Visualize the relative abundance of selected taxa or functions

This function generates various types of plots to visualize the relative abundance of selected taxa or functions in microbiome data. It supports different visualization schemes and plot types for both cross-sectional and longitudinal data.

Usage

plot_feature_diversity(
  data.obj,
  group.var = NULL,
  strata.var = NULL,
  subject.var = NULL,
  time.var = NULL,
  time.point.plot,
  is.plot.change = TRUE,
  feature.change.func = "relative change",
  feature.level = NULL,
  feature.dat.type = c("count", "proportion", "other"),
  features.plot = NULL,
  prop.to.lump = 1e-04,
  top.k.plot = NULL,
  top.k.func = NULL,
  plot.other = TRUE,
  renormalize = FALSE,
  plot.scheme = c("combined", "individual"),
  plot.type = c("barplot", "dotplot", "areaplot", "heatmap", "spaghettiplot", "boxplot",
    "scatterplot")
)

Arguments

data.obj

A list object in a format specific to MicrobiomeStat, which can include components such as feature.tab (matrix), feature.ann (matrix), meta.dat (data.frame), tree, and feature.agg.list (list). The data.obj can be converted from other formats using several functions from the MicrobiomeStat package, including: 'mStat_convert_DGEList_to_data_obj', 'mStat_convert_DESeqDataSet_to_data_obj', 'mStat_convert_phyloseq_to_data_obj', 'mStat_convert_SummarizedExperiment_to_data_obj', 'mStat_import_qiime2_as_data_obj', 'mStat_import_mothur_as_data_obj', 'mStat_import_dada2_as_data_obj', and 'mStat_import_biom_as_data_obj'. Alternatively, users can construct their own data.obj. Note that not all components of data.obj may be required for all functions in the MicrobiomeStat package.

group.var

A string indicating the variable for group identifiers. Default is NULL.

strata.var

A string indicating the variable for strata identifiers. Default is NULL.

subject.var

Character string specifying the subject variable in meta.dat

time.var

Character string specifying the time variable in meta.dat

time.point.plot

Character vector specifying time points to plot

is.plot.change

Logical, whether to plot change from baseline. This parameter is only effective when there are multiple time points (i.e., length(time.point.plot) > 1). If there's only one time point, this parameter has no effect.

feature.change.func

The method or function used to calculate the change in feature abundance between time points. The following options are supported:

- "relative change": Computes the relative change as (time_2 - time_1) / (time_2 + time_1). If both values are zero, the result is zero. - "log fold change": Computes the log2 fold change between time points. Zero values are imputed as half the minimum nonzero value of the respective feature at the given time point before taking the logarithm. - "absolute change": Computes the absolute difference between time points. - A custom function: The provided function should take two numeric vectors as input (values at time 1 and time 2) and return a numeric vector of differences. Users should ensure that their function handles zero values appropriately.

If an unrecognized value or no value is provided for `feature.change.func`, the default behavior will be to compute the absolute difference between time points.

feature.level

The column name in the feature annotation matrix (feature.ann) of data.obj to use for summarization and plotting. This can be the taxonomic level like "Phylum", or any other annotation columns like "Genus" or "OTU_ID". Should be a character vector specifying one or more column names in feature.ann. Multiple columns can be provided, and data will be plotted separately for each column. Default is NULL, which defaults to all columns in feature.ann if `features.plot` is also NULL.

feature.dat.type

The type of the feature data, which determines how the data is handled in downstream analyses. Should be one of: - "count": Raw count data, will be normalized by the function. - "proportion": Data that has already been normalized to proportions/percentages. - "other": Custom abundance data that has unknown scaling. No normalization applied. The choice affects preprocessing steps as well as plot axis labels. Default is "count", which assumes raw OTU table input.

features.plot

A character vector specifying which feature IDs (e.g. OTU IDs) to plot. Default is NULL.

prop.to.lump

Numeric, features with mean proportion less than this will be lumped into "other"

top.k.plot

Integer, plot top k features based on some criterion

top.k.func

Function to order the features

plot.other

Logical, whether to plot the "other" category

renormalize

Logical, whether to renormalize data after removing "other" category

plot.scheme

Character string specifying the plot scheme, one of c("combined", "individual")

plot.type

Character string specifying the plot type, one of c("barplot", "dotplot", "areaplot", "heatmap", "spaghettiplot", "boxplot", "scatterplot")

Value

A list of ggplot objects

Details

This function provides a flexible framework for visualizing microbiome data. It can handle both cross-sectional and longitudinal data, and offers various plot types including bar plots, dot plots, area plots, heatmaps, spaghetti plots, box plots, and scatter plots. The function can also visualize changes over time and supports different grouping and stratification options.

Examples

data(ecam.obj)
plot_feature_diversity(
data.obj = ecam.obj,
group.var = "antiexposedall",
strata.var = NULL,
time.var = "month",
time.point.plot = unique(ecam.obj$meta.dat$month)[1],
is.plot.change = TRUE,
feature.level = c("Phylum", "Family", "Genus"),
feature.dat.type = "proportion",
features.plot = NULL,
prop.to.lump = 0.0001,
top.k.plot = NULL,
top.k.func = NULL,
renormalize = FALSE,
plot.other = TRUE,
plot.scheme = "combined",
plot.type = "barplot"
)
#> Rule 1 passed: data.obj is a list.
#> Rule 2 passed: meta.dat is a data.frame.
#> Rule 3 passed: The row names of feature.tab match the row names of feature.ann.
#> Rule 4 passed: The order of rows in meta.dat has been adjusted to match feature.tab.
#> Rule 5 passed: feature.tab is a matrix.
#> Rule 6 passed: feature.ann is a matrix.
#> Please note: The data components should follow base R data.frame and matrix structures, not phyloseq's formal class.
#> Validation passed.
#> Note: Passing validation does not guarantee the absence of all data issues. Further data exploration may be needed.
#> Data has been subsetted based on the provided condition.
#> Updated metadata to match the subsetted data.
#> The following samples were excluded: 10249.C001.02SS, 10249.C001.03SS, 10249.C001.04SS, 10249.C001.05SS, 10249.C001.06SS, 10249.C001.07SS, 10249.C001.08SS, 10249.C001.09SS, 10249.C001.10SS, 10249.C001.11SS, 10249.C001.12SS, 10249.C001.13SS, 10249.C001.14SS, 10249.C001.15SS, 10249.C001.16SS, 10249.C001.17SS, 10249.C001.18SS, 10249.C001.19SS, 10249.C001.20SS, 10249.C001.25SS, 10249.C001.26SS, 10249.C001.27SS, 10249.C001.29SS, 10249.C001.30SS, 10249.C001.31SS, 10249.C001.32SS, 10249.C001.34SD, 10249.C001.34SS, 10249.C001.35SS, 10249.C001.36SD, 10249.C001.36SS, 10249.C002.02SS, 10249.C002.03SS, 10249.C002.04SS, 10249.C002.05SS, 10249.C002.06SS, 10249.C002.07SS, 10249.C002.08SS, 10249.C002.09SS, 10249.C002.10SS, 10249.C002.11SS, 10249.C002.12SS, 10249.C002.13SS, 10249.C002.15SS, 10249.C002.16SS, 10249.C002.18SS, 10249.C002.19SD, 10249.C002.19SS, 10249.C002.20SS, 10249.C002.21SD, 10249.C002.21SS, 10249.C004.02SS, 10249.C004.03SS, 10249.C004.04SS, 10249.C004.05SS, 10249.C004.06SS, 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10249.C037.17SS, 10249.C037.18SS, 10249.C038.02SS, 10249.C038.04SS, 10249.C038.05SD, 10249.C038.05SS, 10249.C038.06SD, 10249.C038.06SS, 10249.C038.07SD, 10249.C038.07SS, 10249.C038.08SS, 10249.C038.09SS, 10249.C038.10SS, 10249.C038.11SS, 10249.C038.12SD, 10249.C038.12SS, 10249.C038.13SD, 10249.C038.13SS, 10249.C038.14SS, 10249.C038.15SD, 10249.C038.15SS, 10249.C038.16SD, 10249.C038.16SS, 10249.C038.18SS, 10249.C041.02SS, 10249.C041.03SS, 10249.C041.04SS, 10249.C041.05SD, 10249.C041.05SS, 10249.C041.06SD, 10249.C041.06SS, 10249.C041.08SS, 10249.C041.09SS, 10249.C041.10SS, 10249.C041.11SS, 10249.C041.12SS, 10249.C041.13SD, 10249.C041.13SS, 10249.C041.14SD, 10249.C041.14SS, 10249.C041.16SD, 10249.C041.16SS, 10249.C041.17SD, 10249.C041.17SS, 10249.C041.18SS, 10249.C041.19SS, 10249.C042.02SS, 10249.C042.03SS, 10249.C042.04SS, 10249.C042.05SS, 10249.C042.06SD, 10249.C042.06SS, 10249.C042.07SS, 10249.C042.08SS, 10249.C042.09SS, 10249.C042.10SS, 10249.C042.11SD, 10249.C042.11SS, 10249.C042.12SS, 10249.C042.13SS, 10249.C042.14SD, 10249.C042.14SS, 10249.C042.15SD, 10249.C042.15SS, 10249.C042.16SS, 10249.C042.17SS, 10249.C043.02SS, 10249.C043.03SS, 10249.C043.04SD, 10249.C043.04SS, 10249.C043.05SD, 10249.C043.05SS, 10249.C043.06SS, 10249.C043.07SS, 10249.C043.08SS, 10249.C043.09SS, 10249.C043.10SD, 10249.C043.10SS, 10249.C043.11SD, 10249.C043.11SS, 10249.C043.12SD, 10249.C043.12SS, 10249.C043.14SS, 10249.C043.15SD, 10249.C043.15SS, 10249.C043.16SS, 10249.C043.17SS, 10249.C043.18SS, 10249.C043.20SS, 10249.C044.02SS, 10249.C044.03SS, 10249.C044.04SS, 10249.C044.05SS, 10249.C044.06SS, 10249.C044.07SS, 10249.C044.08SS, 10249.C044.09SS, 10249.C044.10SS, 10249.C044.11SS, 10249.C044.12SD, 10249.C044.12SS, 10249.C044.13SD, 10249.C044.13SS, 10249.C044.15SD, 10249.C044.15SS, 10249.C044.16SS, 10249.C044.17SS, 10249.C045.02SS, 10249.C045.03SS, 10249.C045.04SS, 10249.C045.05SD, 10249.C045.05SS, 10249.C045.06SS, 10249.C045.08SD, 10249.C045.08SS, 10249.C045.09SD, 10249.C045.09SS, 10249.C045.10SD, 10249.C045.10SS, 10249.C045.11SS, 10249.C045.12SS, 10249.C045.13SS, 10249.C046.02SS, 10249.C046.03SS, 10249.C046.04SS, 10249.C046.05SS, 10249.C046.06SD, 10249.C046.06SS, 10249.C046.07SD, 10249.C046.07SS, 10249.C046.08SS, 10249.C046.09SD, 10249.C046.09SS, 10249.C046.10SD, 10249.C046.10SS, 10249.C046.11SD, 10249.C046.11SS, 10249.C046.12SS, 10249.C046.13SS, 10249.C046.14SS, 10249.C047.02SD, 10249.C047.02SS, 10249.C047.05SS, 10249.C047.06SD, 10249.C047.06SS, 10249.C047.07SD, 10249.C047.07SS, 10249.C047.08SD, 10249.C047.08SS, 10249.C047.09SS, 10249.C047.10SS, 10249.C047.11SS, 10249.C047.13SS, 10249.C049.03SD, 10249.C049.03SS, 10249.C049.04SS, 10249.C049.07SD, 10249.C049.07SS, 10249.C049.08SD, 10249.C049.08SS, 10249.C049.09SD, 10249.C049.09SS, 10249.C049.10SS, 10249.C049.11SS, 10249.C049.12SS, 10249.C049.13SS, 10249.C049.14SS, 10249.C052.03SD, 10249.C052.03SS, 10249.C052.04SD, 10249.C052.04SS, 10249.C052.05SD, 10249.C052.06SS, 10249.C052.07SS, 10249.C052.08SS, 10249.C052.09SS, 10249.C053.02SD, 10249.C053.02SS, 10249.C053.03SD, 10249.C053.03SS, 10249.C053.04SD, 10249.C053.04SS, 10249.C053.05SD, 10249.C053.05SS, 10249.C053.06SS, 10249.C053.07SS, 10249.C053.08SS, 10249.C053.09SS, 10249.C055.02SD, 10249.C055.02SS, 10249.C055.03SD, 10249.C055.03SS, 10249.C055.04SD, 10249.C055.04SS, 10249.C055.05SD, 10249.C055.05SS, 10249.C055.06SS, 10249.C055.07SS, 10249.C055.08SS, 10249.C055.09SS, 10249.C056.03SD, 10249.C056.03SS, 10249.C056.04SD, 10249.C056.04SS, 10249.C056.05SD, 10249.C056.05SS, 10249.C056.06SS, 10249.C056.07SS, 10249.C056.08SS, 10249.C056.09SS, 10249.C056.10SS, 10249.C057.02SS, 10249.C057.03SD, 10249.C057.03SS, 10249.C057.04SD, 10249.C057.04SS, 10249.C057.05SD, 10249.C057.05SS, 10249.C057.06SS, 10249.C057.08SS, 10249.C057.09SS, 10249.C057.10SS, 10249.C057.11SS
#> Updated feature table to match the subsetted data.
#> Updated feature annotation to match the subsetted data.
#> Data subsetting complete. Returning updated data object.
#> Data has been successfully normalized using TSS method.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Rule 1 passed: data.obj is a list.
#> Rule 2 passed: meta.dat is a data.frame.
#> Rule 3 passed: The row names of feature.tab match the row names of feature.ann.
#> Rule 4 passed: The order of rows in meta.dat has been adjusted to match feature.tab.
#> Rule 5 passed: feature.tab is a matrix.
#> Rule 6 passed: feature.ann is a matrix.
#> Please note: The data components should follow base R data.frame and matrix structures, not phyloseq's formal class.
#> Validation passed.
#> Note: Passing validation does not guarantee the absence of all data issues. Further data exploration may be needed.
#> Data has been subsetted based on the provided condition.
#> Updated metadata to match the subsetted data.
#> The following samples were excluded: 10249.C001.02SS, 10249.C001.03SS, 10249.C001.04SS, 10249.C001.05SS, 10249.C001.06SS, 10249.C001.07SS, 10249.C001.08SS, 10249.C001.09SS, 10249.C001.10SS, 10249.C001.11SS, 10249.C001.12SS, 10249.C001.13SS, 10249.C001.14SS, 10249.C001.15SS, 10249.C001.16SS, 10249.C001.17SS, 10249.C001.18SS, 10249.C001.19SS, 10249.C001.20SS, 10249.C001.25SS, 10249.C001.26SS, 10249.C001.27SS, 10249.C001.29SS, 10249.C001.30SS, 10249.C001.31SS, 10249.C001.32SS, 10249.C001.34SD, 10249.C001.34SS, 10249.C001.35SS, 10249.C001.36SD, 10249.C001.36SS, 10249.C002.02SS, 10249.C002.03SS, 10249.C002.04SS, 10249.C002.05SS, 10249.C002.06SS, 10249.C002.07SS, 10249.C002.08SS, 10249.C002.09SS, 10249.C002.10SS, 10249.C002.11SS, 10249.C002.12SS, 10249.C002.13SS, 10249.C002.15SS, 10249.C002.16SS, 10249.C002.18SS, 10249.C002.19SD, 10249.C002.19SS, 10249.C002.20SS, 10249.C002.21SD, 10249.C002.21SS, 10249.C004.02SS, 10249.C004.03SS, 10249.C004.04SS, 10249.C004.05SS, 10249.C004.06SS, 10249.C004.07SS, 10249.C004.08SS, 10249.C004.09SS, 10249.C004.10SS, 10249.C004.11SS, 10249.C004.12SS, 10249.C004.13SS, 10249.C004.14SS, 10249.C004.15SS, 10249.C005.02SS, 10249.C005.03SS, 10249.C005.04SS, 10249.C005.05SS, 10249.C005.07SS, 10249.C005.08SS, 10249.C005.09SS, 10249.C005.10SS, 10249.C005.11SS, 10249.C005.12SS, 10249.C005.13SS, 10249.C005.14SS, 10249.C005.15SS, 10249.C005.16SS, 10249.C005.17SS, 10249.C005.18SS, 10249.C005.19SD, 10249.C005.19SS, 10249.C005.20SS, 10249.C005.21SD, 10249.C005.21SS, 10249.C005.22SS, 10249.C007.02SS, 10249.C007.03SS, 10249.C007.04SS, 10249.C007.05SS, 10249.C007.06SS, 10249.C007.07SS, 10249.C007.08SS, 10249.C007.09SS, 10249.C007.10SS, 10249.C007.11SS, 10249.C007.12SS, 10249.C007.13SS, 10249.C007.14SS, 10249.C007.15SS, 10249.C007.16SS, 10249.C007.17SS, 10249.C007.18SS, 10249.C007.19SS, 10249.C007.20SS, 10249.C007.21SS, 10249.C007.22SD, 10249.C007.22SS, 10249.C007.23SD, 10249.C007.23SS, 10249.C007.24SD, 10249.C007.24SS, 10249.C007.26SS, 10249.C008.02SS, 10249.C008.03SS, 10249.C008.04SS, 10249.C008.05SS, 10249.C008.06SS, 10249.C008.07SS, 10249.C008.08SS, 10249.C008.09SS, 10249.C008.10SS, 10249.C008.11SS, 10249.C008.12SS, 10249.C008.13SS, 10249.C008.14SS, 10249.C008.15SS, 10249.C008.16SD, 10249.C008.16SS, 10249.C008.18SS, 10249.C009.02SS, 10249.C009.03SS, 10249.C009.04SS, 10249.C009.05SS, 10249.C009.06SS, 10249.C009.07SS, 10249.C009.08SS, 10249.C009.09SS, 10249.C009.10SS, 10249.C009.11SS, 10249.C009.12SS, 10249.C009.13SS, 10249.C009.14SS, 10249.C009.16SS, 10249.C009.17SS, 10249.C009.18SD, 10249.C009.18SS, 10249.C009.19SS, 10249.C009.20SD, 10249.C009.20SS, 10249.C009.21SS, 10249.C010.02SS, 10249.C010.03SS, 10249.C010.04SS, 10249.C010.05SS, 10249.C010.06SS, 10249.C010.07SS, 10249.C010.08SS, 10249.C010.09SS, 10249.C010.10SS, 10249.C010.11SS, 10249.C010.12SS, 10249.C010.13SS, 10249.C010.14SS, 10249.C010.15SS, 10249.C010.16SS, 10249.C010.18SD, 10249.C010.18SS, 10249.C010.19SS, 10249.C010.20SD, 10249.C010.20SS, 10249.C010.21SS, 10249.C011.02SS, 10249.C011.03SS, 10249.C011.04SS, 10249.C011.05SS, 10249.C011.06SS, 10249.C011.07SS, 10249.C011.08SS, 10249.C011.09SS, 10249.C011.10SS, 10249.C011.11SS, 10249.C011.12SS, 10249.C011.13SD, 10249.C011.14SS, 10249.C011.16SS, 10249.C011.17SD, 10249.C011.17SS, 10249.C011.18SS, 10249.C011.19SD, 10249.C011.19SS, 10249.C011.20SS, 10249.C011.21SS, 10249.C012.02SS, 10249.C012.03SS, 10249.C012.04SS, 10249.C012.05SS, 10249.C012.06SS, 10249.C012.07SS, 10249.C012.08SS, 10249.C012.09SS, 10249.C012.10SS, 10249.C012.11SS, 10249.C012.12SS, 10249.C012.13SS, 10249.C012.14SS, 10249.C012.15SS, 10249.C012.16SS, 10249.C012.17SS, 10249.C012.18SS, 10249.C012.19SD, 10249.C012.19SS, 10249.C012.20SS, 10249.C012.21SD, 10249.C012.21SS, 10249.C012.22SD, 10249.C012.22SS, 10249.C014.02SS, 10249.C014.03SS, 10249.C014.04SS, 10249.C014.05SS, 10249.C014.06SS, 10249.C014.07SS, 10249.C014.08SS, 10249.C014.09SS, 10249.C014.10SS, 10249.C014.12SS, 10249.C014.13SS, 10249.C014.15SS, 10249.C014.16SS, 10249.C014.17SS, 10249.C014.18SS, 10249.C014.19SD, 10249.C014.19SS, 10249.C014.20SD, 10249.C014.20SS, 10249.C014.21SS, 10249.C014.22SS, 10249.C016.03SS, 10249.C016.04SS, 10249.C016.05SS, 10249.C016.06SS, 10249.C016.07SS, 10249.C016.08SS, 10249.C016.09SS, 10249.C016.10SS, 10249.C016.11SS, 10249.C016.12SS, 10249.C016.13SS, 10249.C016.14SS, 10249.C016.15SS, 10249.C016.17SS, 10249.C016.18SS, 10249.C016.19SS, 10249.C016.20SS, 10249.C016.21SD, 10249.C016.21SS, 10249.C016.22SD, 10249.C016.22SS, 10249.C016.23SS, 10249.C016.24SS, 10249.C017.04SS, 10249.C017.05SS, 10249.C017.06SS, 10249.C017.07SS, 10249.C017.08SS, 10249.C017.09SS, 10249.C017.10SS, 10249.C017.11SS, 10249.C017.12SS, 10249.C018.02SS, 10249.C018.03SS, 10249.C018.04SS, 10249.C018.05SS, 10249.C018.06SS, 10249.C018.07SS, 10249.C018.08SS, 10249.C018.09SS, 10249.C018.10SS, 10249.C018.11SD, 10249.C018.11SS, 10249.C018.12SD, 10249.C018.12SS, 10249.C018.13SS, 10249.C018.14SS, 10249.C018.15SS, 10249.C018.16SS, 10249.C018.17SS, 10249.C018.18SS, 10249.C018.19SS, 10249.C020.06SS, 10249.C020.07SS, 10249.C020.08SS, 10249.C020.09SS, 10249.C020.10SS, 10249.C020.11SS, 10249.C020.12SS, 10249.C020.13SS, 10249.C020.14SS, 10249.C020.15SS, 10249.C020.16SS, 10249.C020.17SS, 10249.C020.18SS, 10249.C020.19SS, 10249.C020.20SS, 10249.C020.21SS, 10249.C020.22SD, 10249.C020.22SS, 10249.C020.23SD, 10249.C020.23SS, 10249.C020.24SD, 10249.C020.24SS, 10249.C020.25SD, 10249.C020.25SS, 10249.C020.26SD, 10249.C020.26SS, 10249.C020.28SS, 10249.C020.29SS, 10249.C021.03SS, 10249.C021.04SS, 10249.C021.05SS, 10249.C021.06SS, 10249.C021.07SS, 10249.C021.08SS, 10249.C021.09SS, 10249.C021.10SS, 10249.C021.12SS, 10249.C021.13SS, 10249.C022.02SS, 10249.C022.03SS, 10249.C022.04SS, 10249.C022.05SS, 10249.C022.06SS, 10249.C022.07SS, 10249.C022.08SS, 10249.C022.09SS, 10249.C022.10SS, 10249.C022.11SS, 10249.C022.12SS, 10249.C022.13SS, 10249.C022.15SS, 10249.C022.16SS, 10249.C022.18SD, 10249.C022.18SS, 10249.C022.19SS, 10249.C022.20SS, 10249.C022.21SS, 10249.C024.02SS, 10249.C024.03SS, 10249.C024.04SS, 10249.C024.05SS, 10249.C024.06SS, 10249.C024.07SS, 10249.C024.08SS, 10249.C024.09SS, 10249.C024.10SS, 10249.C024.12SS, 10249.C024.13SS, 10249.C024.14SS, 10249.C024.15SS, 10249.C024.16SS, 10249.C024.17SS, 10249.C024.18SS, 10249.C024.19SD, 10249.C024.19SS, 10249.C024.20SD, 10249.C024.20SS, 10249.C024.21SS, 10249.C024.22SS, 10249.C025.02SS, 10249.C025.03SS, 10249.C025.04SS, 10249.C025.05SS, 10249.C025.06SS, 10249.C025.07SS, 10249.C025.08SS, 10249.C025.09SS, 10249.C025.10SS, 10249.C025.11SS, 10249.C025.12SS, 10249.C025.13SD, 10249.C025.13SS, 10249.C025.14SD, 10249.C025.14SS, 10249.C025.15SS, 10249.C025.16SS, 10249.C025.17SS, 10249.C025.18SS, 10249.C025.19SD, 10249.C025.19SS, 10249.C025.20SS, 10249.C025.21SS, 10249.C027.02SS, 10249.C027.03SS, 10249.C027.04SS, 10249.C027.05SS, 10249.C027.06SS, 10249.C027.07SS, 10249.C027.08SS, 10249.C027.09SS, 10249.C027.10SS, 10249.C027.11SD, 10249.C027.12SD, 10249.C027.12SS, 10249.C027.13SS, 10249.C027.14SS, 10249.C027.15SS, 10249.C027.16SS, 10249.C027.17SD, 10249.C027.17SS, 10249.C027.18SS, 10249.C027.19SD, 10249.C027.19SS, 10249.C027.20SD, 10249.C027.20SS, 10249.C027.21SS, 10249.C027.22SS, 10249.C030.02SS, 10249.C030.03SS, 10249.C030.04SS, 10249.C030.05SS, 10249.C030.06SS, 10249.C030.07SS, 10249.C030.08SS, 10249.C030.09SS, 10249.C030.10SS, 10249.C030.11SD, 10249.C030.11SS, 10249.C030.12SS, 10249.C030.13SS, 10249.C030.14SS, 10249.C030.16SS, 10249.C030.17SD, 10249.C030.17SS, 10249.C030.18SS, 10249.C030.19SD, 10249.C030.19SS, 10249.C030.20SS, 10249.C031.02SS, 10249.C031.03SS, 10249.C031.04SS, 10249.C031.05SS, 10249.C031.06SS, 10249.C031.07SS, 10249.C031.08SS, 10249.C031.09SS, 10249.C031.10SS, 10249.C031.11SD, 10249.C031.11SS, 10249.C031.12SS, 10249.C031.13SS, 10249.C031.14SS, 10249.C031.16SS, 10249.C031.17SD, 10249.C031.17SS, 10249.C031.18SS, 10249.C031.19SD, 10249.C031.19SS, 10249.C031.20SS, 10249.C031.21SS, 10249.C032.02SS, 10249.C032.03SS, 10249.C032.04SS, 10249.C032.05SS, 10249.C032.06SS, 10249.C032.07SS, 10249.C032.09SS, 10249.C032.10SS, 10249.C032.11SD, 10249.C032.11SS, 10249.C032.12SD, 10249.C032.13SS, 10249.C032.14SS, 10249.C032.15SS, 10249.C032.16SS, 10249.C032.17SS, 10249.C032.19SD, 10249.C032.19SS, 10249.C032.20SD, 10249.C032.20SS, 10249.C032.21SS, 10249.C032.22SS, 10249.C033.02SS, 10249.C033.03SS, 10249.C033.04SS, 10249.C033.05SS, 10249.C033.06SS, 10249.C033.07SS, 10249.C033.08SS, 10249.C033.09SD, 10249.C033.09SS, 10249.C033.10SD, 10249.C033.10SS, 10249.C033.11SD, 10249.C033.11SS, 10249.C033.12SS, 10249.C033.13SS, 10249.C033.14SS, 10249.C033.15SS, 10249.C033.16SS, 10249.C033.17SD, 10249.C033.17SS, 10249.C033.18SD, 10249.C033.18SS, 10249.C033.19SS, 10249.C034.02SS, 10249.C034.03SS, 10249.C034.04SS, 10249.C034.05SS, 10249.C034.06SS, 10249.C034.07SS, 10249.C034.08SS, 10249.C034.09SS, 10249.C034.10SS, 10249.C034.11SS, 10249.C034.12SS, 10249.C034.13SS, 10249.C034.14SS, 10249.C034.15SD, 10249.C034.15SS, 10249.C034.16SS, 10249.C034.17SD, 10249.C034.17SS, 10249.C035.02SS, 10249.C035.03SS, 10249.C035.04SS, 10249.C035.05SS, 10249.C035.06SD, 10249.C035.06SS, 10249.C035.07SD, 10249.C035.07SS, 10249.C035.08SS, 10249.C035.09SS, 10249.C035.10SS, 10249.C035.11SS, 10249.C035.12SD, 10249.C035.12SS, 10249.C035.13SD, 10249.C035.13SS, 10249.C035.14SD, 10249.C035.14SS, 10249.C035.15SD, 10249.C035.15SS, 10249.C035.16SS, 10249.C035.17SS, 10249.C036.02SS, 10249.C036.03SS, 10249.C036.04SS, 10249.C036.05SD, 10249.C036.05SS, 10249.C036.07SS, 10249.C036.08SS, 10249.C036.09SS, 10249.C036.10SS, 10249.C036.11SS, 10249.C036.12SS, 10249.C036.13SS, 10249.C036.14SD, 10249.C036.14SS, 10249.C036.15SS, 10249.C036.16SS, 10249.C037.02SS, 10249.C037.04SS, 10249.C037.05SS, 10249.C037.06SS, 10249.C037.07SS, 10249.C037.08SS, 10249.C037.09SS, 10249.C037.10SS, 10249.C037.11SS, 10249.C037.12SD, 10249.C037.12SS, 10249.C037.13SD, 10249.C037.13SS, 10249.C037.14SS, 10249.C037.15SS, 10249.C037.16SS, 10249.C037.17SS, 10249.C037.18SS, 10249.C038.02SS, 10249.C038.04SS, 10249.C038.05SD, 10249.C038.05SS, 10249.C038.06SD, 10249.C038.06SS, 10249.C038.07SD, 10249.C038.07SS, 10249.C038.08SS, 10249.C038.09SS, 10249.C038.10SS, 10249.C038.11SS, 10249.C038.12SD, 10249.C038.12SS, 10249.C038.13SD, 10249.C038.13SS, 10249.C038.14SS, 10249.C038.15SD, 10249.C038.15SS, 10249.C038.16SD, 10249.C038.16SS, 10249.C038.18SS, 10249.C041.02SS, 10249.C041.03SS, 10249.C041.04SS, 10249.C041.05SD, 10249.C041.05SS, 10249.C041.06SD, 10249.C041.06SS, 10249.C041.08SS, 10249.C041.09SS, 10249.C041.10SS, 10249.C041.11SS, 10249.C041.12SS, 10249.C041.13SD, 10249.C041.13SS, 10249.C041.14SD, 10249.C041.14SS, 10249.C041.16SD, 10249.C041.16SS, 10249.C041.17SD, 10249.C041.17SS, 10249.C041.18SS, 10249.C041.19SS, 10249.C042.02SS, 10249.C042.03SS, 10249.C042.04SS, 10249.C042.05SS, 10249.C042.06SD, 10249.C042.06SS, 10249.C042.07SS, 10249.C042.08SS, 10249.C042.09SS, 10249.C042.10SS, 10249.C042.11SD, 10249.C042.11SS, 10249.C042.12SS, 10249.C042.13SS, 10249.C042.14SD, 10249.C042.14SS, 10249.C042.15SD, 10249.C042.15SS, 10249.C042.16SS, 10249.C042.17SS, 10249.C043.02SS, 10249.C043.03SS, 10249.C043.04SD, 10249.C043.04SS, 10249.C043.05SD, 10249.C043.05SS, 10249.C043.06SS, 10249.C043.07SS, 10249.C043.08SS, 10249.C043.09SS, 10249.C043.10SD, 10249.C043.10SS, 10249.C043.11SD, 10249.C043.11SS, 10249.C043.12SD, 10249.C043.12SS, 10249.C043.14SS, 10249.C043.15SD, 10249.C043.15SS, 10249.C043.16SS, 10249.C043.17SS, 10249.C043.18SS, 10249.C043.20SS, 10249.C044.02SS, 10249.C044.03SS, 10249.C044.04SS, 10249.C044.05SS, 10249.C044.06SS, 10249.C044.07SS, 10249.C044.08SS, 10249.C044.09SS, 10249.C044.10SS, 10249.C044.11SS, 10249.C044.12SD, 10249.C044.12SS, 10249.C044.13SD, 10249.C044.13SS, 10249.C044.15SD, 10249.C044.15SS, 10249.C044.16SS, 10249.C044.17SS, 10249.C045.02SS, 10249.C045.03SS, 10249.C045.04SS, 10249.C045.05SD, 10249.C045.05SS, 10249.C045.06SS, 10249.C045.08SD, 10249.C045.08SS, 10249.C045.09SD, 10249.C045.09SS, 10249.C045.10SD, 10249.C045.10SS, 10249.C045.11SS, 10249.C045.12SS, 10249.C045.13SS, 10249.C046.02SS, 10249.C046.03SS, 10249.C046.04SS, 10249.C046.05SS, 10249.C046.06SD, 10249.C046.06SS, 10249.C046.07SD, 10249.C046.07SS, 10249.C046.08SS, 10249.C046.09SD, 10249.C046.09SS, 10249.C046.10SD, 10249.C046.10SS, 10249.C046.11SD, 10249.C046.11SS, 10249.C046.12SS, 10249.C046.13SS, 10249.C046.14SS, 10249.C047.02SD, 10249.C047.02SS, 10249.C047.05SS, 10249.C047.06SD, 10249.C047.06SS, 10249.C047.07SD, 10249.C047.07SS, 10249.C047.08SD, 10249.C047.08SS, 10249.C047.09SS, 10249.C047.10SS, 10249.C047.11SS, 10249.C047.13SS, 10249.C049.03SD, 10249.C049.03SS, 10249.C049.04SS, 10249.C049.07SD, 10249.C049.07SS, 10249.C049.08SD, 10249.C049.08SS, 10249.C049.09SD, 10249.C049.09SS, 10249.C049.10SS, 10249.C049.11SS, 10249.C049.12SS, 10249.C049.13SS, 10249.C049.14SS, 10249.C052.03SD, 10249.C052.03SS, 10249.C052.04SD, 10249.C052.04SS, 10249.C052.05SD, 10249.C052.06SS, 10249.C052.07SS, 10249.C052.08SS, 10249.C052.09SS, 10249.C053.02SD, 10249.C053.02SS, 10249.C053.03SD, 10249.C053.03SS, 10249.C053.04SD, 10249.C053.04SS, 10249.C053.05SD, 10249.C053.05SS, 10249.C053.06SS, 10249.C053.07SS, 10249.C053.08SS, 10249.C053.09SS, 10249.C055.02SD, 10249.C055.02SS, 10249.C055.03SD, 10249.C055.03SS, 10249.C055.04SD, 10249.C055.04SS, 10249.C055.05SD, 10249.C055.05SS, 10249.C055.06SS, 10249.C055.07SS, 10249.C055.08SS, 10249.C055.09SS, 10249.C056.03SD, 10249.C056.03SS, 10249.C056.04SD, 10249.C056.04SS, 10249.C056.05SD, 10249.C056.05SS, 10249.C056.06SS, 10249.C056.07SS, 10249.C056.08SS, 10249.C056.09SS, 10249.C056.10SS, 10249.C057.02SS, 10249.C057.03SD, 10249.C057.03SS, 10249.C057.04SD, 10249.C057.04SS, 10249.C057.05SD, 10249.C057.05SS, 10249.C057.06SS, 10249.C057.08SS, 10249.C057.09SS, 10249.C057.10SS, 10249.C057.11SS
#> Updated feature table to match the subsetted data.
#> Updated feature annotation to match the subsetted data.
#> Data subsetting complete. Returning updated data object.
#> Data has been successfully normalized using TSS method.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Rule 1 passed: data.obj is a list.
#> Rule 2 passed: meta.dat is a data.frame.
#> Rule 3 passed: The row names of feature.tab match the row names of feature.ann.
#> Rule 4 passed: The order of rows in meta.dat has been adjusted to match feature.tab.
#> Rule 5 passed: feature.tab is a matrix.
#> Rule 6 passed: feature.ann is a matrix.
#> Please note: The data components should follow base R data.frame and matrix structures, not phyloseq's formal class.
#> Validation passed.
#> Note: Passing validation does not guarantee the absence of all data issues. Further data exploration may be needed.
#> Data has been subsetted based on the provided condition.
#> Updated metadata to match the subsetted data.
#> The following samples were excluded: 10249.C001.02SS, 10249.C001.03SS, 10249.C001.04SS, 10249.C001.05SS, 10249.C001.06SS, 10249.C001.07SS, 10249.C001.08SS, 10249.C001.09SS, 10249.C001.10SS, 10249.C001.11SS, 10249.C001.12SS, 10249.C001.13SS, 10249.C001.14SS, 10249.C001.15SS, 10249.C001.16SS, 10249.C001.17SS, 10249.C001.18SS, 10249.C001.19SS, 10249.C001.20SS, 10249.C001.25SS, 10249.C001.26SS, 10249.C001.27SS, 10249.C001.29SS, 10249.C001.30SS, 10249.C001.31SS, 10249.C001.32SS, 10249.C001.34SD, 10249.C001.34SS, 10249.C001.35SS, 10249.C001.36SD, 10249.C001.36SS, 10249.C002.02SS, 10249.C002.03SS, 10249.C002.04SS, 10249.C002.05SS, 10249.C002.06SS, 10249.C002.07SS, 10249.C002.08SS, 10249.C002.09SS, 10249.C002.10SS, 10249.C002.11SS, 10249.C002.12SS, 10249.C002.13SS, 10249.C002.15SS, 10249.C002.16SS, 10249.C002.18SS, 10249.C002.19SD, 10249.C002.19SS, 10249.C002.20SS, 10249.C002.21SD, 10249.C002.21SS, 10249.C004.02SS, 10249.C004.03SS, 10249.C004.04SS, 10249.C004.05SS, 10249.C004.06SS, 10249.C004.07SS, 10249.C004.08SS, 10249.C004.09SS, 10249.C004.10SS, 10249.C004.11SS, 10249.C004.12SS, 10249.C004.13SS, 10249.C004.14SS, 10249.C004.15SS, 10249.C005.02SS, 10249.C005.03SS, 10249.C005.04SS, 10249.C005.05SS, 10249.C005.07SS, 10249.C005.08SS, 10249.C005.09SS, 10249.C005.10SS, 10249.C005.11SS, 10249.C005.12SS, 10249.C005.13SS, 10249.C005.14SS, 10249.C005.15SS, 10249.C005.16SS, 10249.C005.17SS, 10249.C005.18SS, 10249.C005.19SD, 10249.C005.19SS, 10249.C005.20SS, 10249.C005.21SD, 10249.C005.21SS, 10249.C005.22SS, 10249.C007.02SS, 10249.C007.03SS, 10249.C007.04SS, 10249.C007.05SS, 10249.C007.06SS, 10249.C007.07SS, 10249.C007.08SS, 10249.C007.09SS, 10249.C007.10SS, 10249.C007.11SS, 10249.C007.12SS, 10249.C007.13SS, 10249.C007.14SS, 10249.C007.15SS, 10249.C007.16SS, 10249.C007.17SS, 10249.C007.18SS, 10249.C007.19SS, 10249.C007.20SS, 10249.C007.21SS, 10249.C007.22SD, 10249.C007.22SS, 10249.C007.23SD, 10249.C007.23SS, 10249.C007.24SD, 10249.C007.24SS, 10249.C007.26SS, 10249.C008.02SS, 10249.C008.03SS, 10249.C008.04SS, 10249.C008.05SS, 10249.C008.06SS, 10249.C008.07SS, 10249.C008.08SS, 10249.C008.09SS, 10249.C008.10SS, 10249.C008.11SS, 10249.C008.12SS, 10249.C008.13SS, 10249.C008.14SS, 10249.C008.15SS, 10249.C008.16SD, 10249.C008.16SS, 10249.C008.18SS, 10249.C009.02SS, 10249.C009.03SS, 10249.C009.04SS, 10249.C009.05SS, 10249.C009.06SS, 10249.C009.07SS, 10249.C009.08SS, 10249.C009.09SS, 10249.C009.10SS, 10249.C009.11SS, 10249.C009.12SS, 10249.C009.13SS, 10249.C009.14SS, 10249.C009.16SS, 10249.C009.17SS, 10249.C009.18SD, 10249.C009.18SS, 10249.C009.19SS, 10249.C009.20SD, 10249.C009.20SS, 10249.C009.21SS, 10249.C010.02SS, 10249.C010.03SS, 10249.C010.04SS, 10249.C010.05SS, 10249.C010.06SS, 10249.C010.07SS, 10249.C010.08SS, 10249.C010.09SS, 10249.C010.10SS, 10249.C010.11SS, 10249.C010.12SS, 10249.C010.13SS, 10249.C010.14SS, 10249.C010.15SS, 10249.C010.16SS, 10249.C010.18SD, 10249.C010.18SS, 10249.C010.19SS, 10249.C010.20SD, 10249.C010.20SS, 10249.C010.21SS, 10249.C011.02SS, 10249.C011.03SS, 10249.C011.04SS, 10249.C011.05SS, 10249.C011.06SS, 10249.C011.07SS, 10249.C011.08SS, 10249.C011.09SS, 10249.C011.10SS, 10249.C011.11SS, 10249.C011.12SS, 10249.C011.13SD, 10249.C011.14SS, 10249.C011.16SS, 10249.C011.17SD, 10249.C011.17SS, 10249.C011.18SS, 10249.C011.19SD, 10249.C011.19SS, 10249.C011.20SS, 10249.C011.21SS, 10249.C012.02SS, 10249.C012.03SS, 10249.C012.04SS, 10249.C012.05SS, 10249.C012.06SS, 10249.C012.07SS, 10249.C012.08SS, 10249.C012.09SS, 10249.C012.10SS, 10249.C012.11SS, 10249.C012.12SS, 10249.C012.13SS, 10249.C012.14SS, 10249.C012.15SS, 10249.C012.16SS, 10249.C012.17SS, 10249.C012.18SS, 10249.C012.19SD, 10249.C012.19SS, 10249.C012.20SS, 10249.C012.21SD, 10249.C012.21SS, 10249.C012.22SD, 10249.C012.22SS, 10249.C014.02SS, 10249.C014.03SS, 10249.C014.04SS, 10249.C014.05SS, 10249.C014.06SS, 10249.C014.07SS, 10249.C014.08SS, 10249.C014.09SS, 10249.C014.10SS, 10249.C014.12SS, 10249.C014.13SS, 10249.C014.15SS, 10249.C014.16SS, 10249.C014.17SS, 10249.C014.18SS, 10249.C014.19SD, 10249.C014.19SS, 10249.C014.20SD, 10249.C014.20SS, 10249.C014.21SS, 10249.C014.22SS, 10249.C016.03SS, 10249.C016.04SS, 10249.C016.05SS, 10249.C016.06SS, 10249.C016.07SS, 10249.C016.08SS, 10249.C016.09SS, 10249.C016.10SS, 10249.C016.11SS, 10249.C016.12SS, 10249.C016.13SS, 10249.C016.14SS, 10249.C016.15SS, 10249.C016.17SS, 10249.C016.18SS, 10249.C016.19SS, 10249.C016.20SS, 10249.C016.21SD, 10249.C016.21SS, 10249.C016.22SD, 10249.C016.22SS, 10249.C016.23SS, 10249.C016.24SS, 10249.C017.04SS, 10249.C017.05SS, 10249.C017.06SS, 10249.C017.07SS, 10249.C017.08SS, 10249.C017.09SS, 10249.C017.10SS, 10249.C017.11SS, 10249.C017.12SS, 10249.C018.02SS, 10249.C018.03SS, 10249.C018.04SS, 10249.C018.05SS, 10249.C018.06SS, 10249.C018.07SS, 10249.C018.08SS, 10249.C018.09SS, 10249.C018.10SS, 10249.C018.11SD, 10249.C018.11SS, 10249.C018.12SD, 10249.C018.12SS, 10249.C018.13SS, 10249.C018.14SS, 10249.C018.15SS, 10249.C018.16SS, 10249.C018.17SS, 10249.C018.18SS, 10249.C018.19SS, 10249.C020.06SS, 10249.C020.07SS, 10249.C020.08SS, 10249.C020.09SS, 10249.C020.10SS, 10249.C020.11SS, 10249.C020.12SS, 10249.C020.13SS, 10249.C020.14SS, 10249.C020.15SS, 10249.C020.16SS, 10249.C020.17SS, 10249.C020.18SS, 10249.C020.19SS, 10249.C020.20SS, 10249.C020.21SS, 10249.C020.22SD, 10249.C020.22SS, 10249.C020.23SD, 10249.C020.23SS, 10249.C020.24SD, 10249.C020.24SS, 10249.C020.25SD, 10249.C020.25SS, 10249.C020.26SD, 10249.C020.26SS, 10249.C020.28SS, 10249.C020.29SS, 10249.C021.03SS, 10249.C021.04SS, 10249.C021.05SS, 10249.C021.06SS, 10249.C021.07SS, 10249.C021.08SS, 10249.C021.09SS, 10249.C021.10SS, 10249.C021.12SS, 10249.C021.13SS, 10249.C022.02SS, 10249.C022.03SS, 10249.C022.04SS, 10249.C022.05SS, 10249.C022.06SS, 10249.C022.07SS, 10249.C022.08SS, 10249.C022.09SS, 10249.C022.10SS, 10249.C022.11SS, 10249.C022.12SS, 10249.C022.13SS, 10249.C022.15SS, 10249.C022.16SS, 10249.C022.18SD, 10249.C022.18SS, 10249.C022.19SS, 10249.C022.20SS, 10249.C022.21SS, 10249.C024.02SS, 10249.C024.03SS, 10249.C024.04SS, 10249.C024.05SS, 10249.C024.06SS, 10249.C024.07SS, 10249.C024.08SS, 10249.C024.09SS, 10249.C024.10SS, 10249.C024.12SS, 10249.C024.13SS, 10249.C024.14SS, 10249.C024.15SS, 10249.C024.16SS, 10249.C024.17SS, 10249.C024.18SS, 10249.C024.19SD, 10249.C024.19SS, 10249.C024.20SD, 10249.C024.20SS, 10249.C024.21SS, 10249.C024.22SS, 10249.C025.02SS, 10249.C025.03SS, 10249.C025.04SS, 10249.C025.05SS, 10249.C025.06SS, 10249.C025.07SS, 10249.C025.08SS, 10249.C025.09SS, 10249.C025.10SS, 10249.C025.11SS, 10249.C025.12SS, 10249.C025.13SD, 10249.C025.13SS, 10249.C025.14SD, 10249.C025.14SS, 10249.C025.15SS, 10249.C025.16SS, 10249.C025.17SS, 10249.C025.18SS, 10249.C025.19SD, 10249.C025.19SS, 10249.C025.20SS, 10249.C025.21SS, 10249.C027.02SS, 10249.C027.03SS, 10249.C027.04SS, 10249.C027.05SS, 10249.C027.06SS, 10249.C027.07SS, 10249.C027.08SS, 10249.C027.09SS, 10249.C027.10SS, 10249.C027.11SD, 10249.C027.12SD, 10249.C027.12SS, 10249.C027.13SS, 10249.C027.14SS, 10249.C027.15SS, 10249.C027.16SS, 10249.C027.17SD, 10249.C027.17SS, 10249.C027.18SS, 10249.C027.19SD, 10249.C027.19SS, 10249.C027.20SD, 10249.C027.20SS, 10249.C027.21SS, 10249.C027.22SS, 10249.C030.02SS, 10249.C030.03SS, 10249.C030.04SS, 10249.C030.05SS, 10249.C030.06SS, 10249.C030.07SS, 10249.C030.08SS, 10249.C030.09SS, 10249.C030.10SS, 10249.C030.11SD, 10249.C030.11SS, 10249.C030.12SS, 10249.C030.13SS, 10249.C030.14SS, 10249.C030.16SS, 10249.C030.17SD, 10249.C030.17SS, 10249.C030.18SS, 10249.C030.19SD, 10249.C030.19SS, 10249.C030.20SS, 10249.C031.02SS, 10249.C031.03SS, 10249.C031.04SS, 10249.C031.05SS, 10249.C031.06SS, 10249.C031.07SS, 10249.C031.08SS, 10249.C031.09SS, 10249.C031.10SS, 10249.C031.11SD, 10249.C031.11SS, 10249.C031.12SS, 10249.C031.13SS, 10249.C031.14SS, 10249.C031.16SS, 10249.C031.17SD, 10249.C031.17SS, 10249.C031.18SS, 10249.C031.19SD, 10249.C031.19SS, 10249.C031.20SS, 10249.C031.21SS, 10249.C032.02SS, 10249.C032.03SS, 10249.C032.04SS, 10249.C032.05SS, 10249.C032.06SS, 10249.C032.07SS, 10249.C032.09SS, 10249.C032.10SS, 10249.C032.11SD, 10249.C032.11SS, 10249.C032.12SD, 10249.C032.13SS, 10249.C032.14SS, 10249.C032.15SS, 10249.C032.16SS, 10249.C032.17SS, 10249.C032.19SD, 10249.C032.19SS, 10249.C032.20SD, 10249.C032.20SS, 10249.C032.21SS, 10249.C032.22SS, 10249.C033.02SS, 10249.C033.03SS, 10249.C033.04SS, 10249.C033.05SS, 10249.C033.06SS, 10249.C033.07SS, 10249.C033.08SS, 10249.C033.09SD, 10249.C033.09SS, 10249.C033.10SD, 10249.C033.10SS, 10249.C033.11SD, 10249.C033.11SS, 10249.C033.12SS, 10249.C033.13SS, 10249.C033.14SS, 10249.C033.15SS, 10249.C033.16SS, 10249.C033.17SD, 10249.C033.17SS, 10249.C033.18SD, 10249.C033.18SS, 10249.C033.19SS, 10249.C034.02SS, 10249.C034.03SS, 10249.C034.04SS, 10249.C034.05SS, 10249.C034.06SS, 10249.C034.07SS, 10249.C034.08SS, 10249.C034.09SS, 10249.C034.10SS, 10249.C034.11SS, 10249.C034.12SS, 10249.C034.13SS, 10249.C034.14SS, 10249.C034.15SD, 10249.C034.15SS, 10249.C034.16SS, 10249.C034.17SD, 10249.C034.17SS, 10249.C035.02SS, 10249.C035.03SS, 10249.C035.04SS, 10249.C035.05SS, 10249.C035.06SD, 10249.C035.06SS, 10249.C035.07SD, 10249.C035.07SS, 10249.C035.08SS, 10249.C035.09SS, 10249.C035.10SS, 10249.C035.11SS, 10249.C035.12SD, 10249.C035.12SS, 10249.C035.13SD, 10249.C035.13SS, 10249.C035.14SD, 10249.C035.14SS, 10249.C035.15SD, 10249.C035.15SS, 10249.C035.16SS, 10249.C035.17SS, 10249.C036.02SS, 10249.C036.03SS, 10249.C036.04SS, 10249.C036.05SD, 10249.C036.05SS, 10249.C036.07SS, 10249.C036.08SS, 10249.C036.09SS, 10249.C036.10SS, 10249.C036.11SS, 10249.C036.12SS, 10249.C036.13SS, 10249.C036.14SD, 10249.C036.14SS, 10249.C036.15SS, 10249.C036.16SS, 10249.C037.02SS, 10249.C037.04SS, 10249.C037.05SS, 10249.C037.06SS, 10249.C037.07SS, 10249.C037.08SS, 10249.C037.09SS, 10249.C037.10SS, 10249.C037.11SS, 10249.C037.12SD, 10249.C037.12SS, 10249.C037.13SD, 10249.C037.13SS, 10249.C037.14SS, 10249.C037.15SS, 10249.C037.16SS, 10249.C037.17SS, 10249.C037.18SS, 10249.C038.02SS, 10249.C038.04SS, 10249.C038.05SD, 10249.C038.05SS, 10249.C038.06SD, 10249.C038.06SS, 10249.C038.07SD, 10249.C038.07SS, 10249.C038.08SS, 10249.C038.09SS, 10249.C038.10SS, 10249.C038.11SS, 10249.C038.12SD, 10249.C038.12SS, 10249.C038.13SD, 10249.C038.13SS, 10249.C038.14SS, 10249.C038.15SD, 10249.C038.15SS, 10249.C038.16SD, 10249.C038.16SS, 10249.C038.18SS, 10249.C041.02SS, 10249.C041.03SS, 10249.C041.04SS, 10249.C041.05SD, 10249.C041.05SS, 10249.C041.06SD, 10249.C041.06SS, 10249.C041.08SS, 10249.C041.09SS, 10249.C041.10SS, 10249.C041.11SS, 10249.C041.12SS, 10249.C041.13SD, 10249.C041.13SS, 10249.C041.14SD, 10249.C041.14SS, 10249.C041.16SD, 10249.C041.16SS, 10249.C041.17SD, 10249.C041.17SS, 10249.C041.18SS, 10249.C041.19SS, 10249.C042.02SS, 10249.C042.03SS, 10249.C042.04SS, 10249.C042.05SS, 10249.C042.06SD, 10249.C042.06SS, 10249.C042.07SS, 10249.C042.08SS, 10249.C042.09SS, 10249.C042.10SS, 10249.C042.11SD, 10249.C042.11SS, 10249.C042.12SS, 10249.C042.13SS, 10249.C042.14SD, 10249.C042.14SS, 10249.C042.15SD, 10249.C042.15SS, 10249.C042.16SS, 10249.C042.17SS, 10249.C043.02SS, 10249.C043.03SS, 10249.C043.04SD, 10249.C043.04SS, 10249.C043.05SD, 10249.C043.05SS, 10249.C043.06SS, 10249.C043.07SS, 10249.C043.08SS, 10249.C043.09SS, 10249.C043.10SD, 10249.C043.10SS, 10249.C043.11SD, 10249.C043.11SS, 10249.C043.12SD, 10249.C043.12SS, 10249.C043.14SS, 10249.C043.15SD, 10249.C043.15SS, 10249.C043.16SS, 10249.C043.17SS, 10249.C043.18SS, 10249.C043.20SS, 10249.C044.02SS, 10249.C044.03SS, 10249.C044.04SS, 10249.C044.05SS, 10249.C044.06SS, 10249.C044.07SS, 10249.C044.08SS, 10249.C044.09SS, 10249.C044.10SS, 10249.C044.11SS, 10249.C044.12SD, 10249.C044.12SS, 10249.C044.13SD, 10249.C044.13SS, 10249.C044.15SD, 10249.C044.15SS, 10249.C044.16SS, 10249.C044.17SS, 10249.C045.02SS, 10249.C045.03SS, 10249.C045.04SS, 10249.C045.05SD, 10249.C045.05SS, 10249.C045.06SS, 10249.C045.08SD, 10249.C045.08SS, 10249.C045.09SD, 10249.C045.09SS, 10249.C045.10SD, 10249.C045.10SS, 10249.C045.11SS, 10249.C045.12SS, 10249.C045.13SS, 10249.C046.02SS, 10249.C046.03SS, 10249.C046.04SS, 10249.C046.05SS, 10249.C046.06SD, 10249.C046.06SS, 10249.C046.07SD, 10249.C046.07SS, 10249.C046.08SS, 10249.C046.09SD, 10249.C046.09SS, 10249.C046.10SD, 10249.C046.10SS, 10249.C046.11SD, 10249.C046.11SS, 10249.C046.12SS, 10249.C046.13SS, 10249.C046.14SS, 10249.C047.02SD, 10249.C047.02SS, 10249.C047.05SS, 10249.C047.06SD, 10249.C047.06SS, 10249.C047.07SD, 10249.C047.07SS, 10249.C047.08SD, 10249.C047.08SS, 10249.C047.09SS, 10249.C047.10SS, 10249.C047.11SS, 10249.C047.13SS, 10249.C049.03SD, 10249.C049.03SS, 10249.C049.04SS, 10249.C049.07SD, 10249.C049.07SS, 10249.C049.08SD, 10249.C049.08SS, 10249.C049.09SD, 10249.C049.09SS, 10249.C049.10SS, 10249.C049.11SS, 10249.C049.12SS, 10249.C049.13SS, 10249.C049.14SS, 10249.C052.03SD, 10249.C052.03SS, 10249.C052.04SD, 10249.C052.04SS, 10249.C052.05SD, 10249.C052.06SS, 10249.C052.07SS, 10249.C052.08SS, 10249.C052.09SS, 10249.C053.02SD, 10249.C053.02SS, 10249.C053.03SD, 10249.C053.03SS, 10249.C053.04SD, 10249.C053.04SS, 10249.C053.05SD, 10249.C053.05SS, 10249.C053.06SS, 10249.C053.07SS, 10249.C053.08SS, 10249.C053.09SS, 10249.C055.02SD, 10249.C055.02SS, 10249.C055.03SD, 10249.C055.03SS, 10249.C055.04SD, 10249.C055.04SS, 10249.C055.05SD, 10249.C055.05SS, 10249.C055.06SS, 10249.C055.07SS, 10249.C055.08SS, 10249.C055.09SS, 10249.C056.03SD, 10249.C056.03SS, 10249.C056.04SD, 10249.C056.04SS, 10249.C056.05SD, 10249.C056.05SS, 10249.C056.06SS, 10249.C056.07SS, 10249.C056.08SS, 10249.C056.09SS, 10249.C056.10SS, 10249.C057.02SS, 10249.C057.03SD, 10249.C057.03SS, 10249.C057.04SD, 10249.C057.04SS, 10249.C057.05SD, 10249.C057.05SS, 10249.C057.06SS, 10249.C057.08SS, 10249.C057.09SS, 10249.C057.10SS, 10249.C057.11SS
#> Updated feature table to match the subsetted data.
#> Updated feature annotation to match the subsetted data.
#> Data subsetting complete. Returning updated data object.
#> Data has been successfully normalized using TSS method.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> $Phylum
#> $Phylum$Phylum
#> $Phylum$Phylum$indiv
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.

#> 
#> $Phylum$Phylum$average
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.

#> 
#> 
#> 
#> $Family
#> $Family$Family
#> $Family$Family$indiv
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.

#> 
#> $Family$Family$average
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.

#> 
#> 
#> 
#> $Genus
#> $Genus$Genus
#> $Genus$Genus$indiv
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.

#> 
#> $Genus$Genus$average
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.

#> 
#> 
#> 

plot_feature_diversity(
data.obj = ecam.obj,
group.var = "antiexposedall",
strata.var = "delivery",
time.var = "month",
time.point.plot = unique(ecam.obj$meta.dat$month)[1],
is.plot.change = TRUE,
feature.level = c("Phylum", "Family", "Genus"),
feature.dat.type = "proportion",
features.plot = NULL,
prop.to.lump = 0.0001,
top.k.plot = NULL,
top.k.func = NULL,
renormalize = FALSE,
plot.other = TRUE,
plot.scheme = "combined",
plot.type = "barplot"
)
#> Rule 1 passed: data.obj is a list.
#> Rule 2 passed: meta.dat is a data.frame.
#> Rule 3 passed: The row names of feature.tab match the row names of feature.ann.
#> Rule 4 passed: The order of rows in meta.dat has been adjusted to match feature.tab.
#> Rule 5 passed: feature.tab is a matrix.
#> Rule 6 passed: feature.ann is a matrix.
#> Please note: The data components should follow base R data.frame and matrix structures, not phyloseq's formal class.
#> Validation passed.
#> Note: Passing validation does not guarantee the absence of all data issues. Further data exploration may be needed.
#> Data has been subsetted based on the provided condition.
#> Updated metadata to match the subsetted data.
#> The following samples were excluded: 10249.C001.02SS, 10249.C001.03SS, 10249.C001.04SS, 10249.C001.05SS, 10249.C001.06SS, 10249.C001.07SS, 10249.C001.08SS, 10249.C001.09SS, 10249.C001.10SS, 10249.C001.11SS, 10249.C001.12SS, 10249.C001.13SS, 10249.C001.14SS, 10249.C001.15SS, 10249.C001.16SS, 10249.C001.17SS, 10249.C001.18SS, 10249.C001.19SS, 10249.C001.20SS, 10249.C001.25SS, 10249.C001.26SS, 10249.C001.27SS, 10249.C001.29SS, 10249.C001.30SS, 10249.C001.31SS, 10249.C001.32SS, 10249.C001.34SD, 10249.C001.34SS, 10249.C001.35SS, 10249.C001.36SD, 10249.C001.36SS, 10249.C002.02SS, 10249.C002.03SS, 10249.C002.04SS, 10249.C002.05SS, 10249.C002.06SS, 10249.C002.07SS, 10249.C002.08SS, 10249.C002.09SS, 10249.C002.10SS, 10249.C002.11SS, 10249.C002.12SS, 10249.C002.13SS, 10249.C002.15SS, 10249.C002.16SS, 10249.C002.18SS, 10249.C002.19SD, 10249.C002.19SS, 10249.C002.20SS, 10249.C002.21SD, 10249.C002.21SS, 10249.C004.02SS, 10249.C004.03SS, 10249.C004.04SS, 10249.C004.05SS, 10249.C004.06SS, 10249.C004.07SS, 10249.C004.08SS, 10249.C004.09SS, 10249.C004.10SS, 10249.C004.11SS, 10249.C004.12SS, 10249.C004.13SS, 10249.C004.14SS, 10249.C004.15SS, 10249.C005.02SS, 10249.C005.03SS, 10249.C005.04SS, 10249.C005.05SS, 10249.C005.07SS, 10249.C005.08SS, 10249.C005.09SS, 10249.C005.10SS, 10249.C005.11SS, 10249.C005.12SS, 10249.C005.13SS, 10249.C005.14SS, 10249.C005.15SS, 10249.C005.16SS, 10249.C005.17SS, 10249.C005.18SS, 10249.C005.19SD, 10249.C005.19SS, 10249.C005.20SS, 10249.C005.21SD, 10249.C005.21SS, 10249.C005.22SS, 10249.C007.02SS, 10249.C007.03SS, 10249.C007.04SS, 10249.C007.05SS, 10249.C007.06SS, 10249.C007.07SS, 10249.C007.08SS, 10249.C007.09SS, 10249.C007.10SS, 10249.C007.11SS, 10249.C007.12SS, 10249.C007.13SS, 10249.C007.14SS, 10249.C007.15SS, 10249.C007.16SS, 10249.C007.17SS, 10249.C007.18SS, 10249.C007.19SS, 10249.C007.20SS, 10249.C007.21SS, 10249.C007.22SD, 10249.C007.22SS, 10249.C007.23SD, 10249.C007.23SS, 10249.C007.24SD, 10249.C007.24SS, 10249.C007.26SS, 10249.C008.02SS, 10249.C008.03SS, 10249.C008.04SS, 10249.C008.05SS, 10249.C008.06SS, 10249.C008.07SS, 10249.C008.08SS, 10249.C008.09SS, 10249.C008.10SS, 10249.C008.11SS, 10249.C008.12SS, 10249.C008.13SS, 10249.C008.14SS, 10249.C008.15SS, 10249.C008.16SD, 10249.C008.16SS, 10249.C008.18SS, 10249.C009.02SS, 10249.C009.03SS, 10249.C009.04SS, 10249.C009.05SS, 10249.C009.06SS, 10249.C009.07SS, 10249.C009.08SS, 10249.C009.09SS, 10249.C009.10SS, 10249.C009.11SS, 10249.C009.12SS, 10249.C009.13SS, 10249.C009.14SS, 10249.C009.16SS, 10249.C009.17SS, 10249.C009.18SD, 10249.C009.18SS, 10249.C009.19SS, 10249.C009.20SD, 10249.C009.20SS, 10249.C009.21SS, 10249.C010.02SS, 10249.C010.03SS, 10249.C010.04SS, 10249.C010.05SS, 10249.C010.06SS, 10249.C010.07SS, 10249.C010.08SS, 10249.C010.09SS, 10249.C010.10SS, 10249.C010.11SS, 10249.C010.12SS, 10249.C010.13SS, 10249.C010.14SS, 10249.C010.15SS, 10249.C010.16SS, 10249.C010.18SD, 10249.C010.18SS, 10249.C010.19SS, 10249.C010.20SD, 10249.C010.20SS, 10249.C010.21SS, 10249.C011.02SS, 10249.C011.03SS, 10249.C011.04SS, 10249.C011.05SS, 10249.C011.06SS, 10249.C011.07SS, 10249.C011.08SS, 10249.C011.09SS, 10249.C011.10SS, 10249.C011.11SS, 10249.C011.12SS, 10249.C011.13SD, 10249.C011.14SS, 10249.C011.16SS, 10249.C011.17SD, 10249.C011.17SS, 10249.C011.18SS, 10249.C011.19SD, 10249.C011.19SS, 10249.C011.20SS, 10249.C011.21SS, 10249.C012.02SS, 10249.C012.03SS, 10249.C012.04SS, 10249.C012.05SS, 10249.C012.06SS, 10249.C012.07SS, 10249.C012.08SS, 10249.C012.09SS, 10249.C012.10SS, 10249.C012.11SS, 10249.C012.12SS, 10249.C012.13SS, 10249.C012.14SS, 10249.C012.15SS, 10249.C012.16SS, 10249.C012.17SS, 10249.C012.18SS, 10249.C012.19SD, 10249.C012.19SS, 10249.C012.20SS, 10249.C012.21SD, 10249.C012.21SS, 10249.C012.22SD, 10249.C012.22SS, 10249.C014.02SS, 10249.C014.03SS, 10249.C014.04SS, 10249.C014.05SS, 10249.C014.06SS, 10249.C014.07SS, 10249.C014.08SS, 10249.C014.09SS, 10249.C014.10SS, 10249.C014.12SS, 10249.C014.13SS, 10249.C014.15SS, 10249.C014.16SS, 10249.C014.17SS, 10249.C014.18SS, 10249.C014.19SD, 10249.C014.19SS, 10249.C014.20SD, 10249.C014.20SS, 10249.C014.21SS, 10249.C014.22SS, 10249.C016.03SS, 10249.C016.04SS, 10249.C016.05SS, 10249.C016.06SS, 10249.C016.07SS, 10249.C016.08SS, 10249.C016.09SS, 10249.C016.10SS, 10249.C016.11SS, 10249.C016.12SS, 10249.C016.13SS, 10249.C016.14SS, 10249.C016.15SS, 10249.C016.17SS, 10249.C016.18SS, 10249.C016.19SS, 10249.C016.20SS, 10249.C016.21SD, 10249.C016.21SS, 10249.C016.22SD, 10249.C016.22SS, 10249.C016.23SS, 10249.C016.24SS, 10249.C017.04SS, 10249.C017.05SS, 10249.C017.06SS, 10249.C017.07SS, 10249.C017.08SS, 10249.C017.09SS, 10249.C017.10SS, 10249.C017.11SS, 10249.C017.12SS, 10249.C018.02SS, 10249.C018.03SS, 10249.C018.04SS, 10249.C018.05SS, 10249.C018.06SS, 10249.C018.07SS, 10249.C018.08SS, 10249.C018.09SS, 10249.C018.10SS, 10249.C018.11SD, 10249.C018.11SS, 10249.C018.12SD, 10249.C018.12SS, 10249.C018.13SS, 10249.C018.14SS, 10249.C018.15SS, 10249.C018.16SS, 10249.C018.17SS, 10249.C018.18SS, 10249.C018.19SS, 10249.C020.06SS, 10249.C020.07SS, 10249.C020.08SS, 10249.C020.09SS, 10249.C020.10SS, 10249.C020.11SS, 10249.C020.12SS, 10249.C020.13SS, 10249.C020.14SS, 10249.C020.15SS, 10249.C020.16SS, 10249.C020.17SS, 10249.C020.18SS, 10249.C020.19SS, 10249.C020.20SS, 10249.C020.21SS, 10249.C020.22SD, 10249.C020.22SS, 10249.C020.23SD, 10249.C020.23SS, 10249.C020.24SD, 10249.C020.24SS, 10249.C020.25SD, 10249.C020.25SS, 10249.C020.26SD, 10249.C020.26SS, 10249.C020.28SS, 10249.C020.29SS, 10249.C021.03SS, 10249.C021.04SS, 10249.C021.05SS, 10249.C021.06SS, 10249.C021.07SS, 10249.C021.08SS, 10249.C021.09SS, 10249.C021.10SS, 10249.C021.12SS, 10249.C021.13SS, 10249.C022.02SS, 10249.C022.03SS, 10249.C022.04SS, 10249.C022.05SS, 10249.C022.06SS, 10249.C022.07SS, 10249.C022.08SS, 10249.C022.09SS, 10249.C022.10SS, 10249.C022.11SS, 10249.C022.12SS, 10249.C022.13SS, 10249.C022.15SS, 10249.C022.16SS, 10249.C022.18SD, 10249.C022.18SS, 10249.C022.19SS, 10249.C022.20SS, 10249.C022.21SS, 10249.C024.02SS, 10249.C024.03SS, 10249.C024.04SS, 10249.C024.05SS, 10249.C024.06SS, 10249.C024.07SS, 10249.C024.08SS, 10249.C024.09SS, 10249.C024.10SS, 10249.C024.12SS, 10249.C024.13SS, 10249.C024.14SS, 10249.C024.15SS, 10249.C024.16SS, 10249.C024.17SS, 10249.C024.18SS, 10249.C024.19SD, 10249.C024.19SS, 10249.C024.20SD, 10249.C024.20SS, 10249.C024.21SS, 10249.C024.22SS, 10249.C025.02SS, 10249.C025.03SS, 10249.C025.04SS, 10249.C025.05SS, 10249.C025.06SS, 10249.C025.07SS, 10249.C025.08SS, 10249.C025.09SS, 10249.C025.10SS, 10249.C025.11SS, 10249.C025.12SS, 10249.C025.13SD, 10249.C025.13SS, 10249.C025.14SD, 10249.C025.14SS, 10249.C025.15SS, 10249.C025.16SS, 10249.C025.17SS, 10249.C025.18SS, 10249.C025.19SD, 10249.C025.19SS, 10249.C025.20SS, 10249.C025.21SS, 10249.C027.02SS, 10249.C027.03SS, 10249.C027.04SS, 10249.C027.05SS, 10249.C027.06SS, 10249.C027.07SS, 10249.C027.08SS, 10249.C027.09SS, 10249.C027.10SS, 10249.C027.11SD, 10249.C027.12SD, 10249.C027.12SS, 10249.C027.13SS, 10249.C027.14SS, 10249.C027.15SS, 10249.C027.16SS, 10249.C027.17SD, 10249.C027.17SS, 10249.C027.18SS, 10249.C027.19SD, 10249.C027.19SS, 10249.C027.20SD, 10249.C027.20SS, 10249.C027.21SS, 10249.C027.22SS, 10249.C030.02SS, 10249.C030.03SS, 10249.C030.04SS, 10249.C030.05SS, 10249.C030.06SS, 10249.C030.07SS, 10249.C030.08SS, 10249.C030.09SS, 10249.C030.10SS, 10249.C030.11SD, 10249.C030.11SS, 10249.C030.12SS, 10249.C030.13SS, 10249.C030.14SS, 10249.C030.16SS, 10249.C030.17SD, 10249.C030.17SS, 10249.C030.18SS, 10249.C030.19SD, 10249.C030.19SS, 10249.C030.20SS, 10249.C031.02SS, 10249.C031.03SS, 10249.C031.04SS, 10249.C031.05SS, 10249.C031.06SS, 10249.C031.07SS, 10249.C031.08SS, 10249.C031.09SS, 10249.C031.10SS, 10249.C031.11SD, 10249.C031.11SS, 10249.C031.12SS, 10249.C031.13SS, 10249.C031.14SS, 10249.C031.16SS, 10249.C031.17SD, 10249.C031.17SS, 10249.C031.18SS, 10249.C031.19SD, 10249.C031.19SS, 10249.C031.20SS, 10249.C031.21SS, 10249.C032.02SS, 10249.C032.03SS, 10249.C032.04SS, 10249.C032.05SS, 10249.C032.06SS, 10249.C032.07SS, 10249.C032.09SS, 10249.C032.10SS, 10249.C032.11SD, 10249.C032.11SS, 10249.C032.12SD, 10249.C032.13SS, 10249.C032.14SS, 10249.C032.15SS, 10249.C032.16SS, 10249.C032.17SS, 10249.C032.19SD, 10249.C032.19SS, 10249.C032.20SD, 10249.C032.20SS, 10249.C032.21SS, 10249.C032.22SS, 10249.C033.02SS, 10249.C033.03SS, 10249.C033.04SS, 10249.C033.05SS, 10249.C033.06SS, 10249.C033.07SS, 10249.C033.08SS, 10249.C033.09SD, 10249.C033.09SS, 10249.C033.10SD, 10249.C033.10SS, 10249.C033.11SD, 10249.C033.11SS, 10249.C033.12SS, 10249.C033.13SS, 10249.C033.14SS, 10249.C033.15SS, 10249.C033.16SS, 10249.C033.17SD, 10249.C033.17SS, 10249.C033.18SD, 10249.C033.18SS, 10249.C033.19SS, 10249.C034.02SS, 10249.C034.03SS, 10249.C034.04SS, 10249.C034.05SS, 10249.C034.06SS, 10249.C034.07SS, 10249.C034.08SS, 10249.C034.09SS, 10249.C034.10SS, 10249.C034.11SS, 10249.C034.12SS, 10249.C034.13SS, 10249.C034.14SS, 10249.C034.15SD, 10249.C034.15SS, 10249.C034.16SS, 10249.C034.17SD, 10249.C034.17SS, 10249.C035.02SS, 10249.C035.03SS, 10249.C035.04SS, 10249.C035.05SS, 10249.C035.06SD, 10249.C035.06SS, 10249.C035.07SD, 10249.C035.07SS, 10249.C035.08SS, 10249.C035.09SS, 10249.C035.10SS, 10249.C035.11SS, 10249.C035.12SD, 10249.C035.12SS, 10249.C035.13SD, 10249.C035.13SS, 10249.C035.14SD, 10249.C035.14SS, 10249.C035.15SD, 10249.C035.15SS, 10249.C035.16SS, 10249.C035.17SS, 10249.C036.02SS, 10249.C036.03SS, 10249.C036.04SS, 10249.C036.05SD, 10249.C036.05SS, 10249.C036.07SS, 10249.C036.08SS, 10249.C036.09SS, 10249.C036.10SS, 10249.C036.11SS, 10249.C036.12SS, 10249.C036.13SS, 10249.C036.14SD, 10249.C036.14SS, 10249.C036.15SS, 10249.C036.16SS, 10249.C037.02SS, 10249.C037.04SS, 10249.C037.05SS, 10249.C037.06SS, 10249.C037.07SS, 10249.C037.08SS, 10249.C037.09SS, 10249.C037.10SS, 10249.C037.11SS, 10249.C037.12SD, 10249.C037.12SS, 10249.C037.13SD, 10249.C037.13SS, 10249.C037.14SS, 10249.C037.15SS, 10249.C037.16SS, 10249.C037.17SS, 10249.C037.18SS, 10249.C038.02SS, 10249.C038.04SS, 10249.C038.05SD, 10249.C038.05SS, 10249.C038.06SD, 10249.C038.06SS, 10249.C038.07SD, 10249.C038.07SS, 10249.C038.08SS, 10249.C038.09SS, 10249.C038.10SS, 10249.C038.11SS, 10249.C038.12SD, 10249.C038.12SS, 10249.C038.13SD, 10249.C038.13SS, 10249.C038.14SS, 10249.C038.15SD, 10249.C038.15SS, 10249.C038.16SD, 10249.C038.16SS, 10249.C038.18SS, 10249.C041.02SS, 10249.C041.03SS, 10249.C041.04SS, 10249.C041.05SD, 10249.C041.05SS, 10249.C041.06SD, 10249.C041.06SS, 10249.C041.08SS, 10249.C041.09SS, 10249.C041.10SS, 10249.C041.11SS, 10249.C041.12SS, 10249.C041.13SD, 10249.C041.13SS, 10249.C041.14SD, 10249.C041.14SS, 10249.C041.16SD, 10249.C041.16SS, 10249.C041.17SD, 10249.C041.17SS, 10249.C041.18SS, 10249.C041.19SS, 10249.C042.02SS, 10249.C042.03SS, 10249.C042.04SS, 10249.C042.05SS, 10249.C042.06SD, 10249.C042.06SS, 10249.C042.07SS, 10249.C042.08SS, 10249.C042.09SS, 10249.C042.10SS, 10249.C042.11SD, 10249.C042.11SS, 10249.C042.12SS, 10249.C042.13SS, 10249.C042.14SD, 10249.C042.14SS, 10249.C042.15SD, 10249.C042.15SS, 10249.C042.16SS, 10249.C042.17SS, 10249.C043.02SS, 10249.C043.03SS, 10249.C043.04SD, 10249.C043.04SS, 10249.C043.05SD, 10249.C043.05SS, 10249.C043.06SS, 10249.C043.07SS, 10249.C043.08SS, 10249.C043.09SS, 10249.C043.10SD, 10249.C043.10SS, 10249.C043.11SD, 10249.C043.11SS, 10249.C043.12SD, 10249.C043.12SS, 10249.C043.14SS, 10249.C043.15SD, 10249.C043.15SS, 10249.C043.16SS, 10249.C043.17SS, 10249.C043.18SS, 10249.C043.20SS, 10249.C044.02SS, 10249.C044.03SS, 10249.C044.04SS, 10249.C044.05SS, 10249.C044.06SS, 10249.C044.07SS, 10249.C044.08SS, 10249.C044.09SS, 10249.C044.10SS, 10249.C044.11SS, 10249.C044.12SD, 10249.C044.12SS, 10249.C044.13SD, 10249.C044.13SS, 10249.C044.15SD, 10249.C044.15SS, 10249.C044.16SS, 10249.C044.17SS, 10249.C045.02SS, 10249.C045.03SS, 10249.C045.04SS, 10249.C045.05SD, 10249.C045.05SS, 10249.C045.06SS, 10249.C045.08SD, 10249.C045.08SS, 10249.C045.09SD, 10249.C045.09SS, 10249.C045.10SD, 10249.C045.10SS, 10249.C045.11SS, 10249.C045.12SS, 10249.C045.13SS, 10249.C046.02SS, 10249.C046.03SS, 10249.C046.04SS, 10249.C046.05SS, 10249.C046.06SD, 10249.C046.06SS, 10249.C046.07SD, 10249.C046.07SS, 10249.C046.08SS, 10249.C046.09SD, 10249.C046.09SS, 10249.C046.10SD, 10249.C046.10SS, 10249.C046.11SD, 10249.C046.11SS, 10249.C046.12SS, 10249.C046.13SS, 10249.C046.14SS, 10249.C047.02SD, 10249.C047.02SS, 10249.C047.05SS, 10249.C047.06SD, 10249.C047.06SS, 10249.C047.07SD, 10249.C047.07SS, 10249.C047.08SD, 10249.C047.08SS, 10249.C047.09SS, 10249.C047.10SS, 10249.C047.11SS, 10249.C047.13SS, 10249.C049.03SD, 10249.C049.03SS, 10249.C049.04SS, 10249.C049.07SD, 10249.C049.07SS, 10249.C049.08SD, 10249.C049.08SS, 10249.C049.09SD, 10249.C049.09SS, 10249.C049.10SS, 10249.C049.11SS, 10249.C049.12SS, 10249.C049.13SS, 10249.C049.14SS, 10249.C052.03SD, 10249.C052.03SS, 10249.C052.04SD, 10249.C052.04SS, 10249.C052.05SD, 10249.C052.06SS, 10249.C052.07SS, 10249.C052.08SS, 10249.C052.09SS, 10249.C053.02SD, 10249.C053.02SS, 10249.C053.03SD, 10249.C053.03SS, 10249.C053.04SD, 10249.C053.04SS, 10249.C053.05SD, 10249.C053.05SS, 10249.C053.06SS, 10249.C053.07SS, 10249.C053.08SS, 10249.C053.09SS, 10249.C055.02SD, 10249.C055.02SS, 10249.C055.03SD, 10249.C055.03SS, 10249.C055.04SD, 10249.C055.04SS, 10249.C055.05SD, 10249.C055.05SS, 10249.C055.06SS, 10249.C055.07SS, 10249.C055.08SS, 10249.C055.09SS, 10249.C056.03SD, 10249.C056.03SS, 10249.C056.04SD, 10249.C056.04SS, 10249.C056.05SD, 10249.C056.05SS, 10249.C056.06SS, 10249.C056.07SS, 10249.C056.08SS, 10249.C056.09SS, 10249.C056.10SS, 10249.C057.02SS, 10249.C057.03SD, 10249.C057.03SS, 10249.C057.04SD, 10249.C057.04SS, 10249.C057.05SD, 10249.C057.05SS, 10249.C057.06SS, 10249.C057.08SS, 10249.C057.09SS, 10249.C057.10SS, 10249.C057.11SS
#> Updated feature table to match the subsetted data.
#> Updated feature annotation to match the subsetted data.
#> Data subsetting complete. Returning updated data object.
#> Data has been successfully normalized using TSS method.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Rule 1 passed: data.obj is a list.
#> Rule 2 passed: meta.dat is a data.frame.
#> Rule 3 passed: The row names of feature.tab match the row names of feature.ann.
#> Rule 4 passed: The order of rows in meta.dat has been adjusted to match feature.tab.
#> Rule 5 passed: feature.tab is a matrix.
#> Rule 6 passed: feature.ann is a matrix.
#> Please note: The data components should follow base R data.frame and matrix structures, not phyloseq's formal class.
#> Validation passed.
#> Note: Passing validation does not guarantee the absence of all data issues. Further data exploration may be needed.
#> Data has been subsetted based on the provided condition.
#> Updated metadata to match the subsetted data.
#> The following samples were excluded: 10249.C001.02SS, 10249.C001.03SS, 10249.C001.04SS, 10249.C001.05SS, 10249.C001.06SS, 10249.C001.07SS, 10249.C001.08SS, 10249.C001.09SS, 10249.C001.10SS, 10249.C001.11SS, 10249.C001.12SS, 10249.C001.13SS, 10249.C001.14SS, 10249.C001.15SS, 10249.C001.16SS, 10249.C001.17SS, 10249.C001.18SS, 10249.C001.19SS, 10249.C001.20SS, 10249.C001.25SS, 10249.C001.26SS, 10249.C001.27SS, 10249.C001.29SS, 10249.C001.30SS, 10249.C001.31SS, 10249.C001.32SS, 10249.C001.34SD, 10249.C001.34SS, 10249.C001.35SS, 10249.C001.36SD, 10249.C001.36SS, 10249.C002.02SS, 10249.C002.03SS, 10249.C002.04SS, 10249.C002.05SS, 10249.C002.06SS, 10249.C002.07SS, 10249.C002.08SS, 10249.C002.09SS, 10249.C002.10SS, 10249.C002.11SS, 10249.C002.12SS, 10249.C002.13SS, 10249.C002.15SS, 10249.C002.16SS, 10249.C002.18SS, 10249.C002.19SD, 10249.C002.19SS, 10249.C002.20SS, 10249.C002.21SD, 10249.C002.21SS, 10249.C004.02SS, 10249.C004.03SS, 10249.C004.04SS, 10249.C004.05SS, 10249.C004.06SS, 10249.C004.07SS, 10249.C004.08SS, 10249.C004.09SS, 10249.C004.10SS, 10249.C004.11SS, 10249.C004.12SS, 10249.C004.13SS, 10249.C004.14SS, 10249.C004.15SS, 10249.C005.02SS, 10249.C005.03SS, 10249.C005.04SS, 10249.C005.05SS, 10249.C005.07SS, 10249.C005.08SS, 10249.C005.09SS, 10249.C005.10SS, 10249.C005.11SS, 10249.C005.12SS, 10249.C005.13SS, 10249.C005.14SS, 10249.C005.15SS, 10249.C005.16SS, 10249.C005.17SS, 10249.C005.18SS, 10249.C005.19SD, 10249.C005.19SS, 10249.C005.20SS, 10249.C005.21SD, 10249.C005.21SS, 10249.C005.22SS, 10249.C007.02SS, 10249.C007.03SS, 10249.C007.04SS, 10249.C007.05SS, 10249.C007.06SS, 10249.C007.07SS, 10249.C007.08SS, 10249.C007.09SS, 10249.C007.10SS, 10249.C007.11SS, 10249.C007.12SS, 10249.C007.13SS, 10249.C007.14SS, 10249.C007.15SS, 10249.C007.16SS, 10249.C007.17SS, 10249.C007.18SS, 10249.C007.19SS, 10249.C007.20SS, 10249.C007.21SS, 10249.C007.22SD, 10249.C007.22SS, 10249.C007.23SD, 10249.C007.23SS, 10249.C007.24SD, 10249.C007.24SS, 10249.C007.26SS, 10249.C008.02SS, 10249.C008.03SS, 10249.C008.04SS, 10249.C008.05SS, 10249.C008.06SS, 10249.C008.07SS, 10249.C008.08SS, 10249.C008.09SS, 10249.C008.10SS, 10249.C008.11SS, 10249.C008.12SS, 10249.C008.13SS, 10249.C008.14SS, 10249.C008.15SS, 10249.C008.16SD, 10249.C008.16SS, 10249.C008.18SS, 10249.C009.02SS, 10249.C009.03SS, 10249.C009.04SS, 10249.C009.05SS, 10249.C009.06SS, 10249.C009.07SS, 10249.C009.08SS, 10249.C009.09SS, 10249.C009.10SS, 10249.C009.11SS, 10249.C009.12SS, 10249.C009.13SS, 10249.C009.14SS, 10249.C009.16SS, 10249.C009.17SS, 10249.C009.18SD, 10249.C009.18SS, 10249.C009.19SS, 10249.C009.20SD, 10249.C009.20SS, 10249.C009.21SS, 10249.C010.02SS, 10249.C010.03SS, 10249.C010.04SS, 10249.C010.05SS, 10249.C010.06SS, 10249.C010.07SS, 10249.C010.08SS, 10249.C010.09SS, 10249.C010.10SS, 10249.C010.11SS, 10249.C010.12SS, 10249.C010.13SS, 10249.C010.14SS, 10249.C010.15SS, 10249.C010.16SS, 10249.C010.18SD, 10249.C010.18SS, 10249.C010.19SS, 10249.C010.20SD, 10249.C010.20SS, 10249.C010.21SS, 10249.C011.02SS, 10249.C011.03SS, 10249.C011.04SS, 10249.C011.05SS, 10249.C011.06SS, 10249.C011.07SS, 10249.C011.08SS, 10249.C011.09SS, 10249.C011.10SS, 10249.C011.11SS, 10249.C011.12SS, 10249.C011.13SD, 10249.C011.14SS, 10249.C011.16SS, 10249.C011.17SD, 10249.C011.17SS, 10249.C011.18SS, 10249.C011.19SD, 10249.C011.19SS, 10249.C011.20SS, 10249.C011.21SS, 10249.C012.02SS, 10249.C012.03SS, 10249.C012.04SS, 10249.C012.05SS, 10249.C012.06SS, 10249.C012.07SS, 10249.C012.08SS, 10249.C012.09SS, 10249.C012.10SS, 10249.C012.11SS, 10249.C012.12SS, 10249.C012.13SS, 10249.C012.14SS, 10249.C012.15SS, 10249.C012.16SS, 10249.C012.17SS, 10249.C012.18SS, 10249.C012.19SD, 10249.C012.19SS, 10249.C012.20SS, 10249.C012.21SD, 10249.C012.21SS, 10249.C012.22SD, 10249.C012.22SS, 10249.C014.02SS, 10249.C014.03SS, 10249.C014.04SS, 10249.C014.05SS, 10249.C014.06SS, 10249.C014.07SS, 10249.C014.08SS, 10249.C014.09SS, 10249.C014.10SS, 10249.C014.12SS, 10249.C014.13SS, 10249.C014.15SS, 10249.C014.16SS, 10249.C014.17SS, 10249.C014.18SS, 10249.C014.19SD, 10249.C014.19SS, 10249.C014.20SD, 10249.C014.20SS, 10249.C014.21SS, 10249.C014.22SS, 10249.C016.03SS, 10249.C016.04SS, 10249.C016.05SS, 10249.C016.06SS, 10249.C016.07SS, 10249.C016.08SS, 10249.C016.09SS, 10249.C016.10SS, 10249.C016.11SS, 10249.C016.12SS, 10249.C016.13SS, 10249.C016.14SS, 10249.C016.15SS, 10249.C016.17SS, 10249.C016.18SS, 10249.C016.19SS, 10249.C016.20SS, 10249.C016.21SD, 10249.C016.21SS, 10249.C016.22SD, 10249.C016.22SS, 10249.C016.23SS, 10249.C016.24SS, 10249.C017.04SS, 10249.C017.05SS, 10249.C017.06SS, 10249.C017.07SS, 10249.C017.08SS, 10249.C017.09SS, 10249.C017.10SS, 10249.C017.11SS, 10249.C017.12SS, 10249.C018.02SS, 10249.C018.03SS, 10249.C018.04SS, 10249.C018.05SS, 10249.C018.06SS, 10249.C018.07SS, 10249.C018.08SS, 10249.C018.09SS, 10249.C018.10SS, 10249.C018.11SD, 10249.C018.11SS, 10249.C018.12SD, 10249.C018.12SS, 10249.C018.13SS, 10249.C018.14SS, 10249.C018.15SS, 10249.C018.16SS, 10249.C018.17SS, 10249.C018.18SS, 10249.C018.19SS, 10249.C020.06SS, 10249.C020.07SS, 10249.C020.08SS, 10249.C020.09SS, 10249.C020.10SS, 10249.C020.11SS, 10249.C020.12SS, 10249.C020.13SS, 10249.C020.14SS, 10249.C020.15SS, 10249.C020.16SS, 10249.C020.17SS, 10249.C020.18SS, 10249.C020.19SS, 10249.C020.20SS, 10249.C020.21SS, 10249.C020.22SD, 10249.C020.22SS, 10249.C020.23SD, 10249.C020.23SS, 10249.C020.24SD, 10249.C020.24SS, 10249.C020.25SD, 10249.C020.25SS, 10249.C020.26SD, 10249.C020.26SS, 10249.C020.28SS, 10249.C020.29SS, 10249.C021.03SS, 10249.C021.04SS, 10249.C021.05SS, 10249.C021.06SS, 10249.C021.07SS, 10249.C021.08SS, 10249.C021.09SS, 10249.C021.10SS, 10249.C021.12SS, 10249.C021.13SS, 10249.C022.02SS, 10249.C022.03SS, 10249.C022.04SS, 10249.C022.05SS, 10249.C022.06SS, 10249.C022.07SS, 10249.C022.08SS, 10249.C022.09SS, 10249.C022.10SS, 10249.C022.11SS, 10249.C022.12SS, 10249.C022.13SS, 10249.C022.15SS, 10249.C022.16SS, 10249.C022.18SD, 10249.C022.18SS, 10249.C022.19SS, 10249.C022.20SS, 10249.C022.21SS, 10249.C024.02SS, 10249.C024.03SS, 10249.C024.04SS, 10249.C024.05SS, 10249.C024.06SS, 10249.C024.07SS, 10249.C024.08SS, 10249.C024.09SS, 10249.C024.10SS, 10249.C024.12SS, 10249.C024.13SS, 10249.C024.14SS, 10249.C024.15SS, 10249.C024.16SS, 10249.C024.17SS, 10249.C024.18SS, 10249.C024.19SD, 10249.C024.19SS, 10249.C024.20SD, 10249.C024.20SS, 10249.C024.21SS, 10249.C024.22SS, 10249.C025.02SS, 10249.C025.03SS, 10249.C025.04SS, 10249.C025.05SS, 10249.C025.06SS, 10249.C025.07SS, 10249.C025.08SS, 10249.C025.09SS, 10249.C025.10SS, 10249.C025.11SS, 10249.C025.12SS, 10249.C025.13SD, 10249.C025.13SS, 10249.C025.14SD, 10249.C025.14SS, 10249.C025.15SS, 10249.C025.16SS, 10249.C025.17SS, 10249.C025.18SS, 10249.C025.19SD, 10249.C025.19SS, 10249.C025.20SS, 10249.C025.21SS, 10249.C027.02SS, 10249.C027.03SS, 10249.C027.04SS, 10249.C027.05SS, 10249.C027.06SS, 10249.C027.07SS, 10249.C027.08SS, 10249.C027.09SS, 10249.C027.10SS, 10249.C027.11SD, 10249.C027.12SD, 10249.C027.12SS, 10249.C027.13SS, 10249.C027.14SS, 10249.C027.15SS, 10249.C027.16SS, 10249.C027.17SD, 10249.C027.17SS, 10249.C027.18SS, 10249.C027.19SD, 10249.C027.19SS, 10249.C027.20SD, 10249.C027.20SS, 10249.C027.21SS, 10249.C027.22SS, 10249.C030.02SS, 10249.C030.03SS, 10249.C030.04SS, 10249.C030.05SS, 10249.C030.06SS, 10249.C030.07SS, 10249.C030.08SS, 10249.C030.09SS, 10249.C030.10SS, 10249.C030.11SD, 10249.C030.11SS, 10249.C030.12SS, 10249.C030.13SS, 10249.C030.14SS, 10249.C030.16SS, 10249.C030.17SD, 10249.C030.17SS, 10249.C030.18SS, 10249.C030.19SD, 10249.C030.19SS, 10249.C030.20SS, 10249.C031.02SS, 10249.C031.03SS, 10249.C031.04SS, 10249.C031.05SS, 10249.C031.06SS, 10249.C031.07SS, 10249.C031.08SS, 10249.C031.09SS, 10249.C031.10SS, 10249.C031.11SD, 10249.C031.11SS, 10249.C031.12SS, 10249.C031.13SS, 10249.C031.14SS, 10249.C031.16SS, 10249.C031.17SD, 10249.C031.17SS, 10249.C031.18SS, 10249.C031.19SD, 10249.C031.19SS, 10249.C031.20SS, 10249.C031.21SS, 10249.C032.02SS, 10249.C032.03SS, 10249.C032.04SS, 10249.C032.05SS, 10249.C032.06SS, 10249.C032.07SS, 10249.C032.09SS, 10249.C032.10SS, 10249.C032.11SD, 10249.C032.11SS, 10249.C032.12SD, 10249.C032.13SS, 10249.C032.14SS, 10249.C032.15SS, 10249.C032.16SS, 10249.C032.17SS, 10249.C032.19SD, 10249.C032.19SS, 10249.C032.20SD, 10249.C032.20SS, 10249.C032.21SS, 10249.C032.22SS, 10249.C033.02SS, 10249.C033.03SS, 10249.C033.04SS, 10249.C033.05SS, 10249.C033.06SS, 10249.C033.07SS, 10249.C033.08SS, 10249.C033.09SD, 10249.C033.09SS, 10249.C033.10SD, 10249.C033.10SS, 10249.C033.11SD, 10249.C033.11SS, 10249.C033.12SS, 10249.C033.13SS, 10249.C033.14SS, 10249.C033.15SS, 10249.C033.16SS, 10249.C033.17SD, 10249.C033.17SS, 10249.C033.18SD, 10249.C033.18SS, 10249.C033.19SS, 10249.C034.02SS, 10249.C034.03SS, 10249.C034.04SS, 10249.C034.05SS, 10249.C034.06SS, 10249.C034.07SS, 10249.C034.08SS, 10249.C034.09SS, 10249.C034.10SS, 10249.C034.11SS, 10249.C034.12SS, 10249.C034.13SS, 10249.C034.14SS, 10249.C034.15SD, 10249.C034.15SS, 10249.C034.16SS, 10249.C034.17SD, 10249.C034.17SS, 10249.C035.02SS, 10249.C035.03SS, 10249.C035.04SS, 10249.C035.05SS, 10249.C035.06SD, 10249.C035.06SS, 10249.C035.07SD, 10249.C035.07SS, 10249.C035.08SS, 10249.C035.09SS, 10249.C035.10SS, 10249.C035.11SS, 10249.C035.12SD, 10249.C035.12SS, 10249.C035.13SD, 10249.C035.13SS, 10249.C035.14SD, 10249.C035.14SS, 10249.C035.15SD, 10249.C035.15SS, 10249.C035.16SS, 10249.C035.17SS, 10249.C036.02SS, 10249.C036.03SS, 10249.C036.04SS, 10249.C036.05SD, 10249.C036.05SS, 10249.C036.07SS, 10249.C036.08SS, 10249.C036.09SS, 10249.C036.10SS, 10249.C036.11SS, 10249.C036.12SS, 10249.C036.13SS, 10249.C036.14SD, 10249.C036.14SS, 10249.C036.15SS, 10249.C036.16SS, 10249.C037.02SS, 10249.C037.04SS, 10249.C037.05SS, 10249.C037.06SS, 10249.C037.07SS, 10249.C037.08SS, 10249.C037.09SS, 10249.C037.10SS, 10249.C037.11SS, 10249.C037.12SD, 10249.C037.12SS, 10249.C037.13SD, 10249.C037.13SS, 10249.C037.14SS, 10249.C037.15SS, 10249.C037.16SS, 10249.C037.17SS, 10249.C037.18SS, 10249.C038.02SS, 10249.C038.04SS, 10249.C038.05SD, 10249.C038.05SS, 10249.C038.06SD, 10249.C038.06SS, 10249.C038.07SD, 10249.C038.07SS, 10249.C038.08SS, 10249.C038.09SS, 10249.C038.10SS, 10249.C038.11SS, 10249.C038.12SD, 10249.C038.12SS, 10249.C038.13SD, 10249.C038.13SS, 10249.C038.14SS, 10249.C038.15SD, 10249.C038.15SS, 10249.C038.16SD, 10249.C038.16SS, 10249.C038.18SS, 10249.C041.02SS, 10249.C041.03SS, 10249.C041.04SS, 10249.C041.05SD, 10249.C041.05SS, 10249.C041.06SD, 10249.C041.06SS, 10249.C041.08SS, 10249.C041.09SS, 10249.C041.10SS, 10249.C041.11SS, 10249.C041.12SS, 10249.C041.13SD, 10249.C041.13SS, 10249.C041.14SD, 10249.C041.14SS, 10249.C041.16SD, 10249.C041.16SS, 10249.C041.17SD, 10249.C041.17SS, 10249.C041.18SS, 10249.C041.19SS, 10249.C042.02SS, 10249.C042.03SS, 10249.C042.04SS, 10249.C042.05SS, 10249.C042.06SD, 10249.C042.06SS, 10249.C042.07SS, 10249.C042.08SS, 10249.C042.09SS, 10249.C042.10SS, 10249.C042.11SD, 10249.C042.11SS, 10249.C042.12SS, 10249.C042.13SS, 10249.C042.14SD, 10249.C042.14SS, 10249.C042.15SD, 10249.C042.15SS, 10249.C042.16SS, 10249.C042.17SS, 10249.C043.02SS, 10249.C043.03SS, 10249.C043.04SD, 10249.C043.04SS, 10249.C043.05SD, 10249.C043.05SS, 10249.C043.06SS, 10249.C043.07SS, 10249.C043.08SS, 10249.C043.09SS, 10249.C043.10SD, 10249.C043.10SS, 10249.C043.11SD, 10249.C043.11SS, 10249.C043.12SD, 10249.C043.12SS, 10249.C043.14SS, 10249.C043.15SD, 10249.C043.15SS, 10249.C043.16SS, 10249.C043.17SS, 10249.C043.18SS, 10249.C043.20SS, 10249.C044.02SS, 10249.C044.03SS, 10249.C044.04SS, 10249.C044.05SS, 10249.C044.06SS, 10249.C044.07SS, 10249.C044.08SS, 10249.C044.09SS, 10249.C044.10SS, 10249.C044.11SS, 10249.C044.12SD, 10249.C044.12SS, 10249.C044.13SD, 10249.C044.13SS, 10249.C044.15SD, 10249.C044.15SS, 10249.C044.16SS, 10249.C044.17SS, 10249.C045.02SS, 10249.C045.03SS, 10249.C045.04SS, 10249.C045.05SD, 10249.C045.05SS, 10249.C045.06SS, 10249.C045.08SD, 10249.C045.08SS, 10249.C045.09SD, 10249.C045.09SS, 10249.C045.10SD, 10249.C045.10SS, 10249.C045.11SS, 10249.C045.12SS, 10249.C045.13SS, 10249.C046.02SS, 10249.C046.03SS, 10249.C046.04SS, 10249.C046.05SS, 10249.C046.06SD, 10249.C046.06SS, 10249.C046.07SD, 10249.C046.07SS, 10249.C046.08SS, 10249.C046.09SD, 10249.C046.09SS, 10249.C046.10SD, 10249.C046.10SS, 10249.C046.11SD, 10249.C046.11SS, 10249.C046.12SS, 10249.C046.13SS, 10249.C046.14SS, 10249.C047.02SD, 10249.C047.02SS, 10249.C047.05SS, 10249.C047.06SD, 10249.C047.06SS, 10249.C047.07SD, 10249.C047.07SS, 10249.C047.08SD, 10249.C047.08SS, 10249.C047.09SS, 10249.C047.10SS, 10249.C047.11SS, 10249.C047.13SS, 10249.C049.03SD, 10249.C049.03SS, 10249.C049.04SS, 10249.C049.07SD, 10249.C049.07SS, 10249.C049.08SD, 10249.C049.08SS, 10249.C049.09SD, 10249.C049.09SS, 10249.C049.10SS, 10249.C049.11SS, 10249.C049.12SS, 10249.C049.13SS, 10249.C049.14SS, 10249.C052.03SD, 10249.C052.03SS, 10249.C052.04SD, 10249.C052.04SS, 10249.C052.05SD, 10249.C052.06SS, 10249.C052.07SS, 10249.C052.08SS, 10249.C052.09SS, 10249.C053.02SD, 10249.C053.02SS, 10249.C053.03SD, 10249.C053.03SS, 10249.C053.04SD, 10249.C053.04SS, 10249.C053.05SD, 10249.C053.05SS, 10249.C053.06SS, 10249.C053.07SS, 10249.C053.08SS, 10249.C053.09SS, 10249.C055.02SD, 10249.C055.02SS, 10249.C055.03SD, 10249.C055.03SS, 10249.C055.04SD, 10249.C055.04SS, 10249.C055.05SD, 10249.C055.05SS, 10249.C055.06SS, 10249.C055.07SS, 10249.C055.08SS, 10249.C055.09SS, 10249.C056.03SD, 10249.C056.03SS, 10249.C056.04SD, 10249.C056.04SS, 10249.C056.05SD, 10249.C056.05SS, 10249.C056.06SS, 10249.C056.07SS, 10249.C056.08SS, 10249.C056.09SS, 10249.C056.10SS, 10249.C057.02SS, 10249.C057.03SD, 10249.C057.03SS, 10249.C057.04SD, 10249.C057.04SS, 10249.C057.05SD, 10249.C057.05SS, 10249.C057.06SS, 10249.C057.08SS, 10249.C057.09SS, 10249.C057.10SS, 10249.C057.11SS
#> Updated feature table to match the subsetted data.
#> Updated feature annotation to match the subsetted data.
#> Data subsetting complete. Returning updated data object.
#> Data has been successfully normalized using TSS method.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Rule 1 passed: data.obj is a list.
#> Rule 2 passed: meta.dat is a data.frame.
#> Rule 3 passed: The row names of feature.tab match the row names of feature.ann.
#> Rule 4 passed: The order of rows in meta.dat has been adjusted to match feature.tab.
#> Rule 5 passed: feature.tab is a matrix.
#> Rule 6 passed: feature.ann is a matrix.
#> Please note: The data components should follow base R data.frame and matrix structures, not phyloseq's formal class.
#> Validation passed.
#> Note: Passing validation does not guarantee the absence of all data issues. Further data exploration may be needed.
#> Data has been subsetted based on the provided condition.
#> Updated metadata to match the subsetted data.
#> The following samples were excluded: 10249.C001.02SS, 10249.C001.03SS, 10249.C001.04SS, 10249.C001.05SS, 10249.C001.06SS, 10249.C001.07SS, 10249.C001.08SS, 10249.C001.09SS, 10249.C001.10SS, 10249.C001.11SS, 10249.C001.12SS, 10249.C001.13SS, 10249.C001.14SS, 10249.C001.15SS, 10249.C001.16SS, 10249.C001.17SS, 10249.C001.18SS, 10249.C001.19SS, 10249.C001.20SS, 10249.C001.25SS, 10249.C001.26SS, 10249.C001.27SS, 10249.C001.29SS, 10249.C001.30SS, 10249.C001.31SS, 10249.C001.32SS, 10249.C001.34SD, 10249.C001.34SS, 10249.C001.35SS, 10249.C001.36SD, 10249.C001.36SS, 10249.C002.02SS, 10249.C002.03SS, 10249.C002.04SS, 10249.C002.05SS, 10249.C002.06SS, 10249.C002.07SS, 10249.C002.08SS, 10249.C002.09SS, 10249.C002.10SS, 10249.C002.11SS, 10249.C002.12SS, 10249.C002.13SS, 10249.C002.15SS, 10249.C002.16SS, 10249.C002.18SS, 10249.C002.19SD, 10249.C002.19SS, 10249.C002.20SS, 10249.C002.21SD, 10249.C002.21SS, 10249.C004.02SS, 10249.C004.03SS, 10249.C004.04SS, 10249.C004.05SS, 10249.C004.06SS, 10249.C004.07SS, 10249.C004.08SS, 10249.C004.09SS, 10249.C004.10SS, 10249.C004.11SS, 10249.C004.12SS, 10249.C004.13SS, 10249.C004.14SS, 10249.C004.15SS, 10249.C005.02SS, 10249.C005.03SS, 10249.C005.04SS, 10249.C005.05SS, 10249.C005.07SS, 10249.C005.08SS, 10249.C005.09SS, 10249.C005.10SS, 10249.C005.11SS, 10249.C005.12SS, 10249.C005.13SS, 10249.C005.14SS, 10249.C005.15SS, 10249.C005.16SS, 10249.C005.17SS, 10249.C005.18SS, 10249.C005.19SD, 10249.C005.19SS, 10249.C005.20SS, 10249.C005.21SD, 10249.C005.21SS, 10249.C005.22SS, 10249.C007.02SS, 10249.C007.03SS, 10249.C007.04SS, 10249.C007.05SS, 10249.C007.06SS, 10249.C007.07SS, 10249.C007.08SS, 10249.C007.09SS, 10249.C007.10SS, 10249.C007.11SS, 10249.C007.12SS, 10249.C007.13SS, 10249.C007.14SS, 10249.C007.15SS, 10249.C007.16SS, 10249.C007.17SS, 10249.C007.18SS, 10249.C007.19SS, 10249.C007.20SS, 10249.C007.21SS, 10249.C007.22SD, 10249.C007.22SS, 10249.C007.23SD, 10249.C007.23SS, 10249.C007.24SD, 10249.C007.24SS, 10249.C007.26SS, 10249.C008.02SS, 10249.C008.03SS, 10249.C008.04SS, 10249.C008.05SS, 10249.C008.06SS, 10249.C008.07SS, 10249.C008.08SS, 10249.C008.09SS, 10249.C008.10SS, 10249.C008.11SS, 10249.C008.12SS, 10249.C008.13SS, 10249.C008.14SS, 10249.C008.15SS, 10249.C008.16SD, 10249.C008.16SS, 10249.C008.18SS, 10249.C009.02SS, 10249.C009.03SS, 10249.C009.04SS, 10249.C009.05SS, 10249.C009.06SS, 10249.C009.07SS, 10249.C009.08SS, 10249.C009.09SS, 10249.C009.10SS, 10249.C009.11SS, 10249.C009.12SS, 10249.C009.13SS, 10249.C009.14SS, 10249.C009.16SS, 10249.C009.17SS, 10249.C009.18SD, 10249.C009.18SS, 10249.C009.19SS, 10249.C009.20SD, 10249.C009.20SS, 10249.C009.21SS, 10249.C010.02SS, 10249.C010.03SS, 10249.C010.04SS, 10249.C010.05SS, 10249.C010.06SS, 10249.C010.07SS, 10249.C010.08SS, 10249.C010.09SS, 10249.C010.10SS, 10249.C010.11SS, 10249.C010.12SS, 10249.C010.13SS, 10249.C010.14SS, 10249.C010.15SS, 10249.C010.16SS, 10249.C010.18SD, 10249.C010.18SS, 10249.C010.19SS, 10249.C010.20SD, 10249.C010.20SS, 10249.C010.21SS, 10249.C011.02SS, 10249.C011.03SS, 10249.C011.04SS, 10249.C011.05SS, 10249.C011.06SS, 10249.C011.07SS, 10249.C011.08SS, 10249.C011.09SS, 10249.C011.10SS, 10249.C011.11SS, 10249.C011.12SS, 10249.C011.13SD, 10249.C011.14SS, 10249.C011.16SS, 10249.C011.17SD, 10249.C011.17SS, 10249.C011.18SS, 10249.C011.19SD, 10249.C011.19SS, 10249.C011.20SS, 10249.C011.21SS, 10249.C012.02SS, 10249.C012.03SS, 10249.C012.04SS, 10249.C012.05SS, 10249.C012.06SS, 10249.C012.07SS, 10249.C012.08SS, 10249.C012.09SS, 10249.C012.10SS, 10249.C012.11SS, 10249.C012.12SS, 10249.C012.13SS, 10249.C012.14SS, 10249.C012.15SS, 10249.C012.16SS, 10249.C012.17SS, 10249.C012.18SS, 10249.C012.19SD, 10249.C012.19SS, 10249.C012.20SS, 10249.C012.21SD, 10249.C012.21SS, 10249.C012.22SD, 10249.C012.22SS, 10249.C014.02SS, 10249.C014.03SS, 10249.C014.04SS, 10249.C014.05SS, 10249.C014.06SS, 10249.C014.07SS, 10249.C014.08SS, 10249.C014.09SS, 10249.C014.10SS, 10249.C014.12SS, 10249.C014.13SS, 10249.C014.15SS, 10249.C014.16SS, 10249.C014.17SS, 10249.C014.18SS, 10249.C014.19SD, 10249.C014.19SS, 10249.C014.20SD, 10249.C014.20SS, 10249.C014.21SS, 10249.C014.22SS, 10249.C016.03SS, 10249.C016.04SS, 10249.C016.05SS, 10249.C016.06SS, 10249.C016.07SS, 10249.C016.08SS, 10249.C016.09SS, 10249.C016.10SS, 10249.C016.11SS, 10249.C016.12SS, 10249.C016.13SS, 10249.C016.14SS, 10249.C016.15SS, 10249.C016.17SS, 10249.C016.18SS, 10249.C016.19SS, 10249.C016.20SS, 10249.C016.21SD, 10249.C016.21SS, 10249.C016.22SD, 10249.C016.22SS, 10249.C016.23SS, 10249.C016.24SS, 10249.C017.04SS, 10249.C017.05SS, 10249.C017.06SS, 10249.C017.07SS, 10249.C017.08SS, 10249.C017.09SS, 10249.C017.10SS, 10249.C017.11SS, 10249.C017.12SS, 10249.C018.02SS, 10249.C018.03SS, 10249.C018.04SS, 10249.C018.05SS, 10249.C018.06SS, 10249.C018.07SS, 10249.C018.08SS, 10249.C018.09SS, 10249.C018.10SS, 10249.C018.11SD, 10249.C018.11SS, 10249.C018.12SD, 10249.C018.12SS, 10249.C018.13SS, 10249.C018.14SS, 10249.C018.15SS, 10249.C018.16SS, 10249.C018.17SS, 10249.C018.18SS, 10249.C018.19SS, 10249.C020.06SS, 10249.C020.07SS, 10249.C020.08SS, 10249.C020.09SS, 10249.C020.10SS, 10249.C020.11SS, 10249.C020.12SS, 10249.C020.13SS, 10249.C020.14SS, 10249.C020.15SS, 10249.C020.16SS, 10249.C020.17SS, 10249.C020.18SS, 10249.C020.19SS, 10249.C020.20SS, 10249.C020.21SS, 10249.C020.22SD, 10249.C020.22SS, 10249.C020.23SD, 10249.C020.23SS, 10249.C020.24SD, 10249.C020.24SS, 10249.C020.25SD, 10249.C020.25SS, 10249.C020.26SD, 10249.C020.26SS, 10249.C020.28SS, 10249.C020.29SS, 10249.C021.03SS, 10249.C021.04SS, 10249.C021.05SS, 10249.C021.06SS, 10249.C021.07SS, 10249.C021.08SS, 10249.C021.09SS, 10249.C021.10SS, 10249.C021.12SS, 10249.C021.13SS, 10249.C022.02SS, 10249.C022.03SS, 10249.C022.04SS, 10249.C022.05SS, 10249.C022.06SS, 10249.C022.07SS, 10249.C022.08SS, 10249.C022.09SS, 10249.C022.10SS, 10249.C022.11SS, 10249.C022.12SS, 10249.C022.13SS, 10249.C022.15SS, 10249.C022.16SS, 10249.C022.18SD, 10249.C022.18SS, 10249.C022.19SS, 10249.C022.20SS, 10249.C022.21SS, 10249.C024.02SS, 10249.C024.03SS, 10249.C024.04SS, 10249.C024.05SS, 10249.C024.06SS, 10249.C024.07SS, 10249.C024.08SS, 10249.C024.09SS, 10249.C024.10SS, 10249.C024.12SS, 10249.C024.13SS, 10249.C024.14SS, 10249.C024.15SS, 10249.C024.16SS, 10249.C024.17SS, 10249.C024.18SS, 10249.C024.19SD, 10249.C024.19SS, 10249.C024.20SD, 10249.C024.20SS, 10249.C024.21SS, 10249.C024.22SS, 10249.C025.02SS, 10249.C025.03SS, 10249.C025.04SS, 10249.C025.05SS, 10249.C025.06SS, 10249.C025.07SS, 10249.C025.08SS, 10249.C025.09SS, 10249.C025.10SS, 10249.C025.11SS, 10249.C025.12SS, 10249.C025.13SD, 10249.C025.13SS, 10249.C025.14SD, 10249.C025.14SS, 10249.C025.15SS, 10249.C025.16SS, 10249.C025.17SS, 10249.C025.18SS, 10249.C025.19SD, 10249.C025.19SS, 10249.C025.20SS, 10249.C025.21SS, 10249.C027.02SS, 10249.C027.03SS, 10249.C027.04SS, 10249.C027.05SS, 10249.C027.06SS, 10249.C027.07SS, 10249.C027.08SS, 10249.C027.09SS, 10249.C027.10SS, 10249.C027.11SD, 10249.C027.12SD, 10249.C027.12SS, 10249.C027.13SS, 10249.C027.14SS, 10249.C027.15SS, 10249.C027.16SS, 10249.C027.17SD, 10249.C027.17SS, 10249.C027.18SS, 10249.C027.19SD, 10249.C027.19SS, 10249.C027.20SD, 10249.C027.20SS, 10249.C027.21SS, 10249.C027.22SS, 10249.C030.02SS, 10249.C030.03SS, 10249.C030.04SS, 10249.C030.05SS, 10249.C030.06SS, 10249.C030.07SS, 10249.C030.08SS, 10249.C030.09SS, 10249.C030.10SS, 10249.C030.11SD, 10249.C030.11SS, 10249.C030.12SS, 10249.C030.13SS, 10249.C030.14SS, 10249.C030.16SS, 10249.C030.17SD, 10249.C030.17SS, 10249.C030.18SS, 10249.C030.19SD, 10249.C030.19SS, 10249.C030.20SS, 10249.C031.02SS, 10249.C031.03SS, 10249.C031.04SS, 10249.C031.05SS, 10249.C031.06SS, 10249.C031.07SS, 10249.C031.08SS, 10249.C031.09SS, 10249.C031.10SS, 10249.C031.11SD, 10249.C031.11SS, 10249.C031.12SS, 10249.C031.13SS, 10249.C031.14SS, 10249.C031.16SS, 10249.C031.17SD, 10249.C031.17SS, 10249.C031.18SS, 10249.C031.19SD, 10249.C031.19SS, 10249.C031.20SS, 10249.C031.21SS, 10249.C032.02SS, 10249.C032.03SS, 10249.C032.04SS, 10249.C032.05SS, 10249.C032.06SS, 10249.C032.07SS, 10249.C032.09SS, 10249.C032.10SS, 10249.C032.11SD, 10249.C032.11SS, 10249.C032.12SD, 10249.C032.13SS, 10249.C032.14SS, 10249.C032.15SS, 10249.C032.16SS, 10249.C032.17SS, 10249.C032.19SD, 10249.C032.19SS, 10249.C032.20SD, 10249.C032.20SS, 10249.C032.21SS, 10249.C032.22SS, 10249.C033.02SS, 10249.C033.03SS, 10249.C033.04SS, 10249.C033.05SS, 10249.C033.06SS, 10249.C033.07SS, 10249.C033.08SS, 10249.C033.09SD, 10249.C033.09SS, 10249.C033.10SD, 10249.C033.10SS, 10249.C033.11SD, 10249.C033.11SS, 10249.C033.12SS, 10249.C033.13SS, 10249.C033.14SS, 10249.C033.15SS, 10249.C033.16SS, 10249.C033.17SD, 10249.C033.17SS, 10249.C033.18SD, 10249.C033.18SS, 10249.C033.19SS, 10249.C034.02SS, 10249.C034.03SS, 10249.C034.04SS, 10249.C034.05SS, 10249.C034.06SS, 10249.C034.07SS, 10249.C034.08SS, 10249.C034.09SS, 10249.C034.10SS, 10249.C034.11SS, 10249.C034.12SS, 10249.C034.13SS, 10249.C034.14SS, 10249.C034.15SD, 10249.C034.15SS, 10249.C034.16SS, 10249.C034.17SD, 10249.C034.17SS, 10249.C035.02SS, 10249.C035.03SS, 10249.C035.04SS, 10249.C035.05SS, 10249.C035.06SD, 10249.C035.06SS, 10249.C035.07SD, 10249.C035.07SS, 10249.C035.08SS, 10249.C035.09SS, 10249.C035.10SS, 10249.C035.11SS, 10249.C035.12SD, 10249.C035.12SS, 10249.C035.13SD, 10249.C035.13SS, 10249.C035.14SD, 10249.C035.14SS, 10249.C035.15SD, 10249.C035.15SS, 10249.C035.16SS, 10249.C035.17SS, 10249.C036.02SS, 10249.C036.03SS, 10249.C036.04SS, 10249.C036.05SD, 10249.C036.05SS, 10249.C036.07SS, 10249.C036.08SS, 10249.C036.09SS, 10249.C036.10SS, 10249.C036.11SS, 10249.C036.12SS, 10249.C036.13SS, 10249.C036.14SD, 10249.C036.14SS, 10249.C036.15SS, 10249.C036.16SS, 10249.C037.02SS, 10249.C037.04SS, 10249.C037.05SS, 10249.C037.06SS, 10249.C037.07SS, 10249.C037.08SS, 10249.C037.09SS, 10249.C037.10SS, 10249.C037.11SS, 10249.C037.12SD, 10249.C037.12SS, 10249.C037.13SD, 10249.C037.13SS, 10249.C037.14SS, 10249.C037.15SS, 10249.C037.16SS, 10249.C037.17SS, 10249.C037.18SS, 10249.C038.02SS, 10249.C038.04SS, 10249.C038.05SD, 10249.C038.05SS, 10249.C038.06SD, 10249.C038.06SS, 10249.C038.07SD, 10249.C038.07SS, 10249.C038.08SS, 10249.C038.09SS, 10249.C038.10SS, 10249.C038.11SS, 10249.C038.12SD, 10249.C038.12SS, 10249.C038.13SD, 10249.C038.13SS, 10249.C038.14SS, 10249.C038.15SD, 10249.C038.15SS, 10249.C038.16SD, 10249.C038.16SS, 10249.C038.18SS, 10249.C041.02SS, 10249.C041.03SS, 10249.C041.04SS, 10249.C041.05SD, 10249.C041.05SS, 10249.C041.06SD, 10249.C041.06SS, 10249.C041.08SS, 10249.C041.09SS, 10249.C041.10SS, 10249.C041.11SS, 10249.C041.12SS, 10249.C041.13SD, 10249.C041.13SS, 10249.C041.14SD, 10249.C041.14SS, 10249.C041.16SD, 10249.C041.16SS, 10249.C041.17SD, 10249.C041.17SS, 10249.C041.18SS, 10249.C041.19SS, 10249.C042.02SS, 10249.C042.03SS, 10249.C042.04SS, 10249.C042.05SS, 10249.C042.06SD, 10249.C042.06SS, 10249.C042.07SS, 10249.C042.08SS, 10249.C042.09SS, 10249.C042.10SS, 10249.C042.11SD, 10249.C042.11SS, 10249.C042.12SS, 10249.C042.13SS, 10249.C042.14SD, 10249.C042.14SS, 10249.C042.15SD, 10249.C042.15SS, 10249.C042.16SS, 10249.C042.17SS, 10249.C043.02SS, 10249.C043.03SS, 10249.C043.04SD, 10249.C043.04SS, 10249.C043.05SD, 10249.C043.05SS, 10249.C043.06SS, 10249.C043.07SS, 10249.C043.08SS, 10249.C043.09SS, 10249.C043.10SD, 10249.C043.10SS, 10249.C043.11SD, 10249.C043.11SS, 10249.C043.12SD, 10249.C043.12SS, 10249.C043.14SS, 10249.C043.15SD, 10249.C043.15SS, 10249.C043.16SS, 10249.C043.17SS, 10249.C043.18SS, 10249.C043.20SS, 10249.C044.02SS, 10249.C044.03SS, 10249.C044.04SS, 10249.C044.05SS, 10249.C044.06SS, 10249.C044.07SS, 10249.C044.08SS, 10249.C044.09SS, 10249.C044.10SS, 10249.C044.11SS, 10249.C044.12SD, 10249.C044.12SS, 10249.C044.13SD, 10249.C044.13SS, 10249.C044.15SD, 10249.C044.15SS, 10249.C044.16SS, 10249.C044.17SS, 10249.C045.02SS, 10249.C045.03SS, 10249.C045.04SS, 10249.C045.05SD, 10249.C045.05SS, 10249.C045.06SS, 10249.C045.08SD, 10249.C045.08SS, 10249.C045.09SD, 10249.C045.09SS, 10249.C045.10SD, 10249.C045.10SS, 10249.C045.11SS, 10249.C045.12SS, 10249.C045.13SS, 10249.C046.02SS, 10249.C046.03SS, 10249.C046.04SS, 10249.C046.05SS, 10249.C046.06SD, 10249.C046.06SS, 10249.C046.07SD, 10249.C046.07SS, 10249.C046.08SS, 10249.C046.09SD, 10249.C046.09SS, 10249.C046.10SD, 10249.C046.10SS, 10249.C046.11SD, 10249.C046.11SS, 10249.C046.12SS, 10249.C046.13SS, 10249.C046.14SS, 10249.C047.02SD, 10249.C047.02SS, 10249.C047.05SS, 10249.C047.06SD, 10249.C047.06SS, 10249.C047.07SD, 10249.C047.07SS, 10249.C047.08SD, 10249.C047.08SS, 10249.C047.09SS, 10249.C047.10SS, 10249.C047.11SS, 10249.C047.13SS, 10249.C049.03SD, 10249.C049.03SS, 10249.C049.04SS, 10249.C049.07SD, 10249.C049.07SS, 10249.C049.08SD, 10249.C049.08SS, 10249.C049.09SD, 10249.C049.09SS, 10249.C049.10SS, 10249.C049.11SS, 10249.C049.12SS, 10249.C049.13SS, 10249.C049.14SS, 10249.C052.03SD, 10249.C052.03SS, 10249.C052.04SD, 10249.C052.04SS, 10249.C052.05SD, 10249.C052.06SS, 10249.C052.07SS, 10249.C052.08SS, 10249.C052.09SS, 10249.C053.02SD, 10249.C053.02SS, 10249.C053.03SD, 10249.C053.03SS, 10249.C053.04SD, 10249.C053.04SS, 10249.C053.05SD, 10249.C053.05SS, 10249.C053.06SS, 10249.C053.07SS, 10249.C053.08SS, 10249.C053.09SS, 10249.C055.02SD, 10249.C055.02SS, 10249.C055.03SD, 10249.C055.03SS, 10249.C055.04SD, 10249.C055.04SS, 10249.C055.05SD, 10249.C055.05SS, 10249.C055.06SS, 10249.C055.07SS, 10249.C055.08SS, 10249.C055.09SS, 10249.C056.03SD, 10249.C056.03SS, 10249.C056.04SD, 10249.C056.04SS, 10249.C056.05SD, 10249.C056.05SS, 10249.C056.06SS, 10249.C056.07SS, 10249.C056.08SS, 10249.C056.09SS, 10249.C056.10SS, 10249.C057.02SS, 10249.C057.03SD, 10249.C057.03SS, 10249.C057.04SD, 10249.C057.04SS, 10249.C057.05SD, 10249.C057.05SS, 10249.C057.06SS, 10249.C057.08SS, 10249.C057.09SS, 10249.C057.10SS, 10249.C057.11SS
#> Updated feature table to match the subsetted data.
#> Updated feature annotation to match the subsetted data.
#> Data subsetting complete. Returning updated data object.
#> Data has been successfully normalized using TSS method.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> $Phylum
#> $Phylum$Phylum
#> $Phylum$Phylum$indiv
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.

#> 
#> $Phylum$Phylum$average
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.

#> 
#> 
#> 
#> $Family
#> $Family$Family
#> $Family$Family$indiv
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.

#> 
#> $Family$Family$average
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.

#> 
#> 
#> 
#> $Genus
#> $Genus$Genus
#> $Genus$Genus$indiv
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.

#> 
#> $Genus$Genus$average
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.

#> 
#> 
#> 

plot_feature_diversity(
data.obj = ecam.obj,
group.var = "antiexposedall",
strata.var = "delivery",
time.var = "month",
time.point.plot = unique(ecam.obj$meta.dat$month)[1],
is.plot.change = TRUE,
feature.level = c("Phylum"),
feature.dat.type = "proportion",
features.plot = ecam.obj$feature.ann[,"Phylum"][1:3],
prop.to.lump = 0.0001,
top.k.plot = NULL,
top.k.func = NULL,
renormalize = FALSE,
plot.other = TRUE,
plot.scheme = "combined",
plot.type = "barplot"
)
#> Rule 1 passed: data.obj is a list.
#> Rule 2 passed: meta.dat is a data.frame.
#> Rule 3 passed: The row names of feature.tab match the row names of feature.ann.
#> Rule 4 passed: The order of rows in meta.dat has been adjusted to match feature.tab.
#> Rule 5 passed: feature.tab is a matrix.
#> Rule 6 passed: feature.ann is a matrix.
#> Please note: The data components should follow base R data.frame and matrix structures, not phyloseq's formal class.
#> Validation passed.
#> Note: Passing validation does not guarantee the absence of all data issues. Further data exploration may be needed.
#> Data has been subsetted based on the provided condition.
#> Updated metadata to match the subsetted data.
#> The following samples were excluded: 10249.C001.02SS, 10249.C001.03SS, 10249.C001.04SS, 10249.C001.05SS, 10249.C001.06SS, 10249.C001.07SS, 10249.C001.08SS, 10249.C001.09SS, 10249.C001.10SS, 10249.C001.11SS, 10249.C001.12SS, 10249.C001.13SS, 10249.C001.14SS, 10249.C001.15SS, 10249.C001.16SS, 10249.C001.17SS, 10249.C001.18SS, 10249.C001.19SS, 10249.C001.20SS, 10249.C001.25SS, 10249.C001.26SS, 10249.C001.27SS, 10249.C001.29SS, 10249.C001.30SS, 10249.C001.31SS, 10249.C001.32SS, 10249.C001.34SD, 10249.C001.34SS, 10249.C001.35SS, 10249.C001.36SD, 10249.C001.36SS, 10249.C002.02SS, 10249.C002.03SS, 10249.C002.04SS, 10249.C002.05SS, 10249.C002.06SS, 10249.C002.07SS, 10249.C002.08SS, 10249.C002.09SS, 10249.C002.10SS, 10249.C002.11SS, 10249.C002.12SS, 10249.C002.13SS, 10249.C002.15SS, 10249.C002.16SS, 10249.C002.18SS, 10249.C002.19SD, 10249.C002.19SS, 10249.C002.20SS, 10249.C002.21SD, 10249.C002.21SS, 10249.C004.02SS, 10249.C004.03SS, 10249.C004.04SS, 10249.C004.05SS, 10249.C004.06SS, 10249.C004.07SS, 10249.C004.08SS, 10249.C004.09SS, 10249.C004.10SS, 10249.C004.11SS, 10249.C004.12SS, 10249.C004.13SS, 10249.C004.14SS, 10249.C004.15SS, 10249.C005.02SS, 10249.C005.03SS, 10249.C005.04SS, 10249.C005.05SS, 10249.C005.07SS, 10249.C005.08SS, 10249.C005.09SS, 10249.C005.10SS, 10249.C005.11SS, 10249.C005.12SS, 10249.C005.13SS, 10249.C005.14SS, 10249.C005.15SS, 10249.C005.16SS, 10249.C005.17SS, 10249.C005.18SS, 10249.C005.19SD, 10249.C005.19SS, 10249.C005.20SS, 10249.C005.21SD, 10249.C005.21SS, 10249.C005.22SS, 10249.C007.02SS, 10249.C007.03SS, 10249.C007.04SS, 10249.C007.05SS, 10249.C007.06SS, 10249.C007.07SS, 10249.C007.08SS, 10249.C007.09SS, 10249.C007.10SS, 10249.C007.11SS, 10249.C007.12SS, 10249.C007.13SS, 10249.C007.14SS, 10249.C007.15SS, 10249.C007.16SS, 10249.C007.17SS, 10249.C007.18SS, 10249.C007.19SS, 10249.C007.20SS, 10249.C007.21SS, 10249.C007.22SD, 10249.C007.22SS, 10249.C007.23SD, 10249.C007.23SS, 10249.C007.24SD, 10249.C007.24SS, 10249.C007.26SS, 10249.C008.02SS, 10249.C008.03SS, 10249.C008.04SS, 10249.C008.05SS, 10249.C008.06SS, 10249.C008.07SS, 10249.C008.08SS, 10249.C008.09SS, 10249.C008.10SS, 10249.C008.11SS, 10249.C008.12SS, 10249.C008.13SS, 10249.C008.14SS, 10249.C008.15SS, 10249.C008.16SD, 10249.C008.16SS, 10249.C008.18SS, 10249.C009.02SS, 10249.C009.03SS, 10249.C009.04SS, 10249.C009.05SS, 10249.C009.06SS, 10249.C009.07SS, 10249.C009.08SS, 10249.C009.09SS, 10249.C009.10SS, 10249.C009.11SS, 10249.C009.12SS, 10249.C009.13SS, 10249.C009.14SS, 10249.C009.16SS, 10249.C009.17SS, 10249.C009.18SD, 10249.C009.18SS, 10249.C009.19SS, 10249.C009.20SD, 10249.C009.20SS, 10249.C009.21SS, 10249.C010.02SS, 10249.C010.03SS, 10249.C010.04SS, 10249.C010.05SS, 10249.C010.06SS, 10249.C010.07SS, 10249.C010.08SS, 10249.C010.09SS, 10249.C010.10SS, 10249.C010.11SS, 10249.C010.12SS, 10249.C010.13SS, 10249.C010.14SS, 10249.C010.15SS, 10249.C010.16SS, 10249.C010.18SD, 10249.C010.18SS, 10249.C010.19SS, 10249.C010.20SD, 10249.C010.20SS, 10249.C010.21SS, 10249.C011.02SS, 10249.C011.03SS, 10249.C011.04SS, 10249.C011.05SS, 10249.C011.06SS, 10249.C011.07SS, 10249.C011.08SS, 10249.C011.09SS, 10249.C011.10SS, 10249.C011.11SS, 10249.C011.12SS, 10249.C011.13SD, 10249.C011.14SS, 10249.C011.16SS, 10249.C011.17SD, 10249.C011.17SS, 10249.C011.18SS, 10249.C011.19SD, 10249.C011.19SS, 10249.C011.20SS, 10249.C011.21SS, 10249.C012.02SS, 10249.C012.03SS, 10249.C012.04SS, 10249.C012.05SS, 10249.C012.06SS, 10249.C012.07SS, 10249.C012.08SS, 10249.C012.09SS, 10249.C012.10SS, 10249.C012.11SS, 10249.C012.12SS, 10249.C012.13SS, 10249.C012.14SS, 10249.C012.15SS, 10249.C012.16SS, 10249.C012.17SS, 10249.C012.18SS, 10249.C012.19SD, 10249.C012.19SS, 10249.C012.20SS, 10249.C012.21SD, 10249.C012.21SS, 10249.C012.22SD, 10249.C012.22SS, 10249.C014.02SS, 10249.C014.03SS, 10249.C014.04SS, 10249.C014.05SS, 10249.C014.06SS, 10249.C014.07SS, 10249.C014.08SS, 10249.C014.09SS, 10249.C014.10SS, 10249.C014.12SS, 10249.C014.13SS, 10249.C014.15SS, 10249.C014.16SS, 10249.C014.17SS, 10249.C014.18SS, 10249.C014.19SD, 10249.C014.19SS, 10249.C014.20SD, 10249.C014.20SS, 10249.C014.21SS, 10249.C014.22SS, 10249.C016.03SS, 10249.C016.04SS, 10249.C016.05SS, 10249.C016.06SS, 10249.C016.07SS, 10249.C016.08SS, 10249.C016.09SS, 10249.C016.10SS, 10249.C016.11SS, 10249.C016.12SS, 10249.C016.13SS, 10249.C016.14SS, 10249.C016.15SS, 10249.C016.17SS, 10249.C016.18SS, 10249.C016.19SS, 10249.C016.20SS, 10249.C016.21SD, 10249.C016.21SS, 10249.C016.22SD, 10249.C016.22SS, 10249.C016.23SS, 10249.C016.24SS, 10249.C017.04SS, 10249.C017.05SS, 10249.C017.06SS, 10249.C017.07SS, 10249.C017.08SS, 10249.C017.09SS, 10249.C017.10SS, 10249.C017.11SS, 10249.C017.12SS, 10249.C018.02SS, 10249.C018.03SS, 10249.C018.04SS, 10249.C018.05SS, 10249.C018.06SS, 10249.C018.07SS, 10249.C018.08SS, 10249.C018.09SS, 10249.C018.10SS, 10249.C018.11SD, 10249.C018.11SS, 10249.C018.12SD, 10249.C018.12SS, 10249.C018.13SS, 10249.C018.14SS, 10249.C018.15SS, 10249.C018.16SS, 10249.C018.17SS, 10249.C018.18SS, 10249.C018.19SS, 10249.C020.06SS, 10249.C020.07SS, 10249.C020.08SS, 10249.C020.09SS, 10249.C020.10SS, 10249.C020.11SS, 10249.C020.12SS, 10249.C020.13SS, 10249.C020.14SS, 10249.C020.15SS, 10249.C020.16SS, 10249.C020.17SS, 10249.C020.18SS, 10249.C020.19SS, 10249.C020.20SS, 10249.C020.21SS, 10249.C020.22SD, 10249.C020.22SS, 10249.C020.23SD, 10249.C020.23SS, 10249.C020.24SD, 10249.C020.24SS, 10249.C020.25SD, 10249.C020.25SS, 10249.C020.26SD, 10249.C020.26SS, 10249.C020.28SS, 10249.C020.29SS, 10249.C021.03SS, 10249.C021.04SS, 10249.C021.05SS, 10249.C021.06SS, 10249.C021.07SS, 10249.C021.08SS, 10249.C021.09SS, 10249.C021.10SS, 10249.C021.12SS, 10249.C021.13SS, 10249.C022.02SS, 10249.C022.03SS, 10249.C022.04SS, 10249.C022.05SS, 10249.C022.06SS, 10249.C022.07SS, 10249.C022.08SS, 10249.C022.09SS, 10249.C022.10SS, 10249.C022.11SS, 10249.C022.12SS, 10249.C022.13SS, 10249.C022.15SS, 10249.C022.16SS, 10249.C022.18SD, 10249.C022.18SS, 10249.C022.19SS, 10249.C022.20SS, 10249.C022.21SS, 10249.C024.02SS, 10249.C024.03SS, 10249.C024.04SS, 10249.C024.05SS, 10249.C024.06SS, 10249.C024.07SS, 10249.C024.08SS, 10249.C024.09SS, 10249.C024.10SS, 10249.C024.12SS, 10249.C024.13SS, 10249.C024.14SS, 10249.C024.15SS, 10249.C024.16SS, 10249.C024.17SS, 10249.C024.18SS, 10249.C024.19SD, 10249.C024.19SS, 10249.C024.20SD, 10249.C024.20SS, 10249.C024.21SS, 10249.C024.22SS, 10249.C025.02SS, 10249.C025.03SS, 10249.C025.04SS, 10249.C025.05SS, 10249.C025.06SS, 10249.C025.07SS, 10249.C025.08SS, 10249.C025.09SS, 10249.C025.10SS, 10249.C025.11SS, 10249.C025.12SS, 10249.C025.13SD, 10249.C025.13SS, 10249.C025.14SD, 10249.C025.14SS, 10249.C025.15SS, 10249.C025.16SS, 10249.C025.17SS, 10249.C025.18SS, 10249.C025.19SD, 10249.C025.19SS, 10249.C025.20SS, 10249.C025.21SS, 10249.C027.02SS, 10249.C027.03SS, 10249.C027.04SS, 10249.C027.05SS, 10249.C027.06SS, 10249.C027.07SS, 10249.C027.08SS, 10249.C027.09SS, 10249.C027.10SS, 10249.C027.11SD, 10249.C027.12SD, 10249.C027.12SS, 10249.C027.13SS, 10249.C027.14SS, 10249.C027.15SS, 10249.C027.16SS, 10249.C027.17SD, 10249.C027.17SS, 10249.C027.18SS, 10249.C027.19SD, 10249.C027.19SS, 10249.C027.20SD, 10249.C027.20SS, 10249.C027.21SS, 10249.C027.22SS, 10249.C030.02SS, 10249.C030.03SS, 10249.C030.04SS, 10249.C030.05SS, 10249.C030.06SS, 10249.C030.07SS, 10249.C030.08SS, 10249.C030.09SS, 10249.C030.10SS, 10249.C030.11SD, 10249.C030.11SS, 10249.C030.12SS, 10249.C030.13SS, 10249.C030.14SS, 10249.C030.16SS, 10249.C030.17SD, 10249.C030.17SS, 10249.C030.18SS, 10249.C030.19SD, 10249.C030.19SS, 10249.C030.20SS, 10249.C031.02SS, 10249.C031.03SS, 10249.C031.04SS, 10249.C031.05SS, 10249.C031.06SS, 10249.C031.07SS, 10249.C031.08SS, 10249.C031.09SS, 10249.C031.10SS, 10249.C031.11SD, 10249.C031.11SS, 10249.C031.12SS, 10249.C031.13SS, 10249.C031.14SS, 10249.C031.16SS, 10249.C031.17SD, 10249.C031.17SS, 10249.C031.18SS, 10249.C031.19SD, 10249.C031.19SS, 10249.C031.20SS, 10249.C031.21SS, 10249.C032.02SS, 10249.C032.03SS, 10249.C032.04SS, 10249.C032.05SS, 10249.C032.06SS, 10249.C032.07SS, 10249.C032.09SS, 10249.C032.10SS, 10249.C032.11SD, 10249.C032.11SS, 10249.C032.12SD, 10249.C032.13SS, 10249.C032.14SS, 10249.C032.15SS, 10249.C032.16SS, 10249.C032.17SS, 10249.C032.19SD, 10249.C032.19SS, 10249.C032.20SD, 10249.C032.20SS, 10249.C032.21SS, 10249.C032.22SS, 10249.C033.02SS, 10249.C033.03SS, 10249.C033.04SS, 10249.C033.05SS, 10249.C033.06SS, 10249.C033.07SS, 10249.C033.08SS, 10249.C033.09SD, 10249.C033.09SS, 10249.C033.10SD, 10249.C033.10SS, 10249.C033.11SD, 10249.C033.11SS, 10249.C033.12SS, 10249.C033.13SS, 10249.C033.14SS, 10249.C033.15SS, 10249.C033.16SS, 10249.C033.17SD, 10249.C033.17SS, 10249.C033.18SD, 10249.C033.18SS, 10249.C033.19SS, 10249.C034.02SS, 10249.C034.03SS, 10249.C034.04SS, 10249.C034.05SS, 10249.C034.06SS, 10249.C034.07SS, 10249.C034.08SS, 10249.C034.09SS, 10249.C034.10SS, 10249.C034.11SS, 10249.C034.12SS, 10249.C034.13SS, 10249.C034.14SS, 10249.C034.15SD, 10249.C034.15SS, 10249.C034.16SS, 10249.C034.17SD, 10249.C034.17SS, 10249.C035.02SS, 10249.C035.03SS, 10249.C035.04SS, 10249.C035.05SS, 10249.C035.06SD, 10249.C035.06SS, 10249.C035.07SD, 10249.C035.07SS, 10249.C035.08SS, 10249.C035.09SS, 10249.C035.10SS, 10249.C035.11SS, 10249.C035.12SD, 10249.C035.12SS, 10249.C035.13SD, 10249.C035.13SS, 10249.C035.14SD, 10249.C035.14SS, 10249.C035.15SD, 10249.C035.15SS, 10249.C035.16SS, 10249.C035.17SS, 10249.C036.02SS, 10249.C036.03SS, 10249.C036.04SS, 10249.C036.05SD, 10249.C036.05SS, 10249.C036.07SS, 10249.C036.08SS, 10249.C036.09SS, 10249.C036.10SS, 10249.C036.11SS, 10249.C036.12SS, 10249.C036.13SS, 10249.C036.14SD, 10249.C036.14SS, 10249.C036.15SS, 10249.C036.16SS, 10249.C037.02SS, 10249.C037.04SS, 10249.C037.05SS, 10249.C037.06SS, 10249.C037.07SS, 10249.C037.08SS, 10249.C037.09SS, 10249.C037.10SS, 10249.C037.11SS, 10249.C037.12SD, 10249.C037.12SS, 10249.C037.13SD, 10249.C037.13SS, 10249.C037.14SS, 10249.C037.15SS, 10249.C037.16SS, 10249.C037.17SS, 10249.C037.18SS, 10249.C038.02SS, 10249.C038.04SS, 10249.C038.05SD, 10249.C038.05SS, 10249.C038.06SD, 10249.C038.06SS, 10249.C038.07SD, 10249.C038.07SS, 10249.C038.08SS, 10249.C038.09SS, 10249.C038.10SS, 10249.C038.11SS, 10249.C038.12SD, 10249.C038.12SS, 10249.C038.13SD, 10249.C038.13SS, 10249.C038.14SS, 10249.C038.15SD, 10249.C038.15SS, 10249.C038.16SD, 10249.C038.16SS, 10249.C038.18SS, 10249.C041.02SS, 10249.C041.03SS, 10249.C041.04SS, 10249.C041.05SD, 10249.C041.05SS, 10249.C041.06SD, 10249.C041.06SS, 10249.C041.08SS, 10249.C041.09SS, 10249.C041.10SS, 10249.C041.11SS, 10249.C041.12SS, 10249.C041.13SD, 10249.C041.13SS, 10249.C041.14SD, 10249.C041.14SS, 10249.C041.16SD, 10249.C041.16SS, 10249.C041.17SD, 10249.C041.17SS, 10249.C041.18SS, 10249.C041.19SS, 10249.C042.02SS, 10249.C042.03SS, 10249.C042.04SS, 10249.C042.05SS, 10249.C042.06SD, 10249.C042.06SS, 10249.C042.07SS, 10249.C042.08SS, 10249.C042.09SS, 10249.C042.10SS, 10249.C042.11SD, 10249.C042.11SS, 10249.C042.12SS, 10249.C042.13SS, 10249.C042.14SD, 10249.C042.14SS, 10249.C042.15SD, 10249.C042.15SS, 10249.C042.16SS, 10249.C042.17SS, 10249.C043.02SS, 10249.C043.03SS, 10249.C043.04SD, 10249.C043.04SS, 10249.C043.05SD, 10249.C043.05SS, 10249.C043.06SS, 10249.C043.07SS, 10249.C043.08SS, 10249.C043.09SS, 10249.C043.10SD, 10249.C043.10SS, 10249.C043.11SD, 10249.C043.11SS, 10249.C043.12SD, 10249.C043.12SS, 10249.C043.14SS, 10249.C043.15SD, 10249.C043.15SS, 10249.C043.16SS, 10249.C043.17SS, 10249.C043.18SS, 10249.C043.20SS, 10249.C044.02SS, 10249.C044.03SS, 10249.C044.04SS, 10249.C044.05SS, 10249.C044.06SS, 10249.C044.07SS, 10249.C044.08SS, 10249.C044.09SS, 10249.C044.10SS, 10249.C044.11SS, 10249.C044.12SD, 10249.C044.12SS, 10249.C044.13SD, 10249.C044.13SS, 10249.C044.15SD, 10249.C044.15SS, 10249.C044.16SS, 10249.C044.17SS, 10249.C045.02SS, 10249.C045.03SS, 10249.C045.04SS, 10249.C045.05SD, 10249.C045.05SS, 10249.C045.06SS, 10249.C045.08SD, 10249.C045.08SS, 10249.C045.09SD, 10249.C045.09SS, 10249.C045.10SD, 10249.C045.10SS, 10249.C045.11SS, 10249.C045.12SS, 10249.C045.13SS, 10249.C046.02SS, 10249.C046.03SS, 10249.C046.04SS, 10249.C046.05SS, 10249.C046.06SD, 10249.C046.06SS, 10249.C046.07SD, 10249.C046.07SS, 10249.C046.08SS, 10249.C046.09SD, 10249.C046.09SS, 10249.C046.10SD, 10249.C046.10SS, 10249.C046.11SD, 10249.C046.11SS, 10249.C046.12SS, 10249.C046.13SS, 10249.C046.14SS, 10249.C047.02SD, 10249.C047.02SS, 10249.C047.05SS, 10249.C047.06SD, 10249.C047.06SS, 10249.C047.07SD, 10249.C047.07SS, 10249.C047.08SD, 10249.C047.08SS, 10249.C047.09SS, 10249.C047.10SS, 10249.C047.11SS, 10249.C047.13SS, 10249.C049.03SD, 10249.C049.03SS, 10249.C049.04SS, 10249.C049.07SD, 10249.C049.07SS, 10249.C049.08SD, 10249.C049.08SS, 10249.C049.09SD, 10249.C049.09SS, 10249.C049.10SS, 10249.C049.11SS, 10249.C049.12SS, 10249.C049.13SS, 10249.C049.14SS, 10249.C052.03SD, 10249.C052.03SS, 10249.C052.04SD, 10249.C052.04SS, 10249.C052.05SD, 10249.C052.06SS, 10249.C052.07SS, 10249.C052.08SS, 10249.C052.09SS, 10249.C053.02SD, 10249.C053.02SS, 10249.C053.03SD, 10249.C053.03SS, 10249.C053.04SD, 10249.C053.04SS, 10249.C053.05SD, 10249.C053.05SS, 10249.C053.06SS, 10249.C053.07SS, 10249.C053.08SS, 10249.C053.09SS, 10249.C055.02SD, 10249.C055.02SS, 10249.C055.03SD, 10249.C055.03SS, 10249.C055.04SD, 10249.C055.04SS, 10249.C055.05SD, 10249.C055.05SS, 10249.C055.06SS, 10249.C055.07SS, 10249.C055.08SS, 10249.C055.09SS, 10249.C056.03SD, 10249.C056.03SS, 10249.C056.04SD, 10249.C056.04SS, 10249.C056.05SD, 10249.C056.05SS, 10249.C056.06SS, 10249.C056.07SS, 10249.C056.08SS, 10249.C056.09SS, 10249.C056.10SS, 10249.C057.02SS, 10249.C057.03SD, 10249.C057.03SS, 10249.C057.04SD, 10249.C057.04SS, 10249.C057.05SD, 10249.C057.05SS, 10249.C057.06SS, 10249.C057.08SS, 10249.C057.09SS, 10249.C057.10SS, 10249.C057.11SS
#> Updated feature table to match the subsetted data.
#> Updated feature annotation to match the subsetted data.
#> Data subsetting complete. Returning updated data object.
#> Data has been successfully normalized using TSS method.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: Removed 21 rows containing missing values or values outside the scale range
#> (`geom_bar()`).
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> $Phylum
#> $Phylum$Phylum
#> $Phylum$Phylum$indiv
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: Removed 21 rows containing missing values or values outside the scale range
#> (`geom_bar()`).

#> 
#> $Phylum$Phylum$average
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.

#> 
#> 
#> 

plot_feature_diversity(
data.obj = ecam.obj,
group.var = "antiexposedall",
strata.var = "delivery",
time.var = "month",
time.point.plot = unique(ecam.obj$meta.dat$month)[1],
is.plot.change = TRUE,
feature.level = c("Phylum", "Family", "Genus"),
feature.dat.type = "proportion",
features.plot = NULL,
prop.to.lump = 0.0001,
top.k.plot = NULL,
top.k.func = NULL,
renormalize = FALSE,
plot.other = TRUE,
plot.scheme = "combined",
plot.type = "dotplot"
)
#> Rule 1 passed: data.obj is a list.
#> Rule 2 passed: meta.dat is a data.frame.
#> Rule 3 passed: The row names of feature.tab match the row names of feature.ann.
#> Rule 4 passed: The order of rows in meta.dat has been adjusted to match feature.tab.
#> Rule 5 passed: feature.tab is a matrix.
#> Rule 6 passed: feature.ann is a matrix.
#> Please note: The data components should follow base R data.frame and matrix structures, not phyloseq's formal class.
#> Validation passed.
#> Note: Passing validation does not guarantee the absence of all data issues. Further data exploration may be needed.
#> Data has been subsetted based on the provided condition.
#> Updated metadata to match the subsetted data.
#> The following samples were excluded: 10249.C001.02SS, 10249.C001.03SS, 10249.C001.04SS, 10249.C001.05SS, 10249.C001.06SS, 10249.C001.07SS, 10249.C001.08SS, 10249.C001.09SS, 10249.C001.10SS, 10249.C001.11SS, 10249.C001.12SS, 10249.C001.13SS, 10249.C001.14SS, 10249.C001.15SS, 10249.C001.16SS, 10249.C001.17SS, 10249.C001.18SS, 10249.C001.19SS, 10249.C001.20SS, 10249.C001.25SS, 10249.C001.26SS, 10249.C001.27SS, 10249.C001.29SS, 10249.C001.30SS, 10249.C001.31SS, 10249.C001.32SS, 10249.C001.34SD, 10249.C001.34SS, 10249.C001.35SS, 10249.C001.36SD, 10249.C001.36SS, 10249.C002.02SS, 10249.C002.03SS, 10249.C002.04SS, 10249.C002.05SS, 10249.C002.06SS, 10249.C002.07SS, 10249.C002.08SS, 10249.C002.09SS, 10249.C002.10SS, 10249.C002.11SS, 10249.C002.12SS, 10249.C002.13SS, 10249.C002.15SS, 10249.C002.16SS, 10249.C002.18SS, 10249.C002.19SD, 10249.C002.19SS, 10249.C002.20SS, 10249.C002.21SD, 10249.C002.21SS, 10249.C004.02SS, 10249.C004.03SS, 10249.C004.04SS, 10249.C004.05SS, 10249.C004.06SS, 10249.C004.07SS, 10249.C004.08SS, 10249.C004.09SS, 10249.C004.10SS, 10249.C004.11SS, 10249.C004.12SS, 10249.C004.13SS, 10249.C004.14SS, 10249.C004.15SS, 10249.C005.02SS, 10249.C005.03SS, 10249.C005.04SS, 10249.C005.05SS, 10249.C005.07SS, 10249.C005.08SS, 10249.C005.09SS, 10249.C005.10SS, 10249.C005.11SS, 10249.C005.12SS, 10249.C005.13SS, 10249.C005.14SS, 10249.C005.15SS, 10249.C005.16SS, 10249.C005.17SS, 10249.C005.18SS, 10249.C005.19SD, 10249.C005.19SS, 10249.C005.20SS, 10249.C005.21SD, 10249.C005.21SS, 10249.C005.22SS, 10249.C007.02SS, 10249.C007.03SS, 10249.C007.04SS, 10249.C007.05SS, 10249.C007.06SS, 10249.C007.07SS, 10249.C007.08SS, 10249.C007.09SS, 10249.C007.10SS, 10249.C007.11SS, 10249.C007.12SS, 10249.C007.13SS, 10249.C007.14SS, 10249.C007.15SS, 10249.C007.16SS, 10249.C007.17SS, 10249.C007.18SS, 10249.C007.19SS, 10249.C007.20SS, 10249.C007.21SS, 10249.C007.22SD, 10249.C007.22SS, 10249.C007.23SD, 10249.C007.23SS, 10249.C007.24SD, 10249.C007.24SS, 10249.C007.26SS, 10249.C008.02SS, 10249.C008.03SS, 10249.C008.04SS, 10249.C008.05SS, 10249.C008.06SS, 10249.C008.07SS, 10249.C008.08SS, 10249.C008.09SS, 10249.C008.10SS, 10249.C008.11SS, 10249.C008.12SS, 10249.C008.13SS, 10249.C008.14SS, 10249.C008.15SS, 10249.C008.16SD, 10249.C008.16SS, 10249.C008.18SS, 10249.C009.02SS, 10249.C009.03SS, 10249.C009.04SS, 10249.C009.05SS, 10249.C009.06SS, 10249.C009.07SS, 10249.C009.08SS, 10249.C009.09SS, 10249.C009.10SS, 10249.C009.11SS, 10249.C009.12SS, 10249.C009.13SS, 10249.C009.14SS, 10249.C009.16SS, 10249.C009.17SS, 10249.C009.18SD, 10249.C009.18SS, 10249.C009.19SS, 10249.C009.20SD, 10249.C009.20SS, 10249.C009.21SS, 10249.C010.02SS, 10249.C010.03SS, 10249.C010.04SS, 10249.C010.05SS, 10249.C010.06SS, 10249.C010.07SS, 10249.C010.08SS, 10249.C010.09SS, 10249.C010.10SS, 10249.C010.11SS, 10249.C010.12SS, 10249.C010.13SS, 10249.C010.14SS, 10249.C010.15SS, 10249.C010.16SS, 10249.C010.18SD, 10249.C010.18SS, 10249.C010.19SS, 10249.C010.20SD, 10249.C010.20SS, 10249.C010.21SS, 10249.C011.02SS, 10249.C011.03SS, 10249.C011.04SS, 10249.C011.05SS, 10249.C011.06SS, 10249.C011.07SS, 10249.C011.08SS, 10249.C011.09SS, 10249.C011.10SS, 10249.C011.11SS, 10249.C011.12SS, 10249.C011.13SD, 10249.C011.14SS, 10249.C011.16SS, 10249.C011.17SD, 10249.C011.17SS, 10249.C011.18SS, 10249.C011.19SD, 10249.C011.19SS, 10249.C011.20SS, 10249.C011.21SS, 10249.C012.02SS, 10249.C012.03SS, 10249.C012.04SS, 10249.C012.05SS, 10249.C012.06SS, 10249.C012.07SS, 10249.C012.08SS, 10249.C012.09SS, 10249.C012.10SS, 10249.C012.11SS, 10249.C012.12SS, 10249.C012.13SS, 10249.C012.14SS, 10249.C012.15SS, 10249.C012.16SS, 10249.C012.17SS, 10249.C012.18SS, 10249.C012.19SD, 10249.C012.19SS, 10249.C012.20SS, 10249.C012.21SD, 10249.C012.21SS, 10249.C012.22SD, 10249.C012.22SS, 10249.C014.02SS, 10249.C014.03SS, 10249.C014.04SS, 10249.C014.05SS, 10249.C014.06SS, 10249.C014.07SS, 10249.C014.08SS, 10249.C014.09SS, 10249.C014.10SS, 10249.C014.12SS, 10249.C014.13SS, 10249.C014.15SS, 10249.C014.16SS, 10249.C014.17SS, 10249.C014.18SS, 10249.C014.19SD, 10249.C014.19SS, 10249.C014.20SD, 10249.C014.20SS, 10249.C014.21SS, 10249.C014.22SS, 10249.C016.03SS, 10249.C016.04SS, 10249.C016.05SS, 10249.C016.06SS, 10249.C016.07SS, 10249.C016.08SS, 10249.C016.09SS, 10249.C016.10SS, 10249.C016.11SS, 10249.C016.12SS, 10249.C016.13SS, 10249.C016.14SS, 10249.C016.15SS, 10249.C016.17SS, 10249.C016.18SS, 10249.C016.19SS, 10249.C016.20SS, 10249.C016.21SD, 10249.C016.21SS, 10249.C016.22SD, 10249.C016.22SS, 10249.C016.23SS, 10249.C016.24SS, 10249.C017.04SS, 10249.C017.05SS, 10249.C017.06SS, 10249.C017.07SS, 10249.C017.08SS, 10249.C017.09SS, 10249.C017.10SS, 10249.C017.11SS, 10249.C017.12SS, 10249.C018.02SS, 10249.C018.03SS, 10249.C018.04SS, 10249.C018.05SS, 10249.C018.06SS, 10249.C018.07SS, 10249.C018.08SS, 10249.C018.09SS, 10249.C018.10SS, 10249.C018.11SD, 10249.C018.11SS, 10249.C018.12SD, 10249.C018.12SS, 10249.C018.13SS, 10249.C018.14SS, 10249.C018.15SS, 10249.C018.16SS, 10249.C018.17SS, 10249.C018.18SS, 10249.C018.19SS, 10249.C020.06SS, 10249.C020.07SS, 10249.C020.08SS, 10249.C020.09SS, 10249.C020.10SS, 10249.C020.11SS, 10249.C020.12SS, 10249.C020.13SS, 10249.C020.14SS, 10249.C020.15SS, 10249.C020.16SS, 10249.C020.17SS, 10249.C020.18SS, 10249.C020.19SS, 10249.C020.20SS, 10249.C020.21SS, 10249.C020.22SD, 10249.C020.22SS, 10249.C020.23SD, 10249.C020.23SS, 10249.C020.24SD, 10249.C020.24SS, 10249.C020.25SD, 10249.C020.25SS, 10249.C020.26SD, 10249.C020.26SS, 10249.C020.28SS, 10249.C020.29SS, 10249.C021.03SS, 10249.C021.04SS, 10249.C021.05SS, 10249.C021.06SS, 10249.C021.07SS, 10249.C021.08SS, 10249.C021.09SS, 10249.C021.10SS, 10249.C021.12SS, 10249.C021.13SS, 10249.C022.02SS, 10249.C022.03SS, 10249.C022.04SS, 10249.C022.05SS, 10249.C022.06SS, 10249.C022.07SS, 10249.C022.08SS, 10249.C022.09SS, 10249.C022.10SS, 10249.C022.11SS, 10249.C022.12SS, 10249.C022.13SS, 10249.C022.15SS, 10249.C022.16SS, 10249.C022.18SD, 10249.C022.18SS, 10249.C022.19SS, 10249.C022.20SS, 10249.C022.21SS, 10249.C024.02SS, 10249.C024.03SS, 10249.C024.04SS, 10249.C024.05SS, 10249.C024.06SS, 10249.C024.07SS, 10249.C024.08SS, 10249.C024.09SS, 10249.C024.10SS, 10249.C024.12SS, 10249.C024.13SS, 10249.C024.14SS, 10249.C024.15SS, 10249.C024.16SS, 10249.C024.17SS, 10249.C024.18SS, 10249.C024.19SD, 10249.C024.19SS, 10249.C024.20SD, 10249.C024.20SS, 10249.C024.21SS, 10249.C024.22SS, 10249.C025.02SS, 10249.C025.03SS, 10249.C025.04SS, 10249.C025.05SS, 10249.C025.06SS, 10249.C025.07SS, 10249.C025.08SS, 10249.C025.09SS, 10249.C025.10SS, 10249.C025.11SS, 10249.C025.12SS, 10249.C025.13SD, 10249.C025.13SS, 10249.C025.14SD, 10249.C025.14SS, 10249.C025.15SS, 10249.C025.16SS, 10249.C025.17SS, 10249.C025.18SS, 10249.C025.19SD, 10249.C025.19SS, 10249.C025.20SS, 10249.C025.21SS, 10249.C027.02SS, 10249.C027.03SS, 10249.C027.04SS, 10249.C027.05SS, 10249.C027.06SS, 10249.C027.07SS, 10249.C027.08SS, 10249.C027.09SS, 10249.C027.10SS, 10249.C027.11SD, 10249.C027.12SD, 10249.C027.12SS, 10249.C027.13SS, 10249.C027.14SS, 10249.C027.15SS, 10249.C027.16SS, 10249.C027.17SD, 10249.C027.17SS, 10249.C027.18SS, 10249.C027.19SD, 10249.C027.19SS, 10249.C027.20SD, 10249.C027.20SS, 10249.C027.21SS, 10249.C027.22SS, 10249.C030.02SS, 10249.C030.03SS, 10249.C030.04SS, 10249.C030.05SS, 10249.C030.06SS, 10249.C030.07SS, 10249.C030.08SS, 10249.C030.09SS, 10249.C030.10SS, 10249.C030.11SD, 10249.C030.11SS, 10249.C030.12SS, 10249.C030.13SS, 10249.C030.14SS, 10249.C030.16SS, 10249.C030.17SD, 10249.C030.17SS, 10249.C030.18SS, 10249.C030.19SD, 10249.C030.19SS, 10249.C030.20SS, 10249.C031.02SS, 10249.C031.03SS, 10249.C031.04SS, 10249.C031.05SS, 10249.C031.06SS, 10249.C031.07SS, 10249.C031.08SS, 10249.C031.09SS, 10249.C031.10SS, 10249.C031.11SD, 10249.C031.11SS, 10249.C031.12SS, 10249.C031.13SS, 10249.C031.14SS, 10249.C031.16SS, 10249.C031.17SD, 10249.C031.17SS, 10249.C031.18SS, 10249.C031.19SD, 10249.C031.19SS, 10249.C031.20SS, 10249.C031.21SS, 10249.C032.02SS, 10249.C032.03SS, 10249.C032.04SS, 10249.C032.05SS, 10249.C032.06SS, 10249.C032.07SS, 10249.C032.09SS, 10249.C032.10SS, 10249.C032.11SD, 10249.C032.11SS, 10249.C032.12SD, 10249.C032.13SS, 10249.C032.14SS, 10249.C032.15SS, 10249.C032.16SS, 10249.C032.17SS, 10249.C032.19SD, 10249.C032.19SS, 10249.C032.20SD, 10249.C032.20SS, 10249.C032.21SS, 10249.C032.22SS, 10249.C033.02SS, 10249.C033.03SS, 10249.C033.04SS, 10249.C033.05SS, 10249.C033.06SS, 10249.C033.07SS, 10249.C033.08SS, 10249.C033.09SD, 10249.C033.09SS, 10249.C033.10SD, 10249.C033.10SS, 10249.C033.11SD, 10249.C033.11SS, 10249.C033.12SS, 10249.C033.13SS, 10249.C033.14SS, 10249.C033.15SS, 10249.C033.16SS, 10249.C033.17SD, 10249.C033.17SS, 10249.C033.18SD, 10249.C033.18SS, 10249.C033.19SS, 10249.C034.02SS, 10249.C034.03SS, 10249.C034.04SS, 10249.C034.05SS, 10249.C034.06SS, 10249.C034.07SS, 10249.C034.08SS, 10249.C034.09SS, 10249.C034.10SS, 10249.C034.11SS, 10249.C034.12SS, 10249.C034.13SS, 10249.C034.14SS, 10249.C034.15SD, 10249.C034.15SS, 10249.C034.16SS, 10249.C034.17SD, 10249.C034.17SS, 10249.C035.02SS, 10249.C035.03SS, 10249.C035.04SS, 10249.C035.05SS, 10249.C035.06SD, 10249.C035.06SS, 10249.C035.07SD, 10249.C035.07SS, 10249.C035.08SS, 10249.C035.09SS, 10249.C035.10SS, 10249.C035.11SS, 10249.C035.12SD, 10249.C035.12SS, 10249.C035.13SD, 10249.C035.13SS, 10249.C035.14SD, 10249.C035.14SS, 10249.C035.15SD, 10249.C035.15SS, 10249.C035.16SS, 10249.C035.17SS, 10249.C036.02SS, 10249.C036.03SS, 10249.C036.04SS, 10249.C036.05SD, 10249.C036.05SS, 10249.C036.07SS, 10249.C036.08SS, 10249.C036.09SS, 10249.C036.10SS, 10249.C036.11SS, 10249.C036.12SS, 10249.C036.13SS, 10249.C036.14SD, 10249.C036.14SS, 10249.C036.15SS, 10249.C036.16SS, 10249.C037.02SS, 10249.C037.04SS, 10249.C037.05SS, 10249.C037.06SS, 10249.C037.07SS, 10249.C037.08SS, 10249.C037.09SS, 10249.C037.10SS, 10249.C037.11SS, 10249.C037.12SD, 10249.C037.12SS, 10249.C037.13SD, 10249.C037.13SS, 10249.C037.14SS, 10249.C037.15SS, 10249.C037.16SS, 10249.C037.17SS, 10249.C037.18SS, 10249.C038.02SS, 10249.C038.04SS, 10249.C038.05SD, 10249.C038.05SS, 10249.C038.06SD, 10249.C038.06SS, 10249.C038.07SD, 10249.C038.07SS, 10249.C038.08SS, 10249.C038.09SS, 10249.C038.10SS, 10249.C038.11SS, 10249.C038.12SD, 10249.C038.12SS, 10249.C038.13SD, 10249.C038.13SS, 10249.C038.14SS, 10249.C038.15SD, 10249.C038.15SS, 10249.C038.16SD, 10249.C038.16SS, 10249.C038.18SS, 10249.C041.02SS, 10249.C041.03SS, 10249.C041.04SS, 10249.C041.05SD, 10249.C041.05SS, 10249.C041.06SD, 10249.C041.06SS, 10249.C041.08SS, 10249.C041.09SS, 10249.C041.10SS, 10249.C041.11SS, 10249.C041.12SS, 10249.C041.13SD, 10249.C041.13SS, 10249.C041.14SD, 10249.C041.14SS, 10249.C041.16SD, 10249.C041.16SS, 10249.C041.17SD, 10249.C041.17SS, 10249.C041.18SS, 10249.C041.19SS, 10249.C042.02SS, 10249.C042.03SS, 10249.C042.04SS, 10249.C042.05SS, 10249.C042.06SD, 10249.C042.06SS, 10249.C042.07SS, 10249.C042.08SS, 10249.C042.09SS, 10249.C042.10SS, 10249.C042.11SD, 10249.C042.11SS, 10249.C042.12SS, 10249.C042.13SS, 10249.C042.14SD, 10249.C042.14SS, 10249.C042.15SD, 10249.C042.15SS, 10249.C042.16SS, 10249.C042.17SS, 10249.C043.02SS, 10249.C043.03SS, 10249.C043.04SD, 10249.C043.04SS, 10249.C043.05SD, 10249.C043.05SS, 10249.C043.06SS, 10249.C043.07SS, 10249.C043.08SS, 10249.C043.09SS, 10249.C043.10SD, 10249.C043.10SS, 10249.C043.11SD, 10249.C043.11SS, 10249.C043.12SD, 10249.C043.12SS, 10249.C043.14SS, 10249.C043.15SD, 10249.C043.15SS, 10249.C043.16SS, 10249.C043.17SS, 10249.C043.18SS, 10249.C043.20SS, 10249.C044.02SS, 10249.C044.03SS, 10249.C044.04SS, 10249.C044.05SS, 10249.C044.06SS, 10249.C044.07SS, 10249.C044.08SS, 10249.C044.09SS, 10249.C044.10SS, 10249.C044.11SS, 10249.C044.12SD, 10249.C044.12SS, 10249.C044.13SD, 10249.C044.13SS, 10249.C044.15SD, 10249.C044.15SS, 10249.C044.16SS, 10249.C044.17SS, 10249.C045.02SS, 10249.C045.03SS, 10249.C045.04SS, 10249.C045.05SD, 10249.C045.05SS, 10249.C045.06SS, 10249.C045.08SD, 10249.C045.08SS, 10249.C045.09SD, 10249.C045.09SS, 10249.C045.10SD, 10249.C045.10SS, 10249.C045.11SS, 10249.C045.12SS, 10249.C045.13SS, 10249.C046.02SS, 10249.C046.03SS, 10249.C046.04SS, 10249.C046.05SS, 10249.C046.06SD, 10249.C046.06SS, 10249.C046.07SD, 10249.C046.07SS, 10249.C046.08SS, 10249.C046.09SD, 10249.C046.09SS, 10249.C046.10SD, 10249.C046.10SS, 10249.C046.11SD, 10249.C046.11SS, 10249.C046.12SS, 10249.C046.13SS, 10249.C046.14SS, 10249.C047.02SD, 10249.C047.02SS, 10249.C047.05SS, 10249.C047.06SD, 10249.C047.06SS, 10249.C047.07SD, 10249.C047.07SS, 10249.C047.08SD, 10249.C047.08SS, 10249.C047.09SS, 10249.C047.10SS, 10249.C047.11SS, 10249.C047.13SS, 10249.C049.03SD, 10249.C049.03SS, 10249.C049.04SS, 10249.C049.07SD, 10249.C049.07SS, 10249.C049.08SD, 10249.C049.08SS, 10249.C049.09SD, 10249.C049.09SS, 10249.C049.10SS, 10249.C049.11SS, 10249.C049.12SS, 10249.C049.13SS, 10249.C049.14SS, 10249.C052.03SD, 10249.C052.03SS, 10249.C052.04SD, 10249.C052.04SS, 10249.C052.05SD, 10249.C052.06SS, 10249.C052.07SS, 10249.C052.08SS, 10249.C052.09SS, 10249.C053.02SD, 10249.C053.02SS, 10249.C053.03SD, 10249.C053.03SS, 10249.C053.04SD, 10249.C053.04SS, 10249.C053.05SD, 10249.C053.05SS, 10249.C053.06SS, 10249.C053.07SS, 10249.C053.08SS, 10249.C053.09SS, 10249.C055.02SD, 10249.C055.02SS, 10249.C055.03SD, 10249.C055.03SS, 10249.C055.04SD, 10249.C055.04SS, 10249.C055.05SD, 10249.C055.05SS, 10249.C055.06SS, 10249.C055.07SS, 10249.C055.08SS, 10249.C055.09SS, 10249.C056.03SD, 10249.C056.03SS, 10249.C056.04SD, 10249.C056.04SS, 10249.C056.05SD, 10249.C056.05SS, 10249.C056.06SS, 10249.C056.07SS, 10249.C056.08SS, 10249.C056.09SS, 10249.C056.10SS, 10249.C057.02SS, 10249.C057.03SD, 10249.C057.03SS, 10249.C057.04SD, 10249.C057.04SS, 10249.C057.05SD, 10249.C057.05SS, 10249.C057.06SS, 10249.C057.08SS, 10249.C057.09SS, 10249.C057.10SS, 10249.C057.11SS
#> Updated feature table to match the subsetted data.
#> Updated feature annotation to match the subsetted data.
#> Data subsetting complete. Returning updated data object.
#> Rule 1 passed: data.obj is a list.
#> Rule 2 passed: meta.dat is a data.frame.
#> Rule 3 passed: The row names of feature.tab match the row names of feature.ann.
#> Rule 4 passed: The order of rows in meta.dat has been adjusted to match feature.tab.
#> Rule 5 passed: feature.tab is a matrix.
#> Rule 6 passed: feature.ann is a matrix.
#> Please note: The data components should follow base R data.frame and matrix structures, not phyloseq's formal class.
#> Validation passed.
#> Note: Passing validation does not guarantee the absence of all data issues. Further data exploration may be needed.
#> Data has been subsetted based on the provided condition.
#> Updated metadata to match the subsetted data.
#> The following samples were excluded: 10249.C001.02SS, 10249.C001.03SS, 10249.C001.04SS, 10249.C001.05SS, 10249.C001.06SS, 10249.C001.07SS, 10249.C001.08SS, 10249.C001.09SS, 10249.C001.10SS, 10249.C001.11SS, 10249.C001.12SS, 10249.C001.13SS, 10249.C001.14SS, 10249.C001.15SS, 10249.C001.16SS, 10249.C001.17SS, 10249.C001.18SS, 10249.C001.19SS, 10249.C001.20SS, 10249.C001.25SS, 10249.C001.26SS, 10249.C001.27SS, 10249.C001.29SS, 10249.C001.30SS, 10249.C001.31SS, 10249.C001.32SS, 10249.C001.34SD, 10249.C001.34SS, 10249.C001.35SS, 10249.C001.36SD, 10249.C001.36SS, 10249.C002.02SS, 10249.C002.03SS, 10249.C002.04SS, 10249.C002.05SS, 10249.C002.06SS, 10249.C002.07SS, 10249.C002.08SS, 10249.C002.09SS, 10249.C002.10SS, 10249.C002.11SS, 10249.C002.12SS, 10249.C002.13SS, 10249.C002.15SS, 10249.C002.16SS, 10249.C002.18SS, 10249.C002.19SD, 10249.C002.19SS, 10249.C002.20SS, 10249.C002.21SD, 10249.C002.21SS, 10249.C004.02SS, 10249.C004.03SS, 10249.C004.04SS, 10249.C004.05SS, 10249.C004.06SS, 10249.C004.07SS, 10249.C004.08SS, 10249.C004.09SS, 10249.C004.10SS, 10249.C004.11SS, 10249.C004.12SS, 10249.C004.13SS, 10249.C004.14SS, 10249.C004.15SS, 10249.C005.02SS, 10249.C005.03SS, 10249.C005.04SS, 10249.C005.05SS, 10249.C005.07SS, 10249.C005.08SS, 10249.C005.09SS, 10249.C005.10SS, 10249.C005.11SS, 10249.C005.12SS, 10249.C005.13SS, 10249.C005.14SS, 10249.C005.15SS, 10249.C005.16SS, 10249.C005.17SS, 10249.C005.18SS, 10249.C005.19SD, 10249.C005.19SS, 10249.C005.20SS, 10249.C005.21SD, 10249.C005.21SS, 10249.C005.22SS, 10249.C007.02SS, 10249.C007.03SS, 10249.C007.04SS, 10249.C007.05SS, 10249.C007.06SS, 10249.C007.07SS, 10249.C007.08SS, 10249.C007.09SS, 10249.C007.10SS, 10249.C007.11SS, 10249.C007.12SS, 10249.C007.13SS, 10249.C007.14SS, 10249.C007.15SS, 10249.C007.16SS, 10249.C007.17SS, 10249.C007.18SS, 10249.C007.19SS, 10249.C007.20SS, 10249.C007.21SS, 10249.C007.22SD, 10249.C007.22SS, 10249.C007.23SD, 10249.C007.23SS, 10249.C007.24SD, 10249.C007.24SS, 10249.C007.26SS, 10249.C008.02SS, 10249.C008.03SS, 10249.C008.04SS, 10249.C008.05SS, 10249.C008.06SS, 10249.C008.07SS, 10249.C008.08SS, 10249.C008.09SS, 10249.C008.10SS, 10249.C008.11SS, 10249.C008.12SS, 10249.C008.13SS, 10249.C008.14SS, 10249.C008.15SS, 10249.C008.16SD, 10249.C008.16SS, 10249.C008.18SS, 10249.C009.02SS, 10249.C009.03SS, 10249.C009.04SS, 10249.C009.05SS, 10249.C009.06SS, 10249.C009.07SS, 10249.C009.08SS, 10249.C009.09SS, 10249.C009.10SS, 10249.C009.11SS, 10249.C009.12SS, 10249.C009.13SS, 10249.C009.14SS, 10249.C009.16SS, 10249.C009.17SS, 10249.C009.18SD, 10249.C009.18SS, 10249.C009.19SS, 10249.C009.20SD, 10249.C009.20SS, 10249.C009.21SS, 10249.C010.02SS, 10249.C010.03SS, 10249.C010.04SS, 10249.C010.05SS, 10249.C010.06SS, 10249.C010.07SS, 10249.C010.08SS, 10249.C010.09SS, 10249.C010.10SS, 10249.C010.11SS, 10249.C010.12SS, 10249.C010.13SS, 10249.C010.14SS, 10249.C010.15SS, 10249.C010.16SS, 10249.C010.18SD, 10249.C010.18SS, 10249.C010.19SS, 10249.C010.20SD, 10249.C010.20SS, 10249.C010.21SS, 10249.C011.02SS, 10249.C011.03SS, 10249.C011.04SS, 10249.C011.05SS, 10249.C011.06SS, 10249.C011.07SS, 10249.C011.08SS, 10249.C011.09SS, 10249.C011.10SS, 10249.C011.11SS, 10249.C011.12SS, 10249.C011.13SD, 10249.C011.14SS, 10249.C011.16SS, 10249.C011.17SD, 10249.C011.17SS, 10249.C011.18SS, 10249.C011.19SD, 10249.C011.19SS, 10249.C011.20SS, 10249.C011.21SS, 10249.C012.02SS, 10249.C012.03SS, 10249.C012.04SS, 10249.C012.05SS, 10249.C012.06SS, 10249.C012.07SS, 10249.C012.08SS, 10249.C012.09SS, 10249.C012.10SS, 10249.C012.11SS, 10249.C012.12SS, 10249.C012.13SS, 10249.C012.14SS, 10249.C012.15SS, 10249.C012.16SS, 10249.C012.17SS, 10249.C012.18SS, 10249.C012.19SD, 10249.C012.19SS, 10249.C012.20SS, 10249.C012.21SD, 10249.C012.21SS, 10249.C012.22SD, 10249.C012.22SS, 10249.C014.02SS, 10249.C014.03SS, 10249.C014.04SS, 10249.C014.05SS, 10249.C014.06SS, 10249.C014.07SS, 10249.C014.08SS, 10249.C014.09SS, 10249.C014.10SS, 10249.C014.12SS, 10249.C014.13SS, 10249.C014.15SS, 10249.C014.16SS, 10249.C014.17SS, 10249.C014.18SS, 10249.C014.19SD, 10249.C014.19SS, 10249.C014.20SD, 10249.C014.20SS, 10249.C014.21SS, 10249.C014.22SS, 10249.C016.03SS, 10249.C016.04SS, 10249.C016.05SS, 10249.C016.06SS, 10249.C016.07SS, 10249.C016.08SS, 10249.C016.09SS, 10249.C016.10SS, 10249.C016.11SS, 10249.C016.12SS, 10249.C016.13SS, 10249.C016.14SS, 10249.C016.15SS, 10249.C016.17SS, 10249.C016.18SS, 10249.C016.19SS, 10249.C016.20SS, 10249.C016.21SD, 10249.C016.21SS, 10249.C016.22SD, 10249.C016.22SS, 10249.C016.23SS, 10249.C016.24SS, 10249.C017.04SS, 10249.C017.05SS, 10249.C017.06SS, 10249.C017.07SS, 10249.C017.08SS, 10249.C017.09SS, 10249.C017.10SS, 10249.C017.11SS, 10249.C017.12SS, 10249.C018.02SS, 10249.C018.03SS, 10249.C018.04SS, 10249.C018.05SS, 10249.C018.06SS, 10249.C018.07SS, 10249.C018.08SS, 10249.C018.09SS, 10249.C018.10SS, 10249.C018.11SD, 10249.C018.11SS, 10249.C018.12SD, 10249.C018.12SS, 10249.C018.13SS, 10249.C018.14SS, 10249.C018.15SS, 10249.C018.16SS, 10249.C018.17SS, 10249.C018.18SS, 10249.C018.19SS, 10249.C020.06SS, 10249.C020.07SS, 10249.C020.08SS, 10249.C020.09SS, 10249.C020.10SS, 10249.C020.11SS, 10249.C020.12SS, 10249.C020.13SS, 10249.C020.14SS, 10249.C020.15SS, 10249.C020.16SS, 10249.C020.17SS, 10249.C020.18SS, 10249.C020.19SS, 10249.C020.20SS, 10249.C020.21SS, 10249.C020.22SD, 10249.C020.22SS, 10249.C020.23SD, 10249.C020.23SS, 10249.C020.24SD, 10249.C020.24SS, 10249.C020.25SD, 10249.C020.25SS, 10249.C020.26SD, 10249.C020.26SS, 10249.C020.28SS, 10249.C020.29SS, 10249.C021.03SS, 10249.C021.04SS, 10249.C021.05SS, 10249.C021.06SS, 10249.C021.07SS, 10249.C021.08SS, 10249.C021.09SS, 10249.C021.10SS, 10249.C021.12SS, 10249.C021.13SS, 10249.C022.02SS, 10249.C022.03SS, 10249.C022.04SS, 10249.C022.05SS, 10249.C022.06SS, 10249.C022.07SS, 10249.C022.08SS, 10249.C022.09SS, 10249.C022.10SS, 10249.C022.11SS, 10249.C022.12SS, 10249.C022.13SS, 10249.C022.15SS, 10249.C022.16SS, 10249.C022.18SD, 10249.C022.18SS, 10249.C022.19SS, 10249.C022.20SS, 10249.C022.21SS, 10249.C024.02SS, 10249.C024.03SS, 10249.C024.04SS, 10249.C024.05SS, 10249.C024.06SS, 10249.C024.07SS, 10249.C024.08SS, 10249.C024.09SS, 10249.C024.10SS, 10249.C024.12SS, 10249.C024.13SS, 10249.C024.14SS, 10249.C024.15SS, 10249.C024.16SS, 10249.C024.17SS, 10249.C024.18SS, 10249.C024.19SD, 10249.C024.19SS, 10249.C024.20SD, 10249.C024.20SS, 10249.C024.21SS, 10249.C024.22SS, 10249.C025.02SS, 10249.C025.03SS, 10249.C025.04SS, 10249.C025.05SS, 10249.C025.06SS, 10249.C025.07SS, 10249.C025.08SS, 10249.C025.09SS, 10249.C025.10SS, 10249.C025.11SS, 10249.C025.12SS, 10249.C025.13SD, 10249.C025.13SS, 10249.C025.14SD, 10249.C025.14SS, 10249.C025.15SS, 10249.C025.16SS, 10249.C025.17SS, 10249.C025.18SS, 10249.C025.19SD, 10249.C025.19SS, 10249.C025.20SS, 10249.C025.21SS, 10249.C027.02SS, 10249.C027.03SS, 10249.C027.04SS, 10249.C027.05SS, 10249.C027.06SS, 10249.C027.07SS, 10249.C027.08SS, 10249.C027.09SS, 10249.C027.10SS, 10249.C027.11SD, 10249.C027.12SD, 10249.C027.12SS, 10249.C027.13SS, 10249.C027.14SS, 10249.C027.15SS, 10249.C027.16SS, 10249.C027.17SD, 10249.C027.17SS, 10249.C027.18SS, 10249.C027.19SD, 10249.C027.19SS, 10249.C027.20SD, 10249.C027.20SS, 10249.C027.21SS, 10249.C027.22SS, 10249.C030.02SS, 10249.C030.03SS, 10249.C030.04SS, 10249.C030.05SS, 10249.C030.06SS, 10249.C030.07SS, 10249.C030.08SS, 10249.C030.09SS, 10249.C030.10SS, 10249.C030.11SD, 10249.C030.11SS, 10249.C030.12SS, 10249.C030.13SS, 10249.C030.14SS, 10249.C030.16SS, 10249.C030.17SD, 10249.C030.17SS, 10249.C030.18SS, 10249.C030.19SD, 10249.C030.19SS, 10249.C030.20SS, 10249.C031.02SS, 10249.C031.03SS, 10249.C031.04SS, 10249.C031.05SS, 10249.C031.06SS, 10249.C031.07SS, 10249.C031.08SS, 10249.C031.09SS, 10249.C031.10SS, 10249.C031.11SD, 10249.C031.11SS, 10249.C031.12SS, 10249.C031.13SS, 10249.C031.14SS, 10249.C031.16SS, 10249.C031.17SD, 10249.C031.17SS, 10249.C031.18SS, 10249.C031.19SD, 10249.C031.19SS, 10249.C031.20SS, 10249.C031.21SS, 10249.C032.02SS, 10249.C032.03SS, 10249.C032.04SS, 10249.C032.05SS, 10249.C032.06SS, 10249.C032.07SS, 10249.C032.09SS, 10249.C032.10SS, 10249.C032.11SD, 10249.C032.11SS, 10249.C032.12SD, 10249.C032.13SS, 10249.C032.14SS, 10249.C032.15SS, 10249.C032.16SS, 10249.C032.17SS, 10249.C032.19SD, 10249.C032.19SS, 10249.C032.20SD, 10249.C032.20SS, 10249.C032.21SS, 10249.C032.22SS, 10249.C033.02SS, 10249.C033.03SS, 10249.C033.04SS, 10249.C033.05SS, 10249.C033.06SS, 10249.C033.07SS, 10249.C033.08SS, 10249.C033.09SD, 10249.C033.09SS, 10249.C033.10SD, 10249.C033.10SS, 10249.C033.11SD, 10249.C033.11SS, 10249.C033.12SS, 10249.C033.13SS, 10249.C033.14SS, 10249.C033.15SS, 10249.C033.16SS, 10249.C033.17SD, 10249.C033.17SS, 10249.C033.18SD, 10249.C033.18SS, 10249.C033.19SS, 10249.C034.02SS, 10249.C034.03SS, 10249.C034.04SS, 10249.C034.05SS, 10249.C034.06SS, 10249.C034.07SS, 10249.C034.08SS, 10249.C034.09SS, 10249.C034.10SS, 10249.C034.11SS, 10249.C034.12SS, 10249.C034.13SS, 10249.C034.14SS, 10249.C034.15SD, 10249.C034.15SS, 10249.C034.16SS, 10249.C034.17SD, 10249.C034.17SS, 10249.C035.02SS, 10249.C035.03SS, 10249.C035.04SS, 10249.C035.05SS, 10249.C035.06SD, 10249.C035.06SS, 10249.C035.07SD, 10249.C035.07SS, 10249.C035.08SS, 10249.C035.09SS, 10249.C035.10SS, 10249.C035.11SS, 10249.C035.12SD, 10249.C035.12SS, 10249.C035.13SD, 10249.C035.13SS, 10249.C035.14SD, 10249.C035.14SS, 10249.C035.15SD, 10249.C035.15SS, 10249.C035.16SS, 10249.C035.17SS, 10249.C036.02SS, 10249.C036.03SS, 10249.C036.04SS, 10249.C036.05SD, 10249.C036.05SS, 10249.C036.07SS, 10249.C036.08SS, 10249.C036.09SS, 10249.C036.10SS, 10249.C036.11SS, 10249.C036.12SS, 10249.C036.13SS, 10249.C036.14SD, 10249.C036.14SS, 10249.C036.15SS, 10249.C036.16SS, 10249.C037.02SS, 10249.C037.04SS, 10249.C037.05SS, 10249.C037.06SS, 10249.C037.07SS, 10249.C037.08SS, 10249.C037.09SS, 10249.C037.10SS, 10249.C037.11SS, 10249.C037.12SD, 10249.C037.12SS, 10249.C037.13SD, 10249.C037.13SS, 10249.C037.14SS, 10249.C037.15SS, 10249.C037.16SS, 10249.C037.17SS, 10249.C037.18SS, 10249.C038.02SS, 10249.C038.04SS, 10249.C038.05SD, 10249.C038.05SS, 10249.C038.06SD, 10249.C038.06SS, 10249.C038.07SD, 10249.C038.07SS, 10249.C038.08SS, 10249.C038.09SS, 10249.C038.10SS, 10249.C038.11SS, 10249.C038.12SD, 10249.C038.12SS, 10249.C038.13SD, 10249.C038.13SS, 10249.C038.14SS, 10249.C038.15SD, 10249.C038.15SS, 10249.C038.16SD, 10249.C038.16SS, 10249.C038.18SS, 10249.C041.02SS, 10249.C041.03SS, 10249.C041.04SS, 10249.C041.05SD, 10249.C041.05SS, 10249.C041.06SD, 10249.C041.06SS, 10249.C041.08SS, 10249.C041.09SS, 10249.C041.10SS, 10249.C041.11SS, 10249.C041.12SS, 10249.C041.13SD, 10249.C041.13SS, 10249.C041.14SD, 10249.C041.14SS, 10249.C041.16SD, 10249.C041.16SS, 10249.C041.17SD, 10249.C041.17SS, 10249.C041.18SS, 10249.C041.19SS, 10249.C042.02SS, 10249.C042.03SS, 10249.C042.04SS, 10249.C042.05SS, 10249.C042.06SD, 10249.C042.06SS, 10249.C042.07SS, 10249.C042.08SS, 10249.C042.09SS, 10249.C042.10SS, 10249.C042.11SD, 10249.C042.11SS, 10249.C042.12SS, 10249.C042.13SS, 10249.C042.14SD, 10249.C042.14SS, 10249.C042.15SD, 10249.C042.15SS, 10249.C042.16SS, 10249.C042.17SS, 10249.C043.02SS, 10249.C043.03SS, 10249.C043.04SD, 10249.C043.04SS, 10249.C043.05SD, 10249.C043.05SS, 10249.C043.06SS, 10249.C043.07SS, 10249.C043.08SS, 10249.C043.09SS, 10249.C043.10SD, 10249.C043.10SS, 10249.C043.11SD, 10249.C043.11SS, 10249.C043.12SD, 10249.C043.12SS, 10249.C043.14SS, 10249.C043.15SD, 10249.C043.15SS, 10249.C043.16SS, 10249.C043.17SS, 10249.C043.18SS, 10249.C043.20SS, 10249.C044.02SS, 10249.C044.03SS, 10249.C044.04SS, 10249.C044.05SS, 10249.C044.06SS, 10249.C044.07SS, 10249.C044.08SS, 10249.C044.09SS, 10249.C044.10SS, 10249.C044.11SS, 10249.C044.12SD, 10249.C044.12SS, 10249.C044.13SD, 10249.C044.13SS, 10249.C044.15SD, 10249.C044.15SS, 10249.C044.16SS, 10249.C044.17SS, 10249.C045.02SS, 10249.C045.03SS, 10249.C045.04SS, 10249.C045.05SD, 10249.C045.05SS, 10249.C045.06SS, 10249.C045.08SD, 10249.C045.08SS, 10249.C045.09SD, 10249.C045.09SS, 10249.C045.10SD, 10249.C045.10SS, 10249.C045.11SS, 10249.C045.12SS, 10249.C045.13SS, 10249.C046.02SS, 10249.C046.03SS, 10249.C046.04SS, 10249.C046.05SS, 10249.C046.06SD, 10249.C046.06SS, 10249.C046.07SD, 10249.C046.07SS, 10249.C046.08SS, 10249.C046.09SD, 10249.C046.09SS, 10249.C046.10SD, 10249.C046.10SS, 10249.C046.11SD, 10249.C046.11SS, 10249.C046.12SS, 10249.C046.13SS, 10249.C046.14SS, 10249.C047.02SD, 10249.C047.02SS, 10249.C047.05SS, 10249.C047.06SD, 10249.C047.06SS, 10249.C047.07SD, 10249.C047.07SS, 10249.C047.08SD, 10249.C047.08SS, 10249.C047.09SS, 10249.C047.10SS, 10249.C047.11SS, 10249.C047.13SS, 10249.C049.03SD, 10249.C049.03SS, 10249.C049.04SS, 10249.C049.07SD, 10249.C049.07SS, 10249.C049.08SD, 10249.C049.08SS, 10249.C049.09SD, 10249.C049.09SS, 10249.C049.10SS, 10249.C049.11SS, 10249.C049.12SS, 10249.C049.13SS, 10249.C049.14SS, 10249.C052.03SD, 10249.C052.03SS, 10249.C052.04SD, 10249.C052.04SS, 10249.C052.05SD, 10249.C052.06SS, 10249.C052.07SS, 10249.C052.08SS, 10249.C052.09SS, 10249.C053.02SD, 10249.C053.02SS, 10249.C053.03SD, 10249.C053.03SS, 10249.C053.04SD, 10249.C053.04SS, 10249.C053.05SD, 10249.C053.05SS, 10249.C053.06SS, 10249.C053.07SS, 10249.C053.08SS, 10249.C053.09SS, 10249.C055.02SD, 10249.C055.02SS, 10249.C055.03SD, 10249.C055.03SS, 10249.C055.04SD, 10249.C055.04SS, 10249.C055.05SD, 10249.C055.05SS, 10249.C055.06SS, 10249.C055.07SS, 10249.C055.08SS, 10249.C055.09SS, 10249.C056.03SD, 10249.C056.03SS, 10249.C056.04SD, 10249.C056.04SS, 10249.C056.05SD, 10249.C056.05SS, 10249.C056.06SS, 10249.C056.07SS, 10249.C056.08SS, 10249.C056.09SS, 10249.C056.10SS, 10249.C057.02SS, 10249.C057.03SD, 10249.C057.03SS, 10249.C057.04SD, 10249.C057.04SS, 10249.C057.05SD, 10249.C057.05SS, 10249.C057.06SS, 10249.C057.08SS, 10249.C057.09SS, 10249.C057.10SS, 10249.C057.11SS
#> Updated feature table to match the subsetted data.
#> Updated feature annotation to match the subsetted data.
#> Data subsetting complete. Returning updated data object.
#> Rule 1 passed: data.obj is a list.
#> Rule 2 passed: meta.dat is a data.frame.
#> Rule 3 passed: The row names of feature.tab match the row names of feature.ann.
#> Rule 4 passed: The order of rows in meta.dat has been adjusted to match feature.tab.
#> Rule 5 passed: feature.tab is a matrix.
#> Rule 6 passed: feature.ann is a matrix.
#> Please note: The data components should follow base R data.frame and matrix structures, not phyloseq's formal class.
#> Validation passed.
#> Note: Passing validation does not guarantee the absence of all data issues. Further data exploration may be needed.
#> Data has been subsetted based on the provided condition.
#> Updated metadata to match the subsetted data.
#> The following samples were excluded: 10249.C001.02SS, 10249.C001.03SS, 10249.C001.04SS, 10249.C001.05SS, 10249.C001.06SS, 10249.C001.07SS, 10249.C001.08SS, 10249.C001.09SS, 10249.C001.10SS, 10249.C001.11SS, 10249.C001.12SS, 10249.C001.13SS, 10249.C001.14SS, 10249.C001.15SS, 10249.C001.16SS, 10249.C001.17SS, 10249.C001.18SS, 10249.C001.19SS, 10249.C001.20SS, 10249.C001.25SS, 10249.C001.26SS, 10249.C001.27SS, 10249.C001.29SS, 10249.C001.30SS, 10249.C001.31SS, 10249.C001.32SS, 10249.C001.34SD, 10249.C001.34SS, 10249.C001.35SS, 10249.C001.36SD, 10249.C001.36SS, 10249.C002.02SS, 10249.C002.03SS, 10249.C002.04SS, 10249.C002.05SS, 10249.C002.06SS, 10249.C002.07SS, 10249.C002.08SS, 10249.C002.09SS, 10249.C002.10SS, 10249.C002.11SS, 10249.C002.12SS, 10249.C002.13SS, 10249.C002.15SS, 10249.C002.16SS, 10249.C002.18SS, 10249.C002.19SD, 10249.C002.19SS, 10249.C002.20SS, 10249.C002.21SD, 10249.C002.21SS, 10249.C004.02SS, 10249.C004.03SS, 10249.C004.04SS, 10249.C004.05SS, 10249.C004.06SS, 10249.C004.07SS, 10249.C004.08SS, 10249.C004.09SS, 10249.C004.10SS, 10249.C004.11SS, 10249.C004.12SS, 10249.C004.13SS, 10249.C004.14SS, 10249.C004.15SS, 10249.C005.02SS, 10249.C005.03SS, 10249.C005.04SS, 10249.C005.05SS, 10249.C005.07SS, 10249.C005.08SS, 10249.C005.09SS, 10249.C005.10SS, 10249.C005.11SS, 10249.C005.12SS, 10249.C005.13SS, 10249.C005.14SS, 10249.C005.15SS, 10249.C005.16SS, 10249.C005.17SS, 10249.C005.18SS, 10249.C005.19SD, 10249.C005.19SS, 10249.C005.20SS, 10249.C005.21SD, 10249.C005.21SS, 10249.C005.22SS, 10249.C007.02SS, 10249.C007.03SS, 10249.C007.04SS, 10249.C007.05SS, 10249.C007.06SS, 10249.C007.07SS, 10249.C007.08SS, 10249.C007.09SS, 10249.C007.10SS, 10249.C007.11SS, 10249.C007.12SS, 10249.C007.13SS, 10249.C007.14SS, 10249.C007.15SS, 10249.C007.16SS, 10249.C007.17SS, 10249.C007.18SS, 10249.C007.19SS, 10249.C007.20SS, 10249.C007.21SS, 10249.C007.22SD, 10249.C007.22SS, 10249.C007.23SD, 10249.C007.23SS, 10249.C007.24SD, 10249.C007.24SS, 10249.C007.26SS, 10249.C008.02SS, 10249.C008.03SS, 10249.C008.04SS, 10249.C008.05SS, 10249.C008.06SS, 10249.C008.07SS, 10249.C008.08SS, 10249.C008.09SS, 10249.C008.10SS, 10249.C008.11SS, 10249.C008.12SS, 10249.C008.13SS, 10249.C008.14SS, 10249.C008.15SS, 10249.C008.16SD, 10249.C008.16SS, 10249.C008.18SS, 10249.C009.02SS, 10249.C009.03SS, 10249.C009.04SS, 10249.C009.05SS, 10249.C009.06SS, 10249.C009.07SS, 10249.C009.08SS, 10249.C009.09SS, 10249.C009.10SS, 10249.C009.11SS, 10249.C009.12SS, 10249.C009.13SS, 10249.C009.14SS, 10249.C009.16SS, 10249.C009.17SS, 10249.C009.18SD, 10249.C009.18SS, 10249.C009.19SS, 10249.C009.20SD, 10249.C009.20SS, 10249.C009.21SS, 10249.C010.02SS, 10249.C010.03SS, 10249.C010.04SS, 10249.C010.05SS, 10249.C010.06SS, 10249.C010.07SS, 10249.C010.08SS, 10249.C010.09SS, 10249.C010.10SS, 10249.C010.11SS, 10249.C010.12SS, 10249.C010.13SS, 10249.C010.14SS, 10249.C010.15SS, 10249.C010.16SS, 10249.C010.18SD, 10249.C010.18SS, 10249.C010.19SS, 10249.C010.20SD, 10249.C010.20SS, 10249.C010.21SS, 10249.C011.02SS, 10249.C011.03SS, 10249.C011.04SS, 10249.C011.05SS, 10249.C011.06SS, 10249.C011.07SS, 10249.C011.08SS, 10249.C011.09SS, 10249.C011.10SS, 10249.C011.11SS, 10249.C011.12SS, 10249.C011.13SD, 10249.C011.14SS, 10249.C011.16SS, 10249.C011.17SD, 10249.C011.17SS, 10249.C011.18SS, 10249.C011.19SD, 10249.C011.19SS, 10249.C011.20SS, 10249.C011.21SS, 10249.C012.02SS, 10249.C012.03SS, 10249.C012.04SS, 10249.C012.05SS, 10249.C012.06SS, 10249.C012.07SS, 10249.C012.08SS, 10249.C012.09SS, 10249.C012.10SS, 10249.C012.11SS, 10249.C012.12SS, 10249.C012.13SS, 10249.C012.14SS, 10249.C012.15SS, 10249.C012.16SS, 10249.C012.17SS, 10249.C012.18SS, 10249.C012.19SD, 10249.C012.19SS, 10249.C012.20SS, 10249.C012.21SD, 10249.C012.21SS, 10249.C012.22SD, 10249.C012.22SS, 10249.C014.02SS, 10249.C014.03SS, 10249.C014.04SS, 10249.C014.05SS, 10249.C014.06SS, 10249.C014.07SS, 10249.C014.08SS, 10249.C014.09SS, 10249.C014.10SS, 10249.C014.12SS, 10249.C014.13SS, 10249.C014.15SS, 10249.C014.16SS, 10249.C014.17SS, 10249.C014.18SS, 10249.C014.19SD, 10249.C014.19SS, 10249.C014.20SD, 10249.C014.20SS, 10249.C014.21SS, 10249.C014.22SS, 10249.C016.03SS, 10249.C016.04SS, 10249.C016.05SS, 10249.C016.06SS, 10249.C016.07SS, 10249.C016.08SS, 10249.C016.09SS, 10249.C016.10SS, 10249.C016.11SS, 10249.C016.12SS, 10249.C016.13SS, 10249.C016.14SS, 10249.C016.15SS, 10249.C016.17SS, 10249.C016.18SS, 10249.C016.19SS, 10249.C016.20SS, 10249.C016.21SD, 10249.C016.21SS, 10249.C016.22SD, 10249.C016.22SS, 10249.C016.23SS, 10249.C016.24SS, 10249.C017.04SS, 10249.C017.05SS, 10249.C017.06SS, 10249.C017.07SS, 10249.C017.08SS, 10249.C017.09SS, 10249.C017.10SS, 10249.C017.11SS, 10249.C017.12SS, 10249.C018.02SS, 10249.C018.03SS, 10249.C018.04SS, 10249.C018.05SS, 10249.C018.06SS, 10249.C018.07SS, 10249.C018.08SS, 10249.C018.09SS, 10249.C018.10SS, 10249.C018.11SD, 10249.C018.11SS, 10249.C018.12SD, 10249.C018.12SS, 10249.C018.13SS, 10249.C018.14SS, 10249.C018.15SS, 10249.C018.16SS, 10249.C018.17SS, 10249.C018.18SS, 10249.C018.19SS, 10249.C020.06SS, 10249.C020.07SS, 10249.C020.08SS, 10249.C020.09SS, 10249.C020.10SS, 10249.C020.11SS, 10249.C020.12SS, 10249.C020.13SS, 10249.C020.14SS, 10249.C020.15SS, 10249.C020.16SS, 10249.C020.17SS, 10249.C020.18SS, 10249.C020.19SS, 10249.C020.20SS, 10249.C020.21SS, 10249.C020.22SD, 10249.C020.22SS, 10249.C020.23SD, 10249.C020.23SS, 10249.C020.24SD, 10249.C020.24SS, 10249.C020.25SD, 10249.C020.25SS, 10249.C020.26SD, 10249.C020.26SS, 10249.C020.28SS, 10249.C020.29SS, 10249.C021.03SS, 10249.C021.04SS, 10249.C021.05SS, 10249.C021.06SS, 10249.C021.07SS, 10249.C021.08SS, 10249.C021.09SS, 10249.C021.10SS, 10249.C021.12SS, 10249.C021.13SS, 10249.C022.02SS, 10249.C022.03SS, 10249.C022.04SS, 10249.C022.05SS, 10249.C022.06SS, 10249.C022.07SS, 10249.C022.08SS, 10249.C022.09SS, 10249.C022.10SS, 10249.C022.11SS, 10249.C022.12SS, 10249.C022.13SS, 10249.C022.15SS, 10249.C022.16SS, 10249.C022.18SD, 10249.C022.18SS, 10249.C022.19SS, 10249.C022.20SS, 10249.C022.21SS, 10249.C024.02SS, 10249.C024.03SS, 10249.C024.04SS, 10249.C024.05SS, 10249.C024.06SS, 10249.C024.07SS, 10249.C024.08SS, 10249.C024.09SS, 10249.C024.10SS, 10249.C024.12SS, 10249.C024.13SS, 10249.C024.14SS, 10249.C024.15SS, 10249.C024.16SS, 10249.C024.17SS, 10249.C024.18SS, 10249.C024.19SD, 10249.C024.19SS, 10249.C024.20SD, 10249.C024.20SS, 10249.C024.21SS, 10249.C024.22SS, 10249.C025.02SS, 10249.C025.03SS, 10249.C025.04SS, 10249.C025.05SS, 10249.C025.06SS, 10249.C025.07SS, 10249.C025.08SS, 10249.C025.09SS, 10249.C025.10SS, 10249.C025.11SS, 10249.C025.12SS, 10249.C025.13SD, 10249.C025.13SS, 10249.C025.14SD, 10249.C025.14SS, 10249.C025.15SS, 10249.C025.16SS, 10249.C025.17SS, 10249.C025.18SS, 10249.C025.19SD, 10249.C025.19SS, 10249.C025.20SS, 10249.C025.21SS, 10249.C027.02SS, 10249.C027.03SS, 10249.C027.04SS, 10249.C027.05SS, 10249.C027.06SS, 10249.C027.07SS, 10249.C027.08SS, 10249.C027.09SS, 10249.C027.10SS, 10249.C027.11SD, 10249.C027.12SD, 10249.C027.12SS, 10249.C027.13SS, 10249.C027.14SS, 10249.C027.15SS, 10249.C027.16SS, 10249.C027.17SD, 10249.C027.17SS, 10249.C027.18SS, 10249.C027.19SD, 10249.C027.19SS, 10249.C027.20SD, 10249.C027.20SS, 10249.C027.21SS, 10249.C027.22SS, 10249.C030.02SS, 10249.C030.03SS, 10249.C030.04SS, 10249.C030.05SS, 10249.C030.06SS, 10249.C030.07SS, 10249.C030.08SS, 10249.C030.09SS, 10249.C030.10SS, 10249.C030.11SD, 10249.C030.11SS, 10249.C030.12SS, 10249.C030.13SS, 10249.C030.14SS, 10249.C030.16SS, 10249.C030.17SD, 10249.C030.17SS, 10249.C030.18SS, 10249.C030.19SD, 10249.C030.19SS, 10249.C030.20SS, 10249.C031.02SS, 10249.C031.03SS, 10249.C031.04SS, 10249.C031.05SS, 10249.C031.06SS, 10249.C031.07SS, 10249.C031.08SS, 10249.C031.09SS, 10249.C031.10SS, 10249.C031.11SD, 10249.C031.11SS, 10249.C031.12SS, 10249.C031.13SS, 10249.C031.14SS, 10249.C031.16SS, 10249.C031.17SD, 10249.C031.17SS, 10249.C031.18SS, 10249.C031.19SD, 10249.C031.19SS, 10249.C031.20SS, 10249.C031.21SS, 10249.C032.02SS, 10249.C032.03SS, 10249.C032.04SS, 10249.C032.05SS, 10249.C032.06SS, 10249.C032.07SS, 10249.C032.09SS, 10249.C032.10SS, 10249.C032.11SD, 10249.C032.11SS, 10249.C032.12SD, 10249.C032.13SS, 10249.C032.14SS, 10249.C032.15SS, 10249.C032.16SS, 10249.C032.17SS, 10249.C032.19SD, 10249.C032.19SS, 10249.C032.20SD, 10249.C032.20SS, 10249.C032.21SS, 10249.C032.22SS, 10249.C033.02SS, 10249.C033.03SS, 10249.C033.04SS, 10249.C033.05SS, 10249.C033.06SS, 10249.C033.07SS, 10249.C033.08SS, 10249.C033.09SD, 10249.C033.09SS, 10249.C033.10SD, 10249.C033.10SS, 10249.C033.11SD, 10249.C033.11SS, 10249.C033.12SS, 10249.C033.13SS, 10249.C033.14SS, 10249.C033.15SS, 10249.C033.16SS, 10249.C033.17SD, 10249.C033.17SS, 10249.C033.18SD, 10249.C033.18SS, 10249.C033.19SS, 10249.C034.02SS, 10249.C034.03SS, 10249.C034.04SS, 10249.C034.05SS, 10249.C034.06SS, 10249.C034.07SS, 10249.C034.08SS, 10249.C034.09SS, 10249.C034.10SS, 10249.C034.11SS, 10249.C034.12SS, 10249.C034.13SS, 10249.C034.14SS, 10249.C034.15SD, 10249.C034.15SS, 10249.C034.16SS, 10249.C034.17SD, 10249.C034.17SS, 10249.C035.02SS, 10249.C035.03SS, 10249.C035.04SS, 10249.C035.05SS, 10249.C035.06SD, 10249.C035.06SS, 10249.C035.07SD, 10249.C035.07SS, 10249.C035.08SS, 10249.C035.09SS, 10249.C035.10SS, 10249.C035.11SS, 10249.C035.12SD, 10249.C035.12SS, 10249.C035.13SD, 10249.C035.13SS, 10249.C035.14SD, 10249.C035.14SS, 10249.C035.15SD, 10249.C035.15SS, 10249.C035.16SS, 10249.C035.17SS, 10249.C036.02SS, 10249.C036.03SS, 10249.C036.04SS, 10249.C036.05SD, 10249.C036.05SS, 10249.C036.07SS, 10249.C036.08SS, 10249.C036.09SS, 10249.C036.10SS, 10249.C036.11SS, 10249.C036.12SS, 10249.C036.13SS, 10249.C036.14SD, 10249.C036.14SS, 10249.C036.15SS, 10249.C036.16SS, 10249.C037.02SS, 10249.C037.04SS, 10249.C037.05SS, 10249.C037.06SS, 10249.C037.07SS, 10249.C037.08SS, 10249.C037.09SS, 10249.C037.10SS, 10249.C037.11SS, 10249.C037.12SD, 10249.C037.12SS, 10249.C037.13SD, 10249.C037.13SS, 10249.C037.14SS, 10249.C037.15SS, 10249.C037.16SS, 10249.C037.17SS, 10249.C037.18SS, 10249.C038.02SS, 10249.C038.04SS, 10249.C038.05SD, 10249.C038.05SS, 10249.C038.06SD, 10249.C038.06SS, 10249.C038.07SD, 10249.C038.07SS, 10249.C038.08SS, 10249.C038.09SS, 10249.C038.10SS, 10249.C038.11SS, 10249.C038.12SD, 10249.C038.12SS, 10249.C038.13SD, 10249.C038.13SS, 10249.C038.14SS, 10249.C038.15SD, 10249.C038.15SS, 10249.C038.16SD, 10249.C038.16SS, 10249.C038.18SS, 10249.C041.02SS, 10249.C041.03SS, 10249.C041.04SS, 10249.C041.05SD, 10249.C041.05SS, 10249.C041.06SD, 10249.C041.06SS, 10249.C041.08SS, 10249.C041.09SS, 10249.C041.10SS, 10249.C041.11SS, 10249.C041.12SS, 10249.C041.13SD, 10249.C041.13SS, 10249.C041.14SD, 10249.C041.14SS, 10249.C041.16SD, 10249.C041.16SS, 10249.C041.17SD, 10249.C041.17SS, 10249.C041.18SS, 10249.C041.19SS, 10249.C042.02SS, 10249.C042.03SS, 10249.C042.04SS, 10249.C042.05SS, 10249.C042.06SD, 10249.C042.06SS, 10249.C042.07SS, 10249.C042.08SS, 10249.C042.09SS, 10249.C042.10SS, 10249.C042.11SD, 10249.C042.11SS, 10249.C042.12SS, 10249.C042.13SS, 10249.C042.14SD, 10249.C042.14SS, 10249.C042.15SD, 10249.C042.15SS, 10249.C042.16SS, 10249.C042.17SS, 10249.C043.02SS, 10249.C043.03SS, 10249.C043.04SD, 10249.C043.04SS, 10249.C043.05SD, 10249.C043.05SS, 10249.C043.06SS, 10249.C043.07SS, 10249.C043.08SS, 10249.C043.09SS, 10249.C043.10SD, 10249.C043.10SS, 10249.C043.11SD, 10249.C043.11SS, 10249.C043.12SD, 10249.C043.12SS, 10249.C043.14SS, 10249.C043.15SD, 10249.C043.15SS, 10249.C043.16SS, 10249.C043.17SS, 10249.C043.18SS, 10249.C043.20SS, 10249.C044.02SS, 10249.C044.03SS, 10249.C044.04SS, 10249.C044.05SS, 10249.C044.06SS, 10249.C044.07SS, 10249.C044.08SS, 10249.C044.09SS, 10249.C044.10SS, 10249.C044.11SS, 10249.C044.12SD, 10249.C044.12SS, 10249.C044.13SD, 10249.C044.13SS, 10249.C044.15SD, 10249.C044.15SS, 10249.C044.16SS, 10249.C044.17SS, 10249.C045.02SS, 10249.C045.03SS, 10249.C045.04SS, 10249.C045.05SD, 10249.C045.05SS, 10249.C045.06SS, 10249.C045.08SD, 10249.C045.08SS, 10249.C045.09SD, 10249.C045.09SS, 10249.C045.10SD, 10249.C045.10SS, 10249.C045.11SS, 10249.C045.12SS, 10249.C045.13SS, 10249.C046.02SS, 10249.C046.03SS, 10249.C046.04SS, 10249.C046.05SS, 10249.C046.06SD, 10249.C046.06SS, 10249.C046.07SD, 10249.C046.07SS, 10249.C046.08SS, 10249.C046.09SD, 10249.C046.09SS, 10249.C046.10SD, 10249.C046.10SS, 10249.C046.11SD, 10249.C046.11SS, 10249.C046.12SS, 10249.C046.13SS, 10249.C046.14SS, 10249.C047.02SD, 10249.C047.02SS, 10249.C047.05SS, 10249.C047.06SD, 10249.C047.06SS, 10249.C047.07SD, 10249.C047.07SS, 10249.C047.08SD, 10249.C047.08SS, 10249.C047.09SS, 10249.C047.10SS, 10249.C047.11SS, 10249.C047.13SS, 10249.C049.03SD, 10249.C049.03SS, 10249.C049.04SS, 10249.C049.07SD, 10249.C049.07SS, 10249.C049.08SD, 10249.C049.08SS, 10249.C049.09SD, 10249.C049.09SS, 10249.C049.10SS, 10249.C049.11SS, 10249.C049.12SS, 10249.C049.13SS, 10249.C049.14SS, 10249.C052.03SD, 10249.C052.03SS, 10249.C052.04SD, 10249.C052.04SS, 10249.C052.05SD, 10249.C052.06SS, 10249.C052.07SS, 10249.C052.08SS, 10249.C052.09SS, 10249.C053.02SD, 10249.C053.02SS, 10249.C053.03SD, 10249.C053.03SS, 10249.C053.04SD, 10249.C053.04SS, 10249.C053.05SD, 10249.C053.05SS, 10249.C053.06SS, 10249.C053.07SS, 10249.C053.08SS, 10249.C053.09SS, 10249.C055.02SD, 10249.C055.02SS, 10249.C055.03SD, 10249.C055.03SS, 10249.C055.04SD, 10249.C055.04SS, 10249.C055.05SD, 10249.C055.05SS, 10249.C055.06SS, 10249.C055.07SS, 10249.C055.08SS, 10249.C055.09SS, 10249.C056.03SD, 10249.C056.03SS, 10249.C056.04SD, 10249.C056.04SS, 10249.C056.05SD, 10249.C056.05SS, 10249.C056.06SS, 10249.C056.07SS, 10249.C056.08SS, 10249.C056.09SS, 10249.C056.10SS, 10249.C057.02SS, 10249.C057.03SD, 10249.C057.03SS, 10249.C057.04SD, 10249.C057.04SS, 10249.C057.05SD, 10249.C057.05SS, 10249.C057.06SS, 10249.C057.08SS, 10249.C057.09SS, 10249.C057.10SS, 10249.C057.11SS
#> Updated feature table to match the subsetted data.
#> Updated feature annotation to match the subsetted data.
#> Data subsetting complete. Returning updated data object.
#> $Phylum
#> $Phylum$Phylum

#> 
#> 
#> $Family
#> $Family$Family

#> 
#> 
#> $Genus
#> $Genus$Genus

#> 
#> 

plot_feature_diversity(
data.obj = ecam.obj,
group.var = "antiexposedall",
strata.var = "delivery",
time.var = "month",
time.point.plot = unique(ecam.obj$meta.dat$month)[1],
is.plot.change = TRUE,
feature.level = c("Phylum", "Family", "Genus"),
feature.dat.type = "proportion",
features.plot = NULL,
prop.to.lump = 0.0001,
top.k.plot = NULL,
top.k.func = NULL,
renormalize = FALSE,
plot.other = TRUE,
plot.scheme = "combined",
plot.type = "heatmap"
)
#> Rule 1 passed: data.obj is a list.
#> Rule 2 passed: meta.dat is a data.frame.
#> Rule 3 passed: The row names of feature.tab match the row names of feature.ann.
#> Rule 4 passed: The order of rows in meta.dat has been adjusted to match feature.tab.
#> Rule 5 passed: feature.tab is a matrix.
#> Rule 6 passed: feature.ann is a matrix.
#> Please note: The data components should follow base R data.frame and matrix structures, not phyloseq's formal class.
#> Validation passed.
#> Note: Passing validation does not guarantee the absence of all data issues. Further data exploration may be needed.
#> Data has been subsetted based on the provided condition.
#> Updated metadata to match the subsetted data.
#> The following samples were excluded: 10249.C001.02SS, 10249.C001.03SS, 10249.C001.04SS, 10249.C001.05SS, 10249.C001.06SS, 10249.C001.07SS, 10249.C001.08SS, 10249.C001.09SS, 10249.C001.10SS, 10249.C001.11SS, 10249.C001.12SS, 10249.C001.13SS, 10249.C001.14SS, 10249.C001.15SS, 10249.C001.16SS, 10249.C001.17SS, 10249.C001.18SS, 10249.C001.19SS, 10249.C001.20SS, 10249.C001.25SS, 10249.C001.26SS, 10249.C001.27SS, 10249.C001.29SS, 10249.C001.30SS, 10249.C001.31SS, 10249.C001.32SS, 10249.C001.34SD, 10249.C001.34SS, 10249.C001.35SS, 10249.C001.36SD, 10249.C001.36SS, 10249.C002.02SS, 10249.C002.03SS, 10249.C002.04SS, 10249.C002.05SS, 10249.C002.06SS, 10249.C002.07SS, 10249.C002.08SS, 10249.C002.09SS, 10249.C002.10SS, 10249.C002.11SS, 10249.C002.12SS, 10249.C002.13SS, 10249.C002.15SS, 10249.C002.16SS, 10249.C002.18SS, 10249.C002.19SD, 10249.C002.19SS, 10249.C002.20SS, 10249.C002.21SD, 10249.C002.21SS, 10249.C004.02SS, 10249.C004.03SS, 10249.C004.04SS, 10249.C004.05SS, 10249.C004.06SS, 10249.C004.07SS, 10249.C004.08SS, 10249.C004.09SS, 10249.C004.10SS, 10249.C004.11SS, 10249.C004.12SS, 10249.C004.13SS, 10249.C004.14SS, 10249.C004.15SS, 10249.C005.02SS, 10249.C005.03SS, 10249.C005.04SS, 10249.C005.05SS, 10249.C005.07SS, 10249.C005.08SS, 10249.C005.09SS, 10249.C005.10SS, 10249.C005.11SS, 10249.C005.12SS, 10249.C005.13SS, 10249.C005.14SS, 10249.C005.15SS, 10249.C005.16SS, 10249.C005.17SS, 10249.C005.18SS, 10249.C005.19SD, 10249.C005.19SS, 10249.C005.20SS, 10249.C005.21SD, 10249.C005.21SS, 10249.C005.22SS, 10249.C007.02SS, 10249.C007.03SS, 10249.C007.04SS, 10249.C007.05SS, 10249.C007.06SS, 10249.C007.07SS, 10249.C007.08SS, 10249.C007.09SS, 10249.C007.10SS, 10249.C007.11SS, 10249.C007.12SS, 10249.C007.13SS, 10249.C007.14SS, 10249.C007.15SS, 10249.C007.16SS, 10249.C007.17SS, 10249.C007.18SS, 10249.C007.19SS, 10249.C007.20SS, 10249.C007.21SS, 10249.C007.22SD, 10249.C007.22SS, 10249.C007.23SD, 10249.C007.23SS, 10249.C007.24SD, 10249.C007.24SS, 10249.C007.26SS, 10249.C008.02SS, 10249.C008.03SS, 10249.C008.04SS, 10249.C008.05SS, 10249.C008.06SS, 10249.C008.07SS, 10249.C008.08SS, 10249.C008.09SS, 10249.C008.10SS, 10249.C008.11SS, 10249.C008.12SS, 10249.C008.13SS, 10249.C008.14SS, 10249.C008.15SS, 10249.C008.16SD, 10249.C008.16SS, 10249.C008.18SS, 10249.C009.02SS, 10249.C009.03SS, 10249.C009.04SS, 10249.C009.05SS, 10249.C009.06SS, 10249.C009.07SS, 10249.C009.08SS, 10249.C009.09SS, 10249.C009.10SS, 10249.C009.11SS, 10249.C009.12SS, 10249.C009.13SS, 10249.C009.14SS, 10249.C009.16SS, 10249.C009.17SS, 10249.C009.18SD, 10249.C009.18SS, 10249.C009.19SS, 10249.C009.20SD, 10249.C009.20SS, 10249.C009.21SS, 10249.C010.02SS, 10249.C010.03SS, 10249.C010.04SS, 10249.C010.05SS, 10249.C010.06SS, 10249.C010.07SS, 10249.C010.08SS, 10249.C010.09SS, 10249.C010.10SS, 10249.C010.11SS, 10249.C010.12SS, 10249.C010.13SS, 10249.C010.14SS, 10249.C010.15SS, 10249.C010.16SS, 10249.C010.18SD, 10249.C010.18SS, 10249.C010.19SS, 10249.C010.20SD, 10249.C010.20SS, 10249.C010.21SS, 10249.C011.02SS, 10249.C011.03SS, 10249.C011.04SS, 10249.C011.05SS, 10249.C011.06SS, 10249.C011.07SS, 10249.C011.08SS, 10249.C011.09SS, 10249.C011.10SS, 10249.C011.11SS, 10249.C011.12SS, 10249.C011.13SD, 10249.C011.14SS, 10249.C011.16SS, 10249.C011.17SD, 10249.C011.17SS, 10249.C011.18SS, 10249.C011.19SD, 10249.C011.19SS, 10249.C011.20SS, 10249.C011.21SS, 10249.C012.02SS, 10249.C012.03SS, 10249.C012.04SS, 10249.C012.05SS, 10249.C012.06SS, 10249.C012.07SS, 10249.C012.08SS, 10249.C012.09SS, 10249.C012.10SS, 10249.C012.11SS, 10249.C012.12SS, 10249.C012.13SS, 10249.C012.14SS, 10249.C012.15SS, 10249.C012.16SS, 10249.C012.17SS, 10249.C012.18SS, 10249.C012.19SD, 10249.C012.19SS, 10249.C012.20SS, 10249.C012.21SD, 10249.C012.21SS, 10249.C012.22SD, 10249.C012.22SS, 10249.C014.02SS, 10249.C014.03SS, 10249.C014.04SS, 10249.C014.05SS, 10249.C014.06SS, 10249.C014.07SS, 10249.C014.08SS, 10249.C014.09SS, 10249.C014.10SS, 10249.C014.12SS, 10249.C014.13SS, 10249.C014.15SS, 10249.C014.16SS, 10249.C014.17SS, 10249.C014.18SS, 10249.C014.19SD, 10249.C014.19SS, 10249.C014.20SD, 10249.C014.20SS, 10249.C014.21SS, 10249.C014.22SS, 10249.C016.03SS, 10249.C016.04SS, 10249.C016.05SS, 10249.C016.06SS, 10249.C016.07SS, 10249.C016.08SS, 10249.C016.09SS, 10249.C016.10SS, 10249.C016.11SS, 10249.C016.12SS, 10249.C016.13SS, 10249.C016.14SS, 10249.C016.15SS, 10249.C016.17SS, 10249.C016.18SS, 10249.C016.19SS, 10249.C016.20SS, 10249.C016.21SD, 10249.C016.21SS, 10249.C016.22SD, 10249.C016.22SS, 10249.C016.23SS, 10249.C016.24SS, 10249.C017.04SS, 10249.C017.05SS, 10249.C017.06SS, 10249.C017.07SS, 10249.C017.08SS, 10249.C017.09SS, 10249.C017.10SS, 10249.C017.11SS, 10249.C017.12SS, 10249.C018.02SS, 10249.C018.03SS, 10249.C018.04SS, 10249.C018.05SS, 10249.C018.06SS, 10249.C018.07SS, 10249.C018.08SS, 10249.C018.09SS, 10249.C018.10SS, 10249.C018.11SD, 10249.C018.11SS, 10249.C018.12SD, 10249.C018.12SS, 10249.C018.13SS, 10249.C018.14SS, 10249.C018.15SS, 10249.C018.16SS, 10249.C018.17SS, 10249.C018.18SS, 10249.C018.19SS, 10249.C020.06SS, 10249.C020.07SS, 10249.C020.08SS, 10249.C020.09SS, 10249.C020.10SS, 10249.C020.11SS, 10249.C020.12SS, 10249.C020.13SS, 10249.C020.14SS, 10249.C020.15SS, 10249.C020.16SS, 10249.C020.17SS, 10249.C020.18SS, 10249.C020.19SS, 10249.C020.20SS, 10249.C020.21SS, 10249.C020.22SD, 10249.C020.22SS, 10249.C020.23SD, 10249.C020.23SS, 10249.C020.24SD, 10249.C020.24SS, 10249.C020.25SD, 10249.C020.25SS, 10249.C020.26SD, 10249.C020.26SS, 10249.C020.28SS, 10249.C020.29SS, 10249.C021.03SS, 10249.C021.04SS, 10249.C021.05SS, 10249.C021.06SS, 10249.C021.07SS, 10249.C021.08SS, 10249.C021.09SS, 10249.C021.10SS, 10249.C021.12SS, 10249.C021.13SS, 10249.C022.02SS, 10249.C022.03SS, 10249.C022.04SS, 10249.C022.05SS, 10249.C022.06SS, 10249.C022.07SS, 10249.C022.08SS, 10249.C022.09SS, 10249.C022.10SS, 10249.C022.11SS, 10249.C022.12SS, 10249.C022.13SS, 10249.C022.15SS, 10249.C022.16SS, 10249.C022.18SD, 10249.C022.18SS, 10249.C022.19SS, 10249.C022.20SS, 10249.C022.21SS, 10249.C024.02SS, 10249.C024.03SS, 10249.C024.04SS, 10249.C024.05SS, 10249.C024.06SS, 10249.C024.07SS, 10249.C024.08SS, 10249.C024.09SS, 10249.C024.10SS, 10249.C024.12SS, 10249.C024.13SS, 10249.C024.14SS, 10249.C024.15SS, 10249.C024.16SS, 10249.C024.17SS, 10249.C024.18SS, 10249.C024.19SD, 10249.C024.19SS, 10249.C024.20SD, 10249.C024.20SS, 10249.C024.21SS, 10249.C024.22SS, 10249.C025.02SS, 10249.C025.03SS, 10249.C025.04SS, 10249.C025.05SS, 10249.C025.06SS, 10249.C025.07SS, 10249.C025.08SS, 10249.C025.09SS, 10249.C025.10SS, 10249.C025.11SS, 10249.C025.12SS, 10249.C025.13SD, 10249.C025.13SS, 10249.C025.14SD, 10249.C025.14SS, 10249.C025.15SS, 10249.C025.16SS, 10249.C025.17SS, 10249.C025.18SS, 10249.C025.19SD, 10249.C025.19SS, 10249.C025.20SS, 10249.C025.21SS, 10249.C027.02SS, 10249.C027.03SS, 10249.C027.04SS, 10249.C027.05SS, 10249.C027.06SS, 10249.C027.07SS, 10249.C027.08SS, 10249.C027.09SS, 10249.C027.10SS, 10249.C027.11SD, 10249.C027.12SD, 10249.C027.12SS, 10249.C027.13SS, 10249.C027.14SS, 10249.C027.15SS, 10249.C027.16SS, 10249.C027.17SD, 10249.C027.17SS, 10249.C027.18SS, 10249.C027.19SD, 10249.C027.19SS, 10249.C027.20SD, 10249.C027.20SS, 10249.C027.21SS, 10249.C027.22SS, 10249.C030.02SS, 10249.C030.03SS, 10249.C030.04SS, 10249.C030.05SS, 10249.C030.06SS, 10249.C030.07SS, 10249.C030.08SS, 10249.C030.09SS, 10249.C030.10SS, 10249.C030.11SD, 10249.C030.11SS, 10249.C030.12SS, 10249.C030.13SS, 10249.C030.14SS, 10249.C030.16SS, 10249.C030.17SD, 10249.C030.17SS, 10249.C030.18SS, 10249.C030.19SD, 10249.C030.19SS, 10249.C030.20SS, 10249.C031.02SS, 10249.C031.03SS, 10249.C031.04SS, 10249.C031.05SS, 10249.C031.06SS, 10249.C031.07SS, 10249.C031.08SS, 10249.C031.09SS, 10249.C031.10SS, 10249.C031.11SD, 10249.C031.11SS, 10249.C031.12SS, 10249.C031.13SS, 10249.C031.14SS, 10249.C031.16SS, 10249.C031.17SD, 10249.C031.17SS, 10249.C031.18SS, 10249.C031.19SD, 10249.C031.19SS, 10249.C031.20SS, 10249.C031.21SS, 10249.C032.02SS, 10249.C032.03SS, 10249.C032.04SS, 10249.C032.05SS, 10249.C032.06SS, 10249.C032.07SS, 10249.C032.09SS, 10249.C032.10SS, 10249.C032.11SD, 10249.C032.11SS, 10249.C032.12SD, 10249.C032.13SS, 10249.C032.14SS, 10249.C032.15SS, 10249.C032.16SS, 10249.C032.17SS, 10249.C032.19SD, 10249.C032.19SS, 10249.C032.20SD, 10249.C032.20SS, 10249.C032.21SS, 10249.C032.22SS, 10249.C033.02SS, 10249.C033.03SS, 10249.C033.04SS, 10249.C033.05SS, 10249.C033.06SS, 10249.C033.07SS, 10249.C033.08SS, 10249.C033.09SD, 10249.C033.09SS, 10249.C033.10SD, 10249.C033.10SS, 10249.C033.11SD, 10249.C033.11SS, 10249.C033.12SS, 10249.C033.13SS, 10249.C033.14SS, 10249.C033.15SS, 10249.C033.16SS, 10249.C033.17SD, 10249.C033.17SS, 10249.C033.18SD, 10249.C033.18SS, 10249.C033.19SS, 10249.C034.02SS, 10249.C034.03SS, 10249.C034.04SS, 10249.C034.05SS, 10249.C034.06SS, 10249.C034.07SS, 10249.C034.08SS, 10249.C034.09SS, 10249.C034.10SS, 10249.C034.11SS, 10249.C034.12SS, 10249.C034.13SS, 10249.C034.14SS, 10249.C034.15SD, 10249.C034.15SS, 10249.C034.16SS, 10249.C034.17SD, 10249.C034.17SS, 10249.C035.02SS, 10249.C035.03SS, 10249.C035.04SS, 10249.C035.05SS, 10249.C035.06SD, 10249.C035.06SS, 10249.C035.07SD, 10249.C035.07SS, 10249.C035.08SS, 10249.C035.09SS, 10249.C035.10SS, 10249.C035.11SS, 10249.C035.12SD, 10249.C035.12SS, 10249.C035.13SD, 10249.C035.13SS, 10249.C035.14SD, 10249.C035.14SS, 10249.C035.15SD, 10249.C035.15SS, 10249.C035.16SS, 10249.C035.17SS, 10249.C036.02SS, 10249.C036.03SS, 10249.C036.04SS, 10249.C036.05SD, 10249.C036.05SS, 10249.C036.07SS, 10249.C036.08SS, 10249.C036.09SS, 10249.C036.10SS, 10249.C036.11SS, 10249.C036.12SS, 10249.C036.13SS, 10249.C036.14SD, 10249.C036.14SS, 10249.C036.15SS, 10249.C036.16SS, 10249.C037.02SS, 10249.C037.04SS, 10249.C037.05SS, 10249.C037.06SS, 10249.C037.07SS, 10249.C037.08SS, 10249.C037.09SS, 10249.C037.10SS, 10249.C037.11SS, 10249.C037.12SD, 10249.C037.12SS, 10249.C037.13SD, 10249.C037.13SS, 10249.C037.14SS, 10249.C037.15SS, 10249.C037.16SS, 10249.C037.17SS, 10249.C037.18SS, 10249.C038.02SS, 10249.C038.04SS, 10249.C038.05SD, 10249.C038.05SS, 10249.C038.06SD, 10249.C038.06SS, 10249.C038.07SD, 10249.C038.07SS, 10249.C038.08SS, 10249.C038.09SS, 10249.C038.10SS, 10249.C038.11SS, 10249.C038.12SD, 10249.C038.12SS, 10249.C038.13SD, 10249.C038.13SS, 10249.C038.14SS, 10249.C038.15SD, 10249.C038.15SS, 10249.C038.16SD, 10249.C038.16SS, 10249.C038.18SS, 10249.C041.02SS, 10249.C041.03SS, 10249.C041.04SS, 10249.C041.05SD, 10249.C041.05SS, 10249.C041.06SD, 10249.C041.06SS, 10249.C041.08SS, 10249.C041.09SS, 10249.C041.10SS, 10249.C041.11SS, 10249.C041.12SS, 10249.C041.13SD, 10249.C041.13SS, 10249.C041.14SD, 10249.C041.14SS, 10249.C041.16SD, 10249.C041.16SS, 10249.C041.17SD, 10249.C041.17SS, 10249.C041.18SS, 10249.C041.19SS, 10249.C042.02SS, 10249.C042.03SS, 10249.C042.04SS, 10249.C042.05SS, 10249.C042.06SD, 10249.C042.06SS, 10249.C042.07SS, 10249.C042.08SS, 10249.C042.09SS, 10249.C042.10SS, 10249.C042.11SD, 10249.C042.11SS, 10249.C042.12SS, 10249.C042.13SS, 10249.C042.14SD, 10249.C042.14SS, 10249.C042.15SD, 10249.C042.15SS, 10249.C042.16SS, 10249.C042.17SS, 10249.C043.02SS, 10249.C043.03SS, 10249.C043.04SD, 10249.C043.04SS, 10249.C043.05SD, 10249.C043.05SS, 10249.C043.06SS, 10249.C043.07SS, 10249.C043.08SS, 10249.C043.09SS, 10249.C043.10SD, 10249.C043.10SS, 10249.C043.11SD, 10249.C043.11SS, 10249.C043.12SD, 10249.C043.12SS, 10249.C043.14SS, 10249.C043.15SD, 10249.C043.15SS, 10249.C043.16SS, 10249.C043.17SS, 10249.C043.18SS, 10249.C043.20SS, 10249.C044.02SS, 10249.C044.03SS, 10249.C044.04SS, 10249.C044.05SS, 10249.C044.06SS, 10249.C044.07SS, 10249.C044.08SS, 10249.C044.09SS, 10249.C044.10SS, 10249.C044.11SS, 10249.C044.12SD, 10249.C044.12SS, 10249.C044.13SD, 10249.C044.13SS, 10249.C044.15SD, 10249.C044.15SS, 10249.C044.16SS, 10249.C044.17SS, 10249.C045.02SS, 10249.C045.03SS, 10249.C045.04SS, 10249.C045.05SD, 10249.C045.05SS, 10249.C045.06SS, 10249.C045.08SD, 10249.C045.08SS, 10249.C045.09SD, 10249.C045.09SS, 10249.C045.10SD, 10249.C045.10SS, 10249.C045.11SS, 10249.C045.12SS, 10249.C045.13SS, 10249.C046.02SS, 10249.C046.03SS, 10249.C046.04SS, 10249.C046.05SS, 10249.C046.06SD, 10249.C046.06SS, 10249.C046.07SD, 10249.C046.07SS, 10249.C046.08SS, 10249.C046.09SD, 10249.C046.09SS, 10249.C046.10SD, 10249.C046.10SS, 10249.C046.11SD, 10249.C046.11SS, 10249.C046.12SS, 10249.C046.13SS, 10249.C046.14SS, 10249.C047.02SD, 10249.C047.02SS, 10249.C047.05SS, 10249.C047.06SD, 10249.C047.06SS, 10249.C047.07SD, 10249.C047.07SS, 10249.C047.08SD, 10249.C047.08SS, 10249.C047.09SS, 10249.C047.10SS, 10249.C047.11SS, 10249.C047.13SS, 10249.C049.03SD, 10249.C049.03SS, 10249.C049.04SS, 10249.C049.07SD, 10249.C049.07SS, 10249.C049.08SD, 10249.C049.08SS, 10249.C049.09SD, 10249.C049.09SS, 10249.C049.10SS, 10249.C049.11SS, 10249.C049.12SS, 10249.C049.13SS, 10249.C049.14SS, 10249.C052.03SD, 10249.C052.03SS, 10249.C052.04SD, 10249.C052.04SS, 10249.C052.05SD, 10249.C052.06SS, 10249.C052.07SS, 10249.C052.08SS, 10249.C052.09SS, 10249.C053.02SD, 10249.C053.02SS, 10249.C053.03SD, 10249.C053.03SS, 10249.C053.04SD, 10249.C053.04SS, 10249.C053.05SD, 10249.C053.05SS, 10249.C053.06SS, 10249.C053.07SS, 10249.C053.08SS, 10249.C053.09SS, 10249.C055.02SD, 10249.C055.02SS, 10249.C055.03SD, 10249.C055.03SS, 10249.C055.04SD, 10249.C055.04SS, 10249.C055.05SD, 10249.C055.05SS, 10249.C055.06SS, 10249.C055.07SS, 10249.C055.08SS, 10249.C055.09SS, 10249.C056.03SD, 10249.C056.03SS, 10249.C056.04SD, 10249.C056.04SS, 10249.C056.05SD, 10249.C056.05SS, 10249.C056.06SS, 10249.C056.07SS, 10249.C056.08SS, 10249.C056.09SS, 10249.C056.10SS, 10249.C057.02SS, 10249.C057.03SD, 10249.C057.03SS, 10249.C057.04SD, 10249.C057.04SS, 10249.C057.05SD, 10249.C057.05SS, 10249.C057.06SS, 10249.C057.08SS, 10249.C057.09SS, 10249.C057.10SS, 10249.C057.11SS
#> Updated feature table to match the subsetted data.
#> Updated feature annotation to match the subsetted data.
#> Data subsetting complete. Returning updated data object.
#> Rule 1 passed: data.obj is a list.
#> Rule 2 passed: meta.dat is a data.frame.
#> Rule 3 passed: The row names of feature.tab match the row names of feature.ann.
#> Rule 4 passed: The order of rows in meta.dat has been adjusted to match feature.tab.
#> Rule 5 passed: feature.tab is a matrix.
#> Rule 6 passed: feature.ann is a matrix.
#> Please note: The data components should follow base R data.frame and matrix structures, not phyloseq's formal class.
#> Validation passed.
#> Note: Passing validation does not guarantee the absence of all data issues. Further data exploration may be needed.
#> Data has been subsetted based on the provided condition.
#> Updated metadata to match the subsetted data.
#> The following samples were excluded: 10249.C001.02SS, 10249.C001.03SS, 10249.C001.04SS, 10249.C001.05SS, 10249.C001.06SS, 10249.C001.07SS, 10249.C001.08SS, 10249.C001.09SS, 10249.C001.10SS, 10249.C001.11SS, 10249.C001.12SS, 10249.C001.13SS, 10249.C001.14SS, 10249.C001.15SS, 10249.C001.16SS, 10249.C001.17SS, 10249.C001.18SS, 10249.C001.19SS, 10249.C001.20SS, 10249.C001.25SS, 10249.C001.26SS, 10249.C001.27SS, 10249.C001.29SS, 10249.C001.30SS, 10249.C001.31SS, 10249.C001.32SS, 10249.C001.34SD, 10249.C001.34SS, 10249.C001.35SS, 10249.C001.36SD, 10249.C001.36SS, 10249.C002.02SS, 10249.C002.03SS, 10249.C002.04SS, 10249.C002.05SS, 10249.C002.06SS, 10249.C002.07SS, 10249.C002.08SS, 10249.C002.09SS, 10249.C002.10SS, 10249.C002.11SS, 10249.C002.12SS, 10249.C002.13SS, 10249.C002.15SS, 10249.C002.16SS, 10249.C002.18SS, 10249.C002.19SD, 10249.C002.19SS, 10249.C002.20SS, 10249.C002.21SD, 10249.C002.21SS, 10249.C004.02SS, 10249.C004.03SS, 10249.C004.04SS, 10249.C004.05SS, 10249.C004.06SS, 10249.C004.07SS, 10249.C004.08SS, 10249.C004.09SS, 10249.C004.10SS, 10249.C004.11SS, 10249.C004.12SS, 10249.C004.13SS, 10249.C004.14SS, 10249.C004.15SS, 10249.C005.02SS, 10249.C005.03SS, 10249.C005.04SS, 10249.C005.05SS, 10249.C005.07SS, 10249.C005.08SS, 10249.C005.09SS, 10249.C005.10SS, 10249.C005.11SS, 10249.C005.12SS, 10249.C005.13SS, 10249.C005.14SS, 10249.C005.15SS, 10249.C005.16SS, 10249.C005.17SS, 10249.C005.18SS, 10249.C005.19SD, 10249.C005.19SS, 10249.C005.20SS, 10249.C005.21SD, 10249.C005.21SS, 10249.C005.22SS, 10249.C007.02SS, 10249.C007.03SS, 10249.C007.04SS, 10249.C007.05SS, 10249.C007.06SS, 10249.C007.07SS, 10249.C007.08SS, 10249.C007.09SS, 10249.C007.10SS, 10249.C007.11SS, 10249.C007.12SS, 10249.C007.13SS, 10249.C007.14SS, 10249.C007.15SS, 10249.C007.16SS, 10249.C007.17SS, 10249.C007.18SS, 10249.C007.19SS, 10249.C007.20SS, 10249.C007.21SS, 10249.C007.22SD, 10249.C007.22SS, 10249.C007.23SD, 10249.C007.23SS, 10249.C007.24SD, 10249.C007.24SS, 10249.C007.26SS, 10249.C008.02SS, 10249.C008.03SS, 10249.C008.04SS, 10249.C008.05SS, 10249.C008.06SS, 10249.C008.07SS, 10249.C008.08SS, 10249.C008.09SS, 10249.C008.10SS, 10249.C008.11SS, 10249.C008.12SS, 10249.C008.13SS, 10249.C008.14SS, 10249.C008.15SS, 10249.C008.16SD, 10249.C008.16SS, 10249.C008.18SS, 10249.C009.02SS, 10249.C009.03SS, 10249.C009.04SS, 10249.C009.05SS, 10249.C009.06SS, 10249.C009.07SS, 10249.C009.08SS, 10249.C009.09SS, 10249.C009.10SS, 10249.C009.11SS, 10249.C009.12SS, 10249.C009.13SS, 10249.C009.14SS, 10249.C009.16SS, 10249.C009.17SS, 10249.C009.18SD, 10249.C009.18SS, 10249.C009.19SS, 10249.C009.20SD, 10249.C009.20SS, 10249.C009.21SS, 10249.C010.02SS, 10249.C010.03SS, 10249.C010.04SS, 10249.C010.05SS, 10249.C010.06SS, 10249.C010.07SS, 10249.C010.08SS, 10249.C010.09SS, 10249.C010.10SS, 10249.C010.11SS, 10249.C010.12SS, 10249.C010.13SS, 10249.C010.14SS, 10249.C010.15SS, 10249.C010.16SS, 10249.C010.18SD, 10249.C010.18SS, 10249.C010.19SS, 10249.C010.20SD, 10249.C010.20SS, 10249.C010.21SS, 10249.C011.02SS, 10249.C011.03SS, 10249.C011.04SS, 10249.C011.05SS, 10249.C011.06SS, 10249.C011.07SS, 10249.C011.08SS, 10249.C011.09SS, 10249.C011.10SS, 10249.C011.11SS, 10249.C011.12SS, 10249.C011.13SD, 10249.C011.14SS, 10249.C011.16SS, 10249.C011.17SD, 10249.C011.17SS, 10249.C011.18SS, 10249.C011.19SD, 10249.C011.19SS, 10249.C011.20SS, 10249.C011.21SS, 10249.C012.02SS, 10249.C012.03SS, 10249.C012.04SS, 10249.C012.05SS, 10249.C012.06SS, 10249.C012.07SS, 10249.C012.08SS, 10249.C012.09SS, 10249.C012.10SS, 10249.C012.11SS, 10249.C012.12SS, 10249.C012.13SS, 10249.C012.14SS, 10249.C012.15SS, 10249.C012.16SS, 10249.C012.17SS, 10249.C012.18SS, 10249.C012.19SD, 10249.C012.19SS, 10249.C012.20SS, 10249.C012.21SD, 10249.C012.21SS, 10249.C012.22SD, 10249.C012.22SS, 10249.C014.02SS, 10249.C014.03SS, 10249.C014.04SS, 10249.C014.05SS, 10249.C014.06SS, 10249.C014.07SS, 10249.C014.08SS, 10249.C014.09SS, 10249.C014.10SS, 10249.C014.12SS, 10249.C014.13SS, 10249.C014.15SS, 10249.C014.16SS, 10249.C014.17SS, 10249.C014.18SS, 10249.C014.19SD, 10249.C014.19SS, 10249.C014.20SD, 10249.C014.20SS, 10249.C014.21SS, 10249.C014.22SS, 10249.C016.03SS, 10249.C016.04SS, 10249.C016.05SS, 10249.C016.06SS, 10249.C016.07SS, 10249.C016.08SS, 10249.C016.09SS, 10249.C016.10SS, 10249.C016.11SS, 10249.C016.12SS, 10249.C016.13SS, 10249.C016.14SS, 10249.C016.15SS, 10249.C016.17SS, 10249.C016.18SS, 10249.C016.19SS, 10249.C016.20SS, 10249.C016.21SD, 10249.C016.21SS, 10249.C016.22SD, 10249.C016.22SS, 10249.C016.23SS, 10249.C016.24SS, 10249.C017.04SS, 10249.C017.05SS, 10249.C017.06SS, 10249.C017.07SS, 10249.C017.08SS, 10249.C017.09SS, 10249.C017.10SS, 10249.C017.11SS, 10249.C017.12SS, 10249.C018.02SS, 10249.C018.03SS, 10249.C018.04SS, 10249.C018.05SS, 10249.C018.06SS, 10249.C018.07SS, 10249.C018.08SS, 10249.C018.09SS, 10249.C018.10SS, 10249.C018.11SD, 10249.C018.11SS, 10249.C018.12SD, 10249.C018.12SS, 10249.C018.13SS, 10249.C018.14SS, 10249.C018.15SS, 10249.C018.16SS, 10249.C018.17SS, 10249.C018.18SS, 10249.C018.19SS, 10249.C020.06SS, 10249.C020.07SS, 10249.C020.08SS, 10249.C020.09SS, 10249.C020.10SS, 10249.C020.11SS, 10249.C020.12SS, 10249.C020.13SS, 10249.C020.14SS, 10249.C020.15SS, 10249.C020.16SS, 10249.C020.17SS, 10249.C020.18SS, 10249.C020.19SS, 10249.C020.20SS, 10249.C020.21SS, 10249.C020.22SD, 10249.C020.22SS, 10249.C020.23SD, 10249.C020.23SS, 10249.C020.24SD, 10249.C020.24SS, 10249.C020.25SD, 10249.C020.25SS, 10249.C020.26SD, 10249.C020.26SS, 10249.C020.28SS, 10249.C020.29SS, 10249.C021.03SS, 10249.C021.04SS, 10249.C021.05SS, 10249.C021.06SS, 10249.C021.07SS, 10249.C021.08SS, 10249.C021.09SS, 10249.C021.10SS, 10249.C021.12SS, 10249.C021.13SS, 10249.C022.02SS, 10249.C022.03SS, 10249.C022.04SS, 10249.C022.05SS, 10249.C022.06SS, 10249.C022.07SS, 10249.C022.08SS, 10249.C022.09SS, 10249.C022.10SS, 10249.C022.11SS, 10249.C022.12SS, 10249.C022.13SS, 10249.C022.15SS, 10249.C022.16SS, 10249.C022.18SD, 10249.C022.18SS, 10249.C022.19SS, 10249.C022.20SS, 10249.C022.21SS, 10249.C024.02SS, 10249.C024.03SS, 10249.C024.04SS, 10249.C024.05SS, 10249.C024.06SS, 10249.C024.07SS, 10249.C024.08SS, 10249.C024.09SS, 10249.C024.10SS, 10249.C024.12SS, 10249.C024.13SS, 10249.C024.14SS, 10249.C024.15SS, 10249.C024.16SS, 10249.C024.17SS, 10249.C024.18SS, 10249.C024.19SD, 10249.C024.19SS, 10249.C024.20SD, 10249.C024.20SS, 10249.C024.21SS, 10249.C024.22SS, 10249.C025.02SS, 10249.C025.03SS, 10249.C025.04SS, 10249.C025.05SS, 10249.C025.06SS, 10249.C025.07SS, 10249.C025.08SS, 10249.C025.09SS, 10249.C025.10SS, 10249.C025.11SS, 10249.C025.12SS, 10249.C025.13SD, 10249.C025.13SS, 10249.C025.14SD, 10249.C025.14SS, 10249.C025.15SS, 10249.C025.16SS, 10249.C025.17SS, 10249.C025.18SS, 10249.C025.19SD, 10249.C025.19SS, 10249.C025.20SS, 10249.C025.21SS, 10249.C027.02SS, 10249.C027.03SS, 10249.C027.04SS, 10249.C027.05SS, 10249.C027.06SS, 10249.C027.07SS, 10249.C027.08SS, 10249.C027.09SS, 10249.C027.10SS, 10249.C027.11SD, 10249.C027.12SD, 10249.C027.12SS, 10249.C027.13SS, 10249.C027.14SS, 10249.C027.15SS, 10249.C027.16SS, 10249.C027.17SD, 10249.C027.17SS, 10249.C027.18SS, 10249.C027.19SD, 10249.C027.19SS, 10249.C027.20SD, 10249.C027.20SS, 10249.C027.21SS, 10249.C027.22SS, 10249.C030.02SS, 10249.C030.03SS, 10249.C030.04SS, 10249.C030.05SS, 10249.C030.06SS, 10249.C030.07SS, 10249.C030.08SS, 10249.C030.09SS, 10249.C030.10SS, 10249.C030.11SD, 10249.C030.11SS, 10249.C030.12SS, 10249.C030.13SS, 10249.C030.14SS, 10249.C030.16SS, 10249.C030.17SD, 10249.C030.17SS, 10249.C030.18SS, 10249.C030.19SD, 10249.C030.19SS, 10249.C030.20SS, 10249.C031.02SS, 10249.C031.03SS, 10249.C031.04SS, 10249.C031.05SS, 10249.C031.06SS, 10249.C031.07SS, 10249.C031.08SS, 10249.C031.09SS, 10249.C031.10SS, 10249.C031.11SD, 10249.C031.11SS, 10249.C031.12SS, 10249.C031.13SS, 10249.C031.14SS, 10249.C031.16SS, 10249.C031.17SD, 10249.C031.17SS, 10249.C031.18SS, 10249.C031.19SD, 10249.C031.19SS, 10249.C031.20SS, 10249.C031.21SS, 10249.C032.02SS, 10249.C032.03SS, 10249.C032.04SS, 10249.C032.05SS, 10249.C032.06SS, 10249.C032.07SS, 10249.C032.09SS, 10249.C032.10SS, 10249.C032.11SD, 10249.C032.11SS, 10249.C032.12SD, 10249.C032.13SS, 10249.C032.14SS, 10249.C032.15SS, 10249.C032.16SS, 10249.C032.17SS, 10249.C032.19SD, 10249.C032.19SS, 10249.C032.20SD, 10249.C032.20SS, 10249.C032.21SS, 10249.C032.22SS, 10249.C033.02SS, 10249.C033.03SS, 10249.C033.04SS, 10249.C033.05SS, 10249.C033.06SS, 10249.C033.07SS, 10249.C033.08SS, 10249.C033.09SD, 10249.C033.09SS, 10249.C033.10SD, 10249.C033.10SS, 10249.C033.11SD, 10249.C033.11SS, 10249.C033.12SS, 10249.C033.13SS, 10249.C033.14SS, 10249.C033.15SS, 10249.C033.16SS, 10249.C033.17SD, 10249.C033.17SS, 10249.C033.18SD, 10249.C033.18SS, 10249.C033.19SS, 10249.C034.02SS, 10249.C034.03SS, 10249.C034.04SS, 10249.C034.05SS, 10249.C034.06SS, 10249.C034.07SS, 10249.C034.08SS, 10249.C034.09SS, 10249.C034.10SS, 10249.C034.11SS, 10249.C034.12SS, 10249.C034.13SS, 10249.C034.14SS, 10249.C034.15SD, 10249.C034.15SS, 10249.C034.16SS, 10249.C034.17SD, 10249.C034.17SS, 10249.C035.02SS, 10249.C035.03SS, 10249.C035.04SS, 10249.C035.05SS, 10249.C035.06SD, 10249.C035.06SS, 10249.C035.07SD, 10249.C035.07SS, 10249.C035.08SS, 10249.C035.09SS, 10249.C035.10SS, 10249.C035.11SS, 10249.C035.12SD, 10249.C035.12SS, 10249.C035.13SD, 10249.C035.13SS, 10249.C035.14SD, 10249.C035.14SS, 10249.C035.15SD, 10249.C035.15SS, 10249.C035.16SS, 10249.C035.17SS, 10249.C036.02SS, 10249.C036.03SS, 10249.C036.04SS, 10249.C036.05SD, 10249.C036.05SS, 10249.C036.07SS, 10249.C036.08SS, 10249.C036.09SS, 10249.C036.10SS, 10249.C036.11SS, 10249.C036.12SS, 10249.C036.13SS, 10249.C036.14SD, 10249.C036.14SS, 10249.C036.15SS, 10249.C036.16SS, 10249.C037.02SS, 10249.C037.04SS, 10249.C037.05SS, 10249.C037.06SS, 10249.C037.07SS, 10249.C037.08SS, 10249.C037.09SS, 10249.C037.10SS, 10249.C037.11SS, 10249.C037.12SD, 10249.C037.12SS, 10249.C037.13SD, 10249.C037.13SS, 10249.C037.14SS, 10249.C037.15SS, 10249.C037.16SS, 10249.C037.17SS, 10249.C037.18SS, 10249.C038.02SS, 10249.C038.04SS, 10249.C038.05SD, 10249.C038.05SS, 10249.C038.06SD, 10249.C038.06SS, 10249.C038.07SD, 10249.C038.07SS, 10249.C038.08SS, 10249.C038.09SS, 10249.C038.10SS, 10249.C038.11SS, 10249.C038.12SD, 10249.C038.12SS, 10249.C038.13SD, 10249.C038.13SS, 10249.C038.14SS, 10249.C038.15SD, 10249.C038.15SS, 10249.C038.16SD, 10249.C038.16SS, 10249.C038.18SS, 10249.C041.02SS, 10249.C041.03SS, 10249.C041.04SS, 10249.C041.05SD, 10249.C041.05SS, 10249.C041.06SD, 10249.C041.06SS, 10249.C041.08SS, 10249.C041.09SS, 10249.C041.10SS, 10249.C041.11SS, 10249.C041.12SS, 10249.C041.13SD, 10249.C041.13SS, 10249.C041.14SD, 10249.C041.14SS, 10249.C041.16SD, 10249.C041.16SS, 10249.C041.17SD, 10249.C041.17SS, 10249.C041.18SS, 10249.C041.19SS, 10249.C042.02SS, 10249.C042.03SS, 10249.C042.04SS, 10249.C042.05SS, 10249.C042.06SD, 10249.C042.06SS, 10249.C042.07SS, 10249.C042.08SS, 10249.C042.09SS, 10249.C042.10SS, 10249.C042.11SD, 10249.C042.11SS, 10249.C042.12SS, 10249.C042.13SS, 10249.C042.14SD, 10249.C042.14SS, 10249.C042.15SD, 10249.C042.15SS, 10249.C042.16SS, 10249.C042.17SS, 10249.C043.02SS, 10249.C043.03SS, 10249.C043.04SD, 10249.C043.04SS, 10249.C043.05SD, 10249.C043.05SS, 10249.C043.06SS, 10249.C043.07SS, 10249.C043.08SS, 10249.C043.09SS, 10249.C043.10SD, 10249.C043.10SS, 10249.C043.11SD, 10249.C043.11SS, 10249.C043.12SD, 10249.C043.12SS, 10249.C043.14SS, 10249.C043.15SD, 10249.C043.15SS, 10249.C043.16SS, 10249.C043.17SS, 10249.C043.18SS, 10249.C043.20SS, 10249.C044.02SS, 10249.C044.03SS, 10249.C044.04SS, 10249.C044.05SS, 10249.C044.06SS, 10249.C044.07SS, 10249.C044.08SS, 10249.C044.09SS, 10249.C044.10SS, 10249.C044.11SS, 10249.C044.12SD, 10249.C044.12SS, 10249.C044.13SD, 10249.C044.13SS, 10249.C044.15SD, 10249.C044.15SS, 10249.C044.16SS, 10249.C044.17SS, 10249.C045.02SS, 10249.C045.03SS, 10249.C045.04SS, 10249.C045.05SD, 10249.C045.05SS, 10249.C045.06SS, 10249.C045.08SD, 10249.C045.08SS, 10249.C045.09SD, 10249.C045.09SS, 10249.C045.10SD, 10249.C045.10SS, 10249.C045.11SS, 10249.C045.12SS, 10249.C045.13SS, 10249.C046.02SS, 10249.C046.03SS, 10249.C046.04SS, 10249.C046.05SS, 10249.C046.06SD, 10249.C046.06SS, 10249.C046.07SD, 10249.C046.07SS, 10249.C046.08SS, 10249.C046.09SD, 10249.C046.09SS, 10249.C046.10SD, 10249.C046.10SS, 10249.C046.11SD, 10249.C046.11SS, 10249.C046.12SS, 10249.C046.13SS, 10249.C046.14SS, 10249.C047.02SD, 10249.C047.02SS, 10249.C047.05SS, 10249.C047.06SD, 10249.C047.06SS, 10249.C047.07SD, 10249.C047.07SS, 10249.C047.08SD, 10249.C047.08SS, 10249.C047.09SS, 10249.C047.10SS, 10249.C047.11SS, 10249.C047.13SS, 10249.C049.03SD, 10249.C049.03SS, 10249.C049.04SS, 10249.C049.07SD, 10249.C049.07SS, 10249.C049.08SD, 10249.C049.08SS, 10249.C049.09SD, 10249.C049.09SS, 10249.C049.10SS, 10249.C049.11SS, 10249.C049.12SS, 10249.C049.13SS, 10249.C049.14SS, 10249.C052.03SD, 10249.C052.03SS, 10249.C052.04SD, 10249.C052.04SS, 10249.C052.05SD, 10249.C052.06SS, 10249.C052.07SS, 10249.C052.08SS, 10249.C052.09SS, 10249.C053.02SD, 10249.C053.02SS, 10249.C053.03SD, 10249.C053.03SS, 10249.C053.04SD, 10249.C053.04SS, 10249.C053.05SD, 10249.C053.05SS, 10249.C053.06SS, 10249.C053.07SS, 10249.C053.08SS, 10249.C053.09SS, 10249.C055.02SD, 10249.C055.02SS, 10249.C055.03SD, 10249.C055.03SS, 10249.C055.04SD, 10249.C055.04SS, 10249.C055.05SD, 10249.C055.05SS, 10249.C055.06SS, 10249.C055.07SS, 10249.C055.08SS, 10249.C055.09SS, 10249.C056.03SD, 10249.C056.03SS, 10249.C056.04SD, 10249.C056.04SS, 10249.C056.05SD, 10249.C056.05SS, 10249.C056.06SS, 10249.C056.07SS, 10249.C056.08SS, 10249.C056.09SS, 10249.C056.10SS, 10249.C057.02SS, 10249.C057.03SD, 10249.C057.03SS, 10249.C057.04SD, 10249.C057.04SS, 10249.C057.05SD, 10249.C057.05SS, 10249.C057.06SS, 10249.C057.08SS, 10249.C057.09SS, 10249.C057.10SS, 10249.C057.11SS
#> Updated feature table to match the subsetted data.
#> Updated feature annotation to match the subsetted data.
#> Data subsetting complete. Returning updated data object.
#> Rule 1 passed: data.obj is a list.
#> Rule 2 passed: meta.dat is a data.frame.
#> Rule 3 passed: The row names of feature.tab match the row names of feature.ann.
#> Rule 4 passed: The order of rows in meta.dat has been adjusted to match feature.tab.
#> Rule 5 passed: feature.tab is a matrix.
#> Rule 6 passed: feature.ann is a matrix.
#> Please note: The data components should follow base R data.frame and matrix structures, not phyloseq's formal class.
#> Validation passed.
#> Note: Passing validation does not guarantee the absence of all data issues. Further data exploration may be needed.
#> Data has been subsetted based on the provided condition.
#> Updated metadata to match the subsetted data.
#> The following samples were excluded: 10249.C001.02SS, 10249.C001.03SS, 10249.C001.04SS, 10249.C001.05SS, 10249.C001.06SS, 10249.C001.07SS, 10249.C001.08SS, 10249.C001.09SS, 10249.C001.10SS, 10249.C001.11SS, 10249.C001.12SS, 10249.C001.13SS, 10249.C001.14SS, 10249.C001.15SS, 10249.C001.16SS, 10249.C001.17SS, 10249.C001.18SS, 10249.C001.19SS, 10249.C001.20SS, 10249.C001.25SS, 10249.C001.26SS, 10249.C001.27SS, 10249.C001.29SS, 10249.C001.30SS, 10249.C001.31SS, 10249.C001.32SS, 10249.C001.34SD, 10249.C001.34SS, 10249.C001.35SS, 10249.C001.36SD, 10249.C001.36SS, 10249.C002.02SS, 10249.C002.03SS, 10249.C002.04SS, 10249.C002.05SS, 10249.C002.06SS, 10249.C002.07SS, 10249.C002.08SS, 10249.C002.09SS, 10249.C002.10SS, 10249.C002.11SS, 10249.C002.12SS, 10249.C002.13SS, 10249.C002.15SS, 10249.C002.16SS, 10249.C002.18SS, 10249.C002.19SD, 10249.C002.19SS, 10249.C002.20SS, 10249.C002.21SD, 10249.C002.21SS, 10249.C004.02SS, 10249.C004.03SS, 10249.C004.04SS, 10249.C004.05SS, 10249.C004.06SS, 10249.C004.07SS, 10249.C004.08SS, 10249.C004.09SS, 10249.C004.10SS, 10249.C004.11SS, 10249.C004.12SS, 10249.C004.13SS, 10249.C004.14SS, 10249.C004.15SS, 10249.C005.02SS, 10249.C005.03SS, 10249.C005.04SS, 10249.C005.05SS, 10249.C005.07SS, 10249.C005.08SS, 10249.C005.09SS, 10249.C005.10SS, 10249.C005.11SS, 10249.C005.12SS, 10249.C005.13SS, 10249.C005.14SS, 10249.C005.15SS, 10249.C005.16SS, 10249.C005.17SS, 10249.C005.18SS, 10249.C005.19SD, 10249.C005.19SS, 10249.C005.20SS, 10249.C005.21SD, 10249.C005.21SS, 10249.C005.22SS, 10249.C007.02SS, 10249.C007.03SS, 10249.C007.04SS, 10249.C007.05SS, 10249.C007.06SS, 10249.C007.07SS, 10249.C007.08SS, 10249.C007.09SS, 10249.C007.10SS, 10249.C007.11SS, 10249.C007.12SS, 10249.C007.13SS, 10249.C007.14SS, 10249.C007.15SS, 10249.C007.16SS, 10249.C007.17SS, 10249.C007.18SS, 10249.C007.19SS, 10249.C007.20SS, 10249.C007.21SS, 10249.C007.22SD, 10249.C007.22SS, 10249.C007.23SD, 10249.C007.23SS, 10249.C007.24SD, 10249.C007.24SS, 10249.C007.26SS, 10249.C008.02SS, 10249.C008.03SS, 10249.C008.04SS, 10249.C008.05SS, 10249.C008.06SS, 10249.C008.07SS, 10249.C008.08SS, 10249.C008.09SS, 10249.C008.10SS, 10249.C008.11SS, 10249.C008.12SS, 10249.C008.13SS, 10249.C008.14SS, 10249.C008.15SS, 10249.C008.16SD, 10249.C008.16SS, 10249.C008.18SS, 10249.C009.02SS, 10249.C009.03SS, 10249.C009.04SS, 10249.C009.05SS, 10249.C009.06SS, 10249.C009.07SS, 10249.C009.08SS, 10249.C009.09SS, 10249.C009.10SS, 10249.C009.11SS, 10249.C009.12SS, 10249.C009.13SS, 10249.C009.14SS, 10249.C009.16SS, 10249.C009.17SS, 10249.C009.18SD, 10249.C009.18SS, 10249.C009.19SS, 10249.C009.20SD, 10249.C009.20SS, 10249.C009.21SS, 10249.C010.02SS, 10249.C010.03SS, 10249.C010.04SS, 10249.C010.05SS, 10249.C010.06SS, 10249.C010.07SS, 10249.C010.08SS, 10249.C010.09SS, 10249.C010.10SS, 10249.C010.11SS, 10249.C010.12SS, 10249.C010.13SS, 10249.C010.14SS, 10249.C010.15SS, 10249.C010.16SS, 10249.C010.18SD, 10249.C010.18SS, 10249.C010.19SS, 10249.C010.20SD, 10249.C010.20SS, 10249.C010.21SS, 10249.C011.02SS, 10249.C011.03SS, 10249.C011.04SS, 10249.C011.05SS, 10249.C011.06SS, 10249.C011.07SS, 10249.C011.08SS, 10249.C011.09SS, 10249.C011.10SS, 10249.C011.11SS, 10249.C011.12SS, 10249.C011.13SD, 10249.C011.14SS, 10249.C011.16SS, 10249.C011.17SD, 10249.C011.17SS, 10249.C011.18SS, 10249.C011.19SD, 10249.C011.19SS, 10249.C011.20SS, 10249.C011.21SS, 10249.C012.02SS, 10249.C012.03SS, 10249.C012.04SS, 10249.C012.05SS, 10249.C012.06SS, 10249.C012.07SS, 10249.C012.08SS, 10249.C012.09SS, 10249.C012.10SS, 10249.C012.11SS, 10249.C012.12SS, 10249.C012.13SS, 10249.C012.14SS, 10249.C012.15SS, 10249.C012.16SS, 10249.C012.17SS, 10249.C012.18SS, 10249.C012.19SD, 10249.C012.19SS, 10249.C012.20SS, 10249.C012.21SD, 10249.C012.21SS, 10249.C012.22SD, 10249.C012.22SS, 10249.C014.02SS, 10249.C014.03SS, 10249.C014.04SS, 10249.C014.05SS, 10249.C014.06SS, 10249.C014.07SS, 10249.C014.08SS, 10249.C014.09SS, 10249.C014.10SS, 10249.C014.12SS, 10249.C014.13SS, 10249.C014.15SS, 10249.C014.16SS, 10249.C014.17SS, 10249.C014.18SS, 10249.C014.19SD, 10249.C014.19SS, 10249.C014.20SD, 10249.C014.20SS, 10249.C014.21SS, 10249.C014.22SS, 10249.C016.03SS, 10249.C016.04SS, 10249.C016.05SS, 10249.C016.06SS, 10249.C016.07SS, 10249.C016.08SS, 10249.C016.09SS, 10249.C016.10SS, 10249.C016.11SS, 10249.C016.12SS, 10249.C016.13SS, 10249.C016.14SS, 10249.C016.15SS, 10249.C016.17SS, 10249.C016.18SS, 10249.C016.19SS, 10249.C016.20SS, 10249.C016.21SD, 10249.C016.21SS, 10249.C016.22SD, 10249.C016.22SS, 10249.C016.23SS, 10249.C016.24SS, 10249.C017.04SS, 10249.C017.05SS, 10249.C017.06SS, 10249.C017.07SS, 10249.C017.08SS, 10249.C017.09SS, 10249.C017.10SS, 10249.C017.11SS, 10249.C017.12SS, 10249.C018.02SS, 10249.C018.03SS, 10249.C018.04SS, 10249.C018.05SS, 10249.C018.06SS, 10249.C018.07SS, 10249.C018.08SS, 10249.C018.09SS, 10249.C018.10SS, 10249.C018.11SD, 10249.C018.11SS, 10249.C018.12SD, 10249.C018.12SS, 10249.C018.13SS, 10249.C018.14SS, 10249.C018.15SS, 10249.C018.16SS, 10249.C018.17SS, 10249.C018.18SS, 10249.C018.19SS, 10249.C020.06SS, 10249.C020.07SS, 10249.C020.08SS, 10249.C020.09SS, 10249.C020.10SS, 10249.C020.11SS, 10249.C020.12SS, 10249.C020.13SS, 10249.C020.14SS, 10249.C020.15SS, 10249.C020.16SS, 10249.C020.17SS, 10249.C020.18SS, 10249.C020.19SS, 10249.C020.20SS, 10249.C020.21SS, 10249.C020.22SD, 10249.C020.22SS, 10249.C020.23SD, 10249.C020.23SS, 10249.C020.24SD, 10249.C020.24SS, 10249.C020.25SD, 10249.C020.25SS, 10249.C020.26SD, 10249.C020.26SS, 10249.C020.28SS, 10249.C020.29SS, 10249.C021.03SS, 10249.C021.04SS, 10249.C021.05SS, 10249.C021.06SS, 10249.C021.07SS, 10249.C021.08SS, 10249.C021.09SS, 10249.C021.10SS, 10249.C021.12SS, 10249.C021.13SS, 10249.C022.02SS, 10249.C022.03SS, 10249.C022.04SS, 10249.C022.05SS, 10249.C022.06SS, 10249.C022.07SS, 10249.C022.08SS, 10249.C022.09SS, 10249.C022.10SS, 10249.C022.11SS, 10249.C022.12SS, 10249.C022.13SS, 10249.C022.15SS, 10249.C022.16SS, 10249.C022.18SD, 10249.C022.18SS, 10249.C022.19SS, 10249.C022.20SS, 10249.C022.21SS, 10249.C024.02SS, 10249.C024.03SS, 10249.C024.04SS, 10249.C024.05SS, 10249.C024.06SS, 10249.C024.07SS, 10249.C024.08SS, 10249.C024.09SS, 10249.C024.10SS, 10249.C024.12SS, 10249.C024.13SS, 10249.C024.14SS, 10249.C024.15SS, 10249.C024.16SS, 10249.C024.17SS, 10249.C024.18SS, 10249.C024.19SD, 10249.C024.19SS, 10249.C024.20SD, 10249.C024.20SS, 10249.C024.21SS, 10249.C024.22SS, 10249.C025.02SS, 10249.C025.03SS, 10249.C025.04SS, 10249.C025.05SS, 10249.C025.06SS, 10249.C025.07SS, 10249.C025.08SS, 10249.C025.09SS, 10249.C025.10SS, 10249.C025.11SS, 10249.C025.12SS, 10249.C025.13SD, 10249.C025.13SS, 10249.C025.14SD, 10249.C025.14SS, 10249.C025.15SS, 10249.C025.16SS, 10249.C025.17SS, 10249.C025.18SS, 10249.C025.19SD, 10249.C025.19SS, 10249.C025.20SS, 10249.C025.21SS, 10249.C027.02SS, 10249.C027.03SS, 10249.C027.04SS, 10249.C027.05SS, 10249.C027.06SS, 10249.C027.07SS, 10249.C027.08SS, 10249.C027.09SS, 10249.C027.10SS, 10249.C027.11SD, 10249.C027.12SD, 10249.C027.12SS, 10249.C027.13SS, 10249.C027.14SS, 10249.C027.15SS, 10249.C027.16SS, 10249.C027.17SD, 10249.C027.17SS, 10249.C027.18SS, 10249.C027.19SD, 10249.C027.19SS, 10249.C027.20SD, 10249.C027.20SS, 10249.C027.21SS, 10249.C027.22SS, 10249.C030.02SS, 10249.C030.03SS, 10249.C030.04SS, 10249.C030.05SS, 10249.C030.06SS, 10249.C030.07SS, 10249.C030.08SS, 10249.C030.09SS, 10249.C030.10SS, 10249.C030.11SD, 10249.C030.11SS, 10249.C030.12SS, 10249.C030.13SS, 10249.C030.14SS, 10249.C030.16SS, 10249.C030.17SD, 10249.C030.17SS, 10249.C030.18SS, 10249.C030.19SD, 10249.C030.19SS, 10249.C030.20SS, 10249.C031.02SS, 10249.C031.03SS, 10249.C031.04SS, 10249.C031.05SS, 10249.C031.06SS, 10249.C031.07SS, 10249.C031.08SS, 10249.C031.09SS, 10249.C031.10SS, 10249.C031.11SD, 10249.C031.11SS, 10249.C031.12SS, 10249.C031.13SS, 10249.C031.14SS, 10249.C031.16SS, 10249.C031.17SD, 10249.C031.17SS, 10249.C031.18SS, 10249.C031.19SD, 10249.C031.19SS, 10249.C031.20SS, 10249.C031.21SS, 10249.C032.02SS, 10249.C032.03SS, 10249.C032.04SS, 10249.C032.05SS, 10249.C032.06SS, 10249.C032.07SS, 10249.C032.09SS, 10249.C032.10SS, 10249.C032.11SD, 10249.C032.11SS, 10249.C032.12SD, 10249.C032.13SS, 10249.C032.14SS, 10249.C032.15SS, 10249.C032.16SS, 10249.C032.17SS, 10249.C032.19SD, 10249.C032.19SS, 10249.C032.20SD, 10249.C032.20SS, 10249.C032.21SS, 10249.C032.22SS, 10249.C033.02SS, 10249.C033.03SS, 10249.C033.04SS, 10249.C033.05SS, 10249.C033.06SS, 10249.C033.07SS, 10249.C033.08SS, 10249.C033.09SD, 10249.C033.09SS, 10249.C033.10SD, 10249.C033.10SS, 10249.C033.11SD, 10249.C033.11SS, 10249.C033.12SS, 10249.C033.13SS, 10249.C033.14SS, 10249.C033.15SS, 10249.C033.16SS, 10249.C033.17SD, 10249.C033.17SS, 10249.C033.18SD, 10249.C033.18SS, 10249.C033.19SS, 10249.C034.02SS, 10249.C034.03SS, 10249.C034.04SS, 10249.C034.05SS, 10249.C034.06SS, 10249.C034.07SS, 10249.C034.08SS, 10249.C034.09SS, 10249.C034.10SS, 10249.C034.11SS, 10249.C034.12SS, 10249.C034.13SS, 10249.C034.14SS, 10249.C034.15SD, 10249.C034.15SS, 10249.C034.16SS, 10249.C034.17SD, 10249.C034.17SS, 10249.C035.02SS, 10249.C035.03SS, 10249.C035.04SS, 10249.C035.05SS, 10249.C035.06SD, 10249.C035.06SS, 10249.C035.07SD, 10249.C035.07SS, 10249.C035.08SS, 10249.C035.09SS, 10249.C035.10SS, 10249.C035.11SS, 10249.C035.12SD, 10249.C035.12SS, 10249.C035.13SD, 10249.C035.13SS, 10249.C035.14SD, 10249.C035.14SS, 10249.C035.15SD, 10249.C035.15SS, 10249.C035.16SS, 10249.C035.17SS, 10249.C036.02SS, 10249.C036.03SS, 10249.C036.04SS, 10249.C036.05SD, 10249.C036.05SS, 10249.C036.07SS, 10249.C036.08SS, 10249.C036.09SS, 10249.C036.10SS, 10249.C036.11SS, 10249.C036.12SS, 10249.C036.13SS, 10249.C036.14SD, 10249.C036.14SS, 10249.C036.15SS, 10249.C036.16SS, 10249.C037.02SS, 10249.C037.04SS, 10249.C037.05SS, 10249.C037.06SS, 10249.C037.07SS, 10249.C037.08SS, 10249.C037.09SS, 10249.C037.10SS, 10249.C037.11SS, 10249.C037.12SD, 10249.C037.12SS, 10249.C037.13SD, 10249.C037.13SS, 10249.C037.14SS, 10249.C037.15SS, 10249.C037.16SS, 10249.C037.17SS, 10249.C037.18SS, 10249.C038.02SS, 10249.C038.04SS, 10249.C038.05SD, 10249.C038.05SS, 10249.C038.06SD, 10249.C038.06SS, 10249.C038.07SD, 10249.C038.07SS, 10249.C038.08SS, 10249.C038.09SS, 10249.C038.10SS, 10249.C038.11SS, 10249.C038.12SD, 10249.C038.12SS, 10249.C038.13SD, 10249.C038.13SS, 10249.C038.14SS, 10249.C038.15SD, 10249.C038.15SS, 10249.C038.16SD, 10249.C038.16SS, 10249.C038.18SS, 10249.C041.02SS, 10249.C041.03SS, 10249.C041.04SS, 10249.C041.05SD, 10249.C041.05SS, 10249.C041.06SD, 10249.C041.06SS, 10249.C041.08SS, 10249.C041.09SS, 10249.C041.10SS, 10249.C041.11SS, 10249.C041.12SS, 10249.C041.13SD, 10249.C041.13SS, 10249.C041.14SD, 10249.C041.14SS, 10249.C041.16SD, 10249.C041.16SS, 10249.C041.17SD, 10249.C041.17SS, 10249.C041.18SS, 10249.C041.19SS, 10249.C042.02SS, 10249.C042.03SS, 10249.C042.04SS, 10249.C042.05SS, 10249.C042.06SD, 10249.C042.06SS, 10249.C042.07SS, 10249.C042.08SS, 10249.C042.09SS, 10249.C042.10SS, 10249.C042.11SD, 10249.C042.11SS, 10249.C042.12SS, 10249.C042.13SS, 10249.C042.14SD, 10249.C042.14SS, 10249.C042.15SD, 10249.C042.15SS, 10249.C042.16SS, 10249.C042.17SS, 10249.C043.02SS, 10249.C043.03SS, 10249.C043.04SD, 10249.C043.04SS, 10249.C043.05SD, 10249.C043.05SS, 10249.C043.06SS, 10249.C043.07SS, 10249.C043.08SS, 10249.C043.09SS, 10249.C043.10SD, 10249.C043.10SS, 10249.C043.11SD, 10249.C043.11SS, 10249.C043.12SD, 10249.C043.12SS, 10249.C043.14SS, 10249.C043.15SD, 10249.C043.15SS, 10249.C043.16SS, 10249.C043.17SS, 10249.C043.18SS, 10249.C043.20SS, 10249.C044.02SS, 10249.C044.03SS, 10249.C044.04SS, 10249.C044.05SS, 10249.C044.06SS, 10249.C044.07SS, 10249.C044.08SS, 10249.C044.09SS, 10249.C044.10SS, 10249.C044.11SS, 10249.C044.12SD, 10249.C044.12SS, 10249.C044.13SD, 10249.C044.13SS, 10249.C044.15SD, 10249.C044.15SS, 10249.C044.16SS, 10249.C044.17SS, 10249.C045.02SS, 10249.C045.03SS, 10249.C045.04SS, 10249.C045.05SD, 10249.C045.05SS, 10249.C045.06SS, 10249.C045.08SD, 10249.C045.08SS, 10249.C045.09SD, 10249.C045.09SS, 10249.C045.10SD, 10249.C045.10SS, 10249.C045.11SS, 10249.C045.12SS, 10249.C045.13SS, 10249.C046.02SS, 10249.C046.03SS, 10249.C046.04SS, 10249.C046.05SS, 10249.C046.06SD, 10249.C046.06SS, 10249.C046.07SD, 10249.C046.07SS, 10249.C046.08SS, 10249.C046.09SD, 10249.C046.09SS, 10249.C046.10SD, 10249.C046.10SS, 10249.C046.11SD, 10249.C046.11SS, 10249.C046.12SS, 10249.C046.13SS, 10249.C046.14SS, 10249.C047.02SD, 10249.C047.02SS, 10249.C047.05SS, 10249.C047.06SD, 10249.C047.06SS, 10249.C047.07SD, 10249.C047.07SS, 10249.C047.08SD, 10249.C047.08SS, 10249.C047.09SS, 10249.C047.10SS, 10249.C047.11SS, 10249.C047.13SS, 10249.C049.03SD, 10249.C049.03SS, 10249.C049.04SS, 10249.C049.07SD, 10249.C049.07SS, 10249.C049.08SD, 10249.C049.08SS, 10249.C049.09SD, 10249.C049.09SS, 10249.C049.10SS, 10249.C049.11SS, 10249.C049.12SS, 10249.C049.13SS, 10249.C049.14SS, 10249.C052.03SD, 10249.C052.03SS, 10249.C052.04SD, 10249.C052.04SS, 10249.C052.05SD, 10249.C052.06SS, 10249.C052.07SS, 10249.C052.08SS, 10249.C052.09SS, 10249.C053.02SD, 10249.C053.02SS, 10249.C053.03SD, 10249.C053.03SS, 10249.C053.04SD, 10249.C053.04SS, 10249.C053.05SD, 10249.C053.05SS, 10249.C053.06SS, 10249.C053.07SS, 10249.C053.08SS, 10249.C053.09SS, 10249.C055.02SD, 10249.C055.02SS, 10249.C055.03SD, 10249.C055.03SS, 10249.C055.04SD, 10249.C055.04SS, 10249.C055.05SD, 10249.C055.05SS, 10249.C055.06SS, 10249.C055.07SS, 10249.C055.08SS, 10249.C055.09SS, 10249.C056.03SD, 10249.C056.03SS, 10249.C056.04SD, 10249.C056.04SS, 10249.C056.05SD, 10249.C056.05SS, 10249.C056.06SS, 10249.C056.07SS, 10249.C056.08SS, 10249.C056.09SS, 10249.C056.10SS, 10249.C057.02SS, 10249.C057.03SD, 10249.C057.03SS, 10249.C057.04SD, 10249.C057.04SS, 10249.C057.05SD, 10249.C057.05SS, 10249.C057.06SS, 10249.C057.08SS, 10249.C057.09SS, 10249.C057.10SS, 10249.C057.11SS
#> Updated feature table to match the subsetted data.
#> Updated feature annotation to match the subsetted data.
#> Data subsetting complete. Returning updated data object.
#> $Phylum
#> $Phylum$Phylum

#> 
#> 
#> $Family
#> $Family$Family

#> 
#> 
#> $Genus
#> $Genus$Genus

#> 
#> 

plot_feature_diversity(
data.obj = ecam.obj,
group.var = "antiexposedall",
strata.var = "delivery",
time.var = "month",
time.point.plot = unique(ecam.obj$meta.dat$month)[1],
is.plot.change = TRUE,
feature.level = c("Phylum", "Family", "Genus"),
feature.dat.type = "proportion",
features.plot = NULL,
prop.to.lump = 0.0001,
top.k.plot = NULL,
top.k.func = NULL,
renormalize = FALSE,
plot.other = TRUE,
plot.scheme = "combined",
plot.type = "boxplot"
)
#> Rule 1 passed: data.obj is a list.
#> Rule 2 passed: meta.dat is a data.frame.
#> Rule 3 passed: The row names of feature.tab match the row names of feature.ann.
#> Rule 4 passed: The order of rows in meta.dat has been adjusted to match feature.tab.
#> Rule 5 passed: feature.tab is a matrix.
#> Rule 6 passed: feature.ann is a matrix.
#> Please note: The data components should follow base R data.frame and matrix structures, not phyloseq's formal class.
#> Validation passed.
#> Note: Passing validation does not guarantee the absence of all data issues. Further data exploration may be needed.
#> Data has been subsetted based on the provided condition.
#> Updated metadata to match the subsetted data.
#> The following samples were excluded: 10249.C001.02SS, 10249.C001.03SS, 10249.C001.04SS, 10249.C001.05SS, 10249.C001.06SS, 10249.C001.07SS, 10249.C001.08SS, 10249.C001.09SS, 10249.C001.10SS, 10249.C001.11SS, 10249.C001.12SS, 10249.C001.13SS, 10249.C001.14SS, 10249.C001.15SS, 10249.C001.16SS, 10249.C001.17SS, 10249.C001.18SS, 10249.C001.19SS, 10249.C001.20SS, 10249.C001.25SS, 10249.C001.26SS, 10249.C001.27SS, 10249.C001.29SS, 10249.C001.30SS, 10249.C001.31SS, 10249.C001.32SS, 10249.C001.34SD, 10249.C001.34SS, 10249.C001.35SS, 10249.C001.36SD, 10249.C001.36SS, 10249.C002.02SS, 10249.C002.03SS, 10249.C002.04SS, 10249.C002.05SS, 10249.C002.06SS, 10249.C002.07SS, 10249.C002.08SS, 10249.C002.09SS, 10249.C002.10SS, 10249.C002.11SS, 10249.C002.12SS, 10249.C002.13SS, 10249.C002.15SS, 10249.C002.16SS, 10249.C002.18SS, 10249.C002.19SD, 10249.C002.19SS, 10249.C002.20SS, 10249.C002.21SD, 10249.C002.21SS, 10249.C004.02SS, 10249.C004.03SS, 10249.C004.04SS, 10249.C004.05SS, 10249.C004.06SS, 10249.C004.07SS, 10249.C004.08SS, 10249.C004.09SS, 10249.C004.10SS, 10249.C004.11SS, 10249.C004.12SS, 10249.C004.13SS, 10249.C004.14SS, 10249.C004.15SS, 10249.C005.02SS, 10249.C005.03SS, 10249.C005.04SS, 10249.C005.05SS, 10249.C005.07SS, 10249.C005.08SS, 10249.C005.09SS, 10249.C005.10SS, 10249.C005.11SS, 10249.C005.12SS, 10249.C005.13SS, 10249.C005.14SS, 10249.C005.15SS, 10249.C005.16SS, 10249.C005.17SS, 10249.C005.18SS, 10249.C005.19SD, 10249.C005.19SS, 10249.C005.20SS, 10249.C005.21SD, 10249.C005.21SS, 10249.C005.22SS, 10249.C007.02SS, 10249.C007.03SS, 10249.C007.04SS, 10249.C007.05SS, 10249.C007.06SS, 10249.C007.07SS, 10249.C007.08SS, 10249.C007.09SS, 10249.C007.10SS, 10249.C007.11SS, 10249.C007.12SS, 10249.C007.13SS, 10249.C007.14SS, 10249.C007.15SS, 10249.C007.16SS, 10249.C007.17SS, 10249.C007.18SS, 10249.C007.19SS, 10249.C007.20SS, 10249.C007.21SS, 10249.C007.22SD, 10249.C007.22SS, 10249.C007.23SD, 10249.C007.23SS, 10249.C007.24SD, 10249.C007.24SS, 10249.C007.26SS, 10249.C008.02SS, 10249.C008.03SS, 10249.C008.04SS, 10249.C008.05SS, 10249.C008.06SS, 10249.C008.07SS, 10249.C008.08SS, 10249.C008.09SS, 10249.C008.10SS, 10249.C008.11SS, 10249.C008.12SS, 10249.C008.13SS, 10249.C008.14SS, 10249.C008.15SS, 10249.C008.16SD, 10249.C008.16SS, 10249.C008.18SS, 10249.C009.02SS, 10249.C009.03SS, 10249.C009.04SS, 10249.C009.05SS, 10249.C009.06SS, 10249.C009.07SS, 10249.C009.08SS, 10249.C009.09SS, 10249.C009.10SS, 10249.C009.11SS, 10249.C009.12SS, 10249.C009.13SS, 10249.C009.14SS, 10249.C009.16SS, 10249.C009.17SS, 10249.C009.18SD, 10249.C009.18SS, 10249.C009.19SS, 10249.C009.20SD, 10249.C009.20SS, 10249.C009.21SS, 10249.C010.02SS, 10249.C010.03SS, 10249.C010.04SS, 10249.C010.05SS, 10249.C010.06SS, 10249.C010.07SS, 10249.C010.08SS, 10249.C010.09SS, 10249.C010.10SS, 10249.C010.11SS, 10249.C010.12SS, 10249.C010.13SS, 10249.C010.14SS, 10249.C010.15SS, 10249.C010.16SS, 10249.C010.18SD, 10249.C010.18SS, 10249.C010.19SS, 10249.C010.20SD, 10249.C010.20SS, 10249.C010.21SS, 10249.C011.02SS, 10249.C011.03SS, 10249.C011.04SS, 10249.C011.05SS, 10249.C011.06SS, 10249.C011.07SS, 10249.C011.08SS, 10249.C011.09SS, 10249.C011.10SS, 10249.C011.11SS, 10249.C011.12SS, 10249.C011.13SD, 10249.C011.14SS, 10249.C011.16SS, 10249.C011.17SD, 10249.C011.17SS, 10249.C011.18SS, 10249.C011.19SD, 10249.C011.19SS, 10249.C011.20SS, 10249.C011.21SS, 10249.C012.02SS, 10249.C012.03SS, 10249.C012.04SS, 10249.C012.05SS, 10249.C012.06SS, 10249.C012.07SS, 10249.C012.08SS, 10249.C012.09SS, 10249.C012.10SS, 10249.C012.11SS, 10249.C012.12SS, 10249.C012.13SS, 10249.C012.14SS, 10249.C012.15SS, 10249.C012.16SS, 10249.C012.17SS, 10249.C012.18SS, 10249.C012.19SD, 10249.C012.19SS, 10249.C012.20SS, 10249.C012.21SD, 10249.C012.21SS, 10249.C012.22SD, 10249.C012.22SS, 10249.C014.02SS, 10249.C014.03SS, 10249.C014.04SS, 10249.C014.05SS, 10249.C014.06SS, 10249.C014.07SS, 10249.C014.08SS, 10249.C014.09SS, 10249.C014.10SS, 10249.C014.12SS, 10249.C014.13SS, 10249.C014.15SS, 10249.C014.16SS, 10249.C014.17SS, 10249.C014.18SS, 10249.C014.19SD, 10249.C014.19SS, 10249.C014.20SD, 10249.C014.20SS, 10249.C014.21SS, 10249.C014.22SS, 10249.C016.03SS, 10249.C016.04SS, 10249.C016.05SS, 10249.C016.06SS, 10249.C016.07SS, 10249.C016.08SS, 10249.C016.09SS, 10249.C016.10SS, 10249.C016.11SS, 10249.C016.12SS, 10249.C016.13SS, 10249.C016.14SS, 10249.C016.15SS, 10249.C016.17SS, 10249.C016.18SS, 10249.C016.19SS, 10249.C016.20SS, 10249.C016.21SD, 10249.C016.21SS, 10249.C016.22SD, 10249.C016.22SS, 10249.C016.23SS, 10249.C016.24SS, 10249.C017.04SS, 10249.C017.05SS, 10249.C017.06SS, 10249.C017.07SS, 10249.C017.08SS, 10249.C017.09SS, 10249.C017.10SS, 10249.C017.11SS, 10249.C017.12SS, 10249.C018.02SS, 10249.C018.03SS, 10249.C018.04SS, 10249.C018.05SS, 10249.C018.06SS, 10249.C018.07SS, 10249.C018.08SS, 10249.C018.09SS, 10249.C018.10SS, 10249.C018.11SD, 10249.C018.11SS, 10249.C018.12SD, 10249.C018.12SS, 10249.C018.13SS, 10249.C018.14SS, 10249.C018.15SS, 10249.C018.16SS, 10249.C018.17SS, 10249.C018.18SS, 10249.C018.19SS, 10249.C020.06SS, 10249.C020.07SS, 10249.C020.08SS, 10249.C020.09SS, 10249.C020.10SS, 10249.C020.11SS, 10249.C020.12SS, 10249.C020.13SS, 10249.C020.14SS, 10249.C020.15SS, 10249.C020.16SS, 10249.C020.17SS, 10249.C020.18SS, 10249.C020.19SS, 10249.C020.20SS, 10249.C020.21SS, 10249.C020.22SD, 10249.C020.22SS, 10249.C020.23SD, 10249.C020.23SS, 10249.C020.24SD, 10249.C020.24SS, 10249.C020.25SD, 10249.C020.25SS, 10249.C020.26SD, 10249.C020.26SS, 10249.C020.28SS, 10249.C020.29SS, 10249.C021.03SS, 10249.C021.04SS, 10249.C021.05SS, 10249.C021.06SS, 10249.C021.07SS, 10249.C021.08SS, 10249.C021.09SS, 10249.C021.10SS, 10249.C021.12SS, 10249.C021.13SS, 10249.C022.02SS, 10249.C022.03SS, 10249.C022.04SS, 10249.C022.05SS, 10249.C022.06SS, 10249.C022.07SS, 10249.C022.08SS, 10249.C022.09SS, 10249.C022.10SS, 10249.C022.11SS, 10249.C022.12SS, 10249.C022.13SS, 10249.C022.15SS, 10249.C022.16SS, 10249.C022.18SD, 10249.C022.18SS, 10249.C022.19SS, 10249.C022.20SS, 10249.C022.21SS, 10249.C024.02SS, 10249.C024.03SS, 10249.C024.04SS, 10249.C024.05SS, 10249.C024.06SS, 10249.C024.07SS, 10249.C024.08SS, 10249.C024.09SS, 10249.C024.10SS, 10249.C024.12SS, 10249.C024.13SS, 10249.C024.14SS, 10249.C024.15SS, 10249.C024.16SS, 10249.C024.17SS, 10249.C024.18SS, 10249.C024.19SD, 10249.C024.19SS, 10249.C024.20SD, 10249.C024.20SS, 10249.C024.21SS, 10249.C024.22SS, 10249.C025.02SS, 10249.C025.03SS, 10249.C025.04SS, 10249.C025.05SS, 10249.C025.06SS, 10249.C025.07SS, 10249.C025.08SS, 10249.C025.09SS, 10249.C025.10SS, 10249.C025.11SS, 10249.C025.12SS, 10249.C025.13SD, 10249.C025.13SS, 10249.C025.14SD, 10249.C025.14SS, 10249.C025.15SS, 10249.C025.16SS, 10249.C025.17SS, 10249.C025.18SS, 10249.C025.19SD, 10249.C025.19SS, 10249.C025.20SS, 10249.C025.21SS, 10249.C027.02SS, 10249.C027.03SS, 10249.C027.04SS, 10249.C027.05SS, 10249.C027.06SS, 10249.C027.07SS, 10249.C027.08SS, 10249.C027.09SS, 10249.C027.10SS, 10249.C027.11SD, 10249.C027.12SD, 10249.C027.12SS, 10249.C027.13SS, 10249.C027.14SS, 10249.C027.15SS, 10249.C027.16SS, 10249.C027.17SD, 10249.C027.17SS, 10249.C027.18SS, 10249.C027.19SD, 10249.C027.19SS, 10249.C027.20SD, 10249.C027.20SS, 10249.C027.21SS, 10249.C027.22SS, 10249.C030.02SS, 10249.C030.03SS, 10249.C030.04SS, 10249.C030.05SS, 10249.C030.06SS, 10249.C030.07SS, 10249.C030.08SS, 10249.C030.09SS, 10249.C030.10SS, 10249.C030.11SD, 10249.C030.11SS, 10249.C030.12SS, 10249.C030.13SS, 10249.C030.14SS, 10249.C030.16SS, 10249.C030.17SD, 10249.C030.17SS, 10249.C030.18SS, 10249.C030.19SD, 10249.C030.19SS, 10249.C030.20SS, 10249.C031.02SS, 10249.C031.03SS, 10249.C031.04SS, 10249.C031.05SS, 10249.C031.06SS, 10249.C031.07SS, 10249.C031.08SS, 10249.C031.09SS, 10249.C031.10SS, 10249.C031.11SD, 10249.C031.11SS, 10249.C031.12SS, 10249.C031.13SS, 10249.C031.14SS, 10249.C031.16SS, 10249.C031.17SD, 10249.C031.17SS, 10249.C031.18SS, 10249.C031.19SD, 10249.C031.19SS, 10249.C031.20SS, 10249.C031.21SS, 10249.C032.02SS, 10249.C032.03SS, 10249.C032.04SS, 10249.C032.05SS, 10249.C032.06SS, 10249.C032.07SS, 10249.C032.09SS, 10249.C032.10SS, 10249.C032.11SD, 10249.C032.11SS, 10249.C032.12SD, 10249.C032.13SS, 10249.C032.14SS, 10249.C032.15SS, 10249.C032.16SS, 10249.C032.17SS, 10249.C032.19SD, 10249.C032.19SS, 10249.C032.20SD, 10249.C032.20SS, 10249.C032.21SS, 10249.C032.22SS, 10249.C033.02SS, 10249.C033.03SS, 10249.C033.04SS, 10249.C033.05SS, 10249.C033.06SS, 10249.C033.07SS, 10249.C033.08SS, 10249.C033.09SD, 10249.C033.09SS, 10249.C033.10SD, 10249.C033.10SS, 10249.C033.11SD, 10249.C033.11SS, 10249.C033.12SS, 10249.C033.13SS, 10249.C033.14SS, 10249.C033.15SS, 10249.C033.16SS, 10249.C033.17SD, 10249.C033.17SS, 10249.C033.18SD, 10249.C033.18SS, 10249.C033.19SS, 10249.C034.02SS, 10249.C034.03SS, 10249.C034.04SS, 10249.C034.05SS, 10249.C034.06SS, 10249.C034.07SS, 10249.C034.08SS, 10249.C034.09SS, 10249.C034.10SS, 10249.C034.11SS, 10249.C034.12SS, 10249.C034.13SS, 10249.C034.14SS, 10249.C034.15SD, 10249.C034.15SS, 10249.C034.16SS, 10249.C034.17SD, 10249.C034.17SS, 10249.C035.02SS, 10249.C035.03SS, 10249.C035.04SS, 10249.C035.05SS, 10249.C035.06SD, 10249.C035.06SS, 10249.C035.07SD, 10249.C035.07SS, 10249.C035.08SS, 10249.C035.09SS, 10249.C035.10SS, 10249.C035.11SS, 10249.C035.12SD, 10249.C035.12SS, 10249.C035.13SD, 10249.C035.13SS, 10249.C035.14SD, 10249.C035.14SS, 10249.C035.15SD, 10249.C035.15SS, 10249.C035.16SS, 10249.C035.17SS, 10249.C036.02SS, 10249.C036.03SS, 10249.C036.04SS, 10249.C036.05SD, 10249.C036.05SS, 10249.C036.07SS, 10249.C036.08SS, 10249.C036.09SS, 10249.C036.10SS, 10249.C036.11SS, 10249.C036.12SS, 10249.C036.13SS, 10249.C036.14SD, 10249.C036.14SS, 10249.C036.15SS, 10249.C036.16SS, 10249.C037.02SS, 10249.C037.04SS, 10249.C037.05SS, 10249.C037.06SS, 10249.C037.07SS, 10249.C037.08SS, 10249.C037.09SS, 10249.C037.10SS, 10249.C037.11SS, 10249.C037.12SD, 10249.C037.12SS, 10249.C037.13SD, 10249.C037.13SS, 10249.C037.14SS, 10249.C037.15SS, 10249.C037.16SS, 10249.C037.17SS, 10249.C037.18SS, 10249.C038.02SS, 10249.C038.04SS, 10249.C038.05SD, 10249.C038.05SS, 10249.C038.06SD, 10249.C038.06SS, 10249.C038.07SD, 10249.C038.07SS, 10249.C038.08SS, 10249.C038.09SS, 10249.C038.10SS, 10249.C038.11SS, 10249.C038.12SD, 10249.C038.12SS, 10249.C038.13SD, 10249.C038.13SS, 10249.C038.14SS, 10249.C038.15SD, 10249.C038.15SS, 10249.C038.16SD, 10249.C038.16SS, 10249.C038.18SS, 10249.C041.02SS, 10249.C041.03SS, 10249.C041.04SS, 10249.C041.05SD, 10249.C041.05SS, 10249.C041.06SD, 10249.C041.06SS, 10249.C041.08SS, 10249.C041.09SS, 10249.C041.10SS, 10249.C041.11SS, 10249.C041.12SS, 10249.C041.13SD, 10249.C041.13SS, 10249.C041.14SD, 10249.C041.14SS, 10249.C041.16SD, 10249.C041.16SS, 10249.C041.17SD, 10249.C041.17SS, 10249.C041.18SS, 10249.C041.19SS, 10249.C042.02SS, 10249.C042.03SS, 10249.C042.04SS, 10249.C042.05SS, 10249.C042.06SD, 10249.C042.06SS, 10249.C042.07SS, 10249.C042.08SS, 10249.C042.09SS, 10249.C042.10SS, 10249.C042.11SD, 10249.C042.11SS, 10249.C042.12SS, 10249.C042.13SS, 10249.C042.14SD, 10249.C042.14SS, 10249.C042.15SD, 10249.C042.15SS, 10249.C042.16SS, 10249.C042.17SS, 10249.C043.02SS, 10249.C043.03SS, 10249.C043.04SD, 10249.C043.04SS, 10249.C043.05SD, 10249.C043.05SS, 10249.C043.06SS, 10249.C043.07SS, 10249.C043.08SS, 10249.C043.09SS, 10249.C043.10SD, 10249.C043.10SS, 10249.C043.11SD, 10249.C043.11SS, 10249.C043.12SD, 10249.C043.12SS, 10249.C043.14SS, 10249.C043.15SD, 10249.C043.15SS, 10249.C043.16SS, 10249.C043.17SS, 10249.C043.18SS, 10249.C043.20SS, 10249.C044.02SS, 10249.C044.03SS, 10249.C044.04SS, 10249.C044.05SS, 10249.C044.06SS, 10249.C044.07SS, 10249.C044.08SS, 10249.C044.09SS, 10249.C044.10SS, 10249.C044.11SS, 10249.C044.12SD, 10249.C044.12SS, 10249.C044.13SD, 10249.C044.13SS, 10249.C044.15SD, 10249.C044.15SS, 10249.C044.16SS, 10249.C044.17SS, 10249.C045.02SS, 10249.C045.03SS, 10249.C045.04SS, 10249.C045.05SD, 10249.C045.05SS, 10249.C045.06SS, 10249.C045.08SD, 10249.C045.08SS, 10249.C045.09SD, 10249.C045.09SS, 10249.C045.10SD, 10249.C045.10SS, 10249.C045.11SS, 10249.C045.12SS, 10249.C045.13SS, 10249.C046.02SS, 10249.C046.03SS, 10249.C046.04SS, 10249.C046.05SS, 10249.C046.06SD, 10249.C046.06SS, 10249.C046.07SD, 10249.C046.07SS, 10249.C046.08SS, 10249.C046.09SD, 10249.C046.09SS, 10249.C046.10SD, 10249.C046.10SS, 10249.C046.11SD, 10249.C046.11SS, 10249.C046.12SS, 10249.C046.13SS, 10249.C046.14SS, 10249.C047.02SD, 10249.C047.02SS, 10249.C047.05SS, 10249.C047.06SD, 10249.C047.06SS, 10249.C047.07SD, 10249.C047.07SS, 10249.C047.08SD, 10249.C047.08SS, 10249.C047.09SS, 10249.C047.10SS, 10249.C047.11SS, 10249.C047.13SS, 10249.C049.03SD, 10249.C049.03SS, 10249.C049.04SS, 10249.C049.07SD, 10249.C049.07SS, 10249.C049.08SD, 10249.C049.08SS, 10249.C049.09SD, 10249.C049.09SS, 10249.C049.10SS, 10249.C049.11SS, 10249.C049.12SS, 10249.C049.13SS, 10249.C049.14SS, 10249.C052.03SD, 10249.C052.03SS, 10249.C052.04SD, 10249.C052.04SS, 10249.C052.05SD, 10249.C052.06SS, 10249.C052.07SS, 10249.C052.08SS, 10249.C052.09SS, 10249.C053.02SD, 10249.C053.02SS, 10249.C053.03SD, 10249.C053.03SS, 10249.C053.04SD, 10249.C053.04SS, 10249.C053.05SD, 10249.C053.05SS, 10249.C053.06SS, 10249.C053.07SS, 10249.C053.08SS, 10249.C053.09SS, 10249.C055.02SD, 10249.C055.02SS, 10249.C055.03SD, 10249.C055.03SS, 10249.C055.04SD, 10249.C055.04SS, 10249.C055.05SD, 10249.C055.05SS, 10249.C055.06SS, 10249.C055.07SS, 10249.C055.08SS, 10249.C055.09SS, 10249.C056.03SD, 10249.C056.03SS, 10249.C056.04SD, 10249.C056.04SS, 10249.C056.05SD, 10249.C056.05SS, 10249.C056.06SS, 10249.C056.07SS, 10249.C056.08SS, 10249.C056.09SS, 10249.C056.10SS, 10249.C057.02SS, 10249.C057.03SD, 10249.C057.03SS, 10249.C057.04SD, 10249.C057.04SS, 10249.C057.05SD, 10249.C057.05SS, 10249.C057.06SS, 10249.C057.08SS, 10249.C057.09SS, 10249.C057.10SS, 10249.C057.11SS
#> Updated feature table to match the subsetted data.
#> Updated feature annotation to match the subsetted data.
#> Data subsetting complete. Returning updated data object.
#> Rule 1 passed: data.obj is a list.
#> Rule 2 passed: meta.dat is a data.frame.
#> Rule 3 passed: The row names of feature.tab match the row names of feature.ann.
#> Rule 4 passed: The order of rows in meta.dat has been adjusted to match feature.tab.
#> Rule 5 passed: feature.tab is a matrix.
#> Rule 6 passed: feature.ann is a matrix.
#> Please note: The data components should follow base R data.frame and matrix structures, not phyloseq's formal class.
#> Validation passed.
#> Note: Passing validation does not guarantee the absence of all data issues. Further data exploration may be needed.
#> Data has been subsetted based on the provided condition.
#> Updated metadata to match the subsetted data.
#> The following samples were excluded: 10249.C001.02SS, 10249.C001.03SS, 10249.C001.04SS, 10249.C001.05SS, 10249.C001.06SS, 10249.C001.07SS, 10249.C001.08SS, 10249.C001.09SS, 10249.C001.10SS, 10249.C001.11SS, 10249.C001.12SS, 10249.C001.13SS, 10249.C001.14SS, 10249.C001.15SS, 10249.C001.16SS, 10249.C001.17SS, 10249.C001.18SS, 10249.C001.19SS, 10249.C001.20SS, 10249.C001.25SS, 10249.C001.26SS, 10249.C001.27SS, 10249.C001.29SS, 10249.C001.30SS, 10249.C001.31SS, 10249.C001.32SS, 10249.C001.34SD, 10249.C001.34SS, 10249.C001.35SS, 10249.C001.36SD, 10249.C001.36SS, 10249.C002.02SS, 10249.C002.03SS, 10249.C002.04SS, 10249.C002.05SS, 10249.C002.06SS, 10249.C002.07SS, 10249.C002.08SS, 10249.C002.09SS, 10249.C002.10SS, 10249.C002.11SS, 10249.C002.12SS, 10249.C002.13SS, 10249.C002.15SS, 10249.C002.16SS, 10249.C002.18SS, 10249.C002.19SD, 10249.C002.19SS, 10249.C002.20SS, 10249.C002.21SD, 10249.C002.21SS, 10249.C004.02SS, 10249.C004.03SS, 10249.C004.04SS, 10249.C004.05SS, 10249.C004.06SS, 10249.C004.07SS, 10249.C004.08SS, 10249.C004.09SS, 10249.C004.10SS, 10249.C004.11SS, 10249.C004.12SS, 10249.C004.13SS, 10249.C004.14SS, 10249.C004.15SS, 10249.C005.02SS, 10249.C005.03SS, 10249.C005.04SS, 10249.C005.05SS, 10249.C005.07SS, 10249.C005.08SS, 10249.C005.09SS, 10249.C005.10SS, 10249.C005.11SS, 10249.C005.12SS, 10249.C005.13SS, 10249.C005.14SS, 10249.C005.15SS, 10249.C005.16SS, 10249.C005.17SS, 10249.C005.18SS, 10249.C005.19SD, 10249.C005.19SS, 10249.C005.20SS, 10249.C005.21SD, 10249.C005.21SS, 10249.C005.22SS, 10249.C007.02SS, 10249.C007.03SS, 10249.C007.04SS, 10249.C007.05SS, 10249.C007.06SS, 10249.C007.07SS, 10249.C007.08SS, 10249.C007.09SS, 10249.C007.10SS, 10249.C007.11SS, 10249.C007.12SS, 10249.C007.13SS, 10249.C007.14SS, 10249.C007.15SS, 10249.C007.16SS, 10249.C007.17SS, 10249.C007.18SS, 10249.C007.19SS, 10249.C007.20SS, 10249.C007.21SS, 10249.C007.22SD, 10249.C007.22SS, 10249.C007.23SD, 10249.C007.23SS, 10249.C007.24SD, 10249.C007.24SS, 10249.C007.26SS, 10249.C008.02SS, 10249.C008.03SS, 10249.C008.04SS, 10249.C008.05SS, 10249.C008.06SS, 10249.C008.07SS, 10249.C008.08SS, 10249.C008.09SS, 10249.C008.10SS, 10249.C008.11SS, 10249.C008.12SS, 10249.C008.13SS, 10249.C008.14SS, 10249.C008.15SS, 10249.C008.16SD, 10249.C008.16SS, 10249.C008.18SS, 10249.C009.02SS, 10249.C009.03SS, 10249.C009.04SS, 10249.C009.05SS, 10249.C009.06SS, 10249.C009.07SS, 10249.C009.08SS, 10249.C009.09SS, 10249.C009.10SS, 10249.C009.11SS, 10249.C009.12SS, 10249.C009.13SS, 10249.C009.14SS, 10249.C009.16SS, 10249.C009.17SS, 10249.C009.18SD, 10249.C009.18SS, 10249.C009.19SS, 10249.C009.20SD, 10249.C009.20SS, 10249.C009.21SS, 10249.C010.02SS, 10249.C010.03SS, 10249.C010.04SS, 10249.C010.05SS, 10249.C010.06SS, 10249.C010.07SS, 10249.C010.08SS, 10249.C010.09SS, 10249.C010.10SS, 10249.C010.11SS, 10249.C010.12SS, 10249.C010.13SS, 10249.C010.14SS, 10249.C010.15SS, 10249.C010.16SS, 10249.C010.18SD, 10249.C010.18SS, 10249.C010.19SS, 10249.C010.20SD, 10249.C010.20SS, 10249.C010.21SS, 10249.C011.02SS, 10249.C011.03SS, 10249.C011.04SS, 10249.C011.05SS, 10249.C011.06SS, 10249.C011.07SS, 10249.C011.08SS, 10249.C011.09SS, 10249.C011.10SS, 10249.C011.11SS, 10249.C011.12SS, 10249.C011.13SD, 10249.C011.14SS, 10249.C011.16SS, 10249.C011.17SD, 10249.C011.17SS, 10249.C011.18SS, 10249.C011.19SD, 10249.C011.19SS, 10249.C011.20SS, 10249.C011.21SS, 10249.C012.02SS, 10249.C012.03SS, 10249.C012.04SS, 10249.C012.05SS, 10249.C012.06SS, 10249.C012.07SS, 10249.C012.08SS, 10249.C012.09SS, 10249.C012.10SS, 10249.C012.11SS, 10249.C012.12SS, 10249.C012.13SS, 10249.C012.14SS, 10249.C012.15SS, 10249.C012.16SS, 10249.C012.17SS, 10249.C012.18SS, 10249.C012.19SD, 10249.C012.19SS, 10249.C012.20SS, 10249.C012.21SD, 10249.C012.21SS, 10249.C012.22SD, 10249.C012.22SS, 10249.C014.02SS, 10249.C014.03SS, 10249.C014.04SS, 10249.C014.05SS, 10249.C014.06SS, 10249.C014.07SS, 10249.C014.08SS, 10249.C014.09SS, 10249.C014.10SS, 10249.C014.12SS, 10249.C014.13SS, 10249.C014.15SS, 10249.C014.16SS, 10249.C014.17SS, 10249.C014.18SS, 10249.C014.19SD, 10249.C014.19SS, 10249.C014.20SD, 10249.C014.20SS, 10249.C014.21SS, 10249.C014.22SS, 10249.C016.03SS, 10249.C016.04SS, 10249.C016.05SS, 10249.C016.06SS, 10249.C016.07SS, 10249.C016.08SS, 10249.C016.09SS, 10249.C016.10SS, 10249.C016.11SS, 10249.C016.12SS, 10249.C016.13SS, 10249.C016.14SS, 10249.C016.15SS, 10249.C016.17SS, 10249.C016.18SS, 10249.C016.19SS, 10249.C016.20SS, 10249.C016.21SD, 10249.C016.21SS, 10249.C016.22SD, 10249.C016.22SS, 10249.C016.23SS, 10249.C016.24SS, 10249.C017.04SS, 10249.C017.05SS, 10249.C017.06SS, 10249.C017.07SS, 10249.C017.08SS, 10249.C017.09SS, 10249.C017.10SS, 10249.C017.11SS, 10249.C017.12SS, 10249.C018.02SS, 10249.C018.03SS, 10249.C018.04SS, 10249.C018.05SS, 10249.C018.06SS, 10249.C018.07SS, 10249.C018.08SS, 10249.C018.09SS, 10249.C018.10SS, 10249.C018.11SD, 10249.C018.11SS, 10249.C018.12SD, 10249.C018.12SS, 10249.C018.13SS, 10249.C018.14SS, 10249.C018.15SS, 10249.C018.16SS, 10249.C018.17SS, 10249.C018.18SS, 10249.C018.19SS, 10249.C020.06SS, 10249.C020.07SS, 10249.C020.08SS, 10249.C020.09SS, 10249.C020.10SS, 10249.C020.11SS, 10249.C020.12SS, 10249.C020.13SS, 10249.C020.14SS, 10249.C020.15SS, 10249.C020.16SS, 10249.C020.17SS, 10249.C020.18SS, 10249.C020.19SS, 10249.C020.20SS, 10249.C020.21SS, 10249.C020.22SD, 10249.C020.22SS, 10249.C020.23SD, 10249.C020.23SS, 10249.C020.24SD, 10249.C020.24SS, 10249.C020.25SD, 10249.C020.25SS, 10249.C020.26SD, 10249.C020.26SS, 10249.C020.28SS, 10249.C020.29SS, 10249.C021.03SS, 10249.C021.04SS, 10249.C021.05SS, 10249.C021.06SS, 10249.C021.07SS, 10249.C021.08SS, 10249.C021.09SS, 10249.C021.10SS, 10249.C021.12SS, 10249.C021.13SS, 10249.C022.02SS, 10249.C022.03SS, 10249.C022.04SS, 10249.C022.05SS, 10249.C022.06SS, 10249.C022.07SS, 10249.C022.08SS, 10249.C022.09SS, 10249.C022.10SS, 10249.C022.11SS, 10249.C022.12SS, 10249.C022.13SS, 10249.C022.15SS, 10249.C022.16SS, 10249.C022.18SD, 10249.C022.18SS, 10249.C022.19SS, 10249.C022.20SS, 10249.C022.21SS, 10249.C024.02SS, 10249.C024.03SS, 10249.C024.04SS, 10249.C024.05SS, 10249.C024.06SS, 10249.C024.07SS, 10249.C024.08SS, 10249.C024.09SS, 10249.C024.10SS, 10249.C024.12SS, 10249.C024.13SS, 10249.C024.14SS, 10249.C024.15SS, 10249.C024.16SS, 10249.C024.17SS, 10249.C024.18SS, 10249.C024.19SD, 10249.C024.19SS, 10249.C024.20SD, 10249.C024.20SS, 10249.C024.21SS, 10249.C024.22SS, 10249.C025.02SS, 10249.C025.03SS, 10249.C025.04SS, 10249.C025.05SS, 10249.C025.06SS, 10249.C025.07SS, 10249.C025.08SS, 10249.C025.09SS, 10249.C025.10SS, 10249.C025.11SS, 10249.C025.12SS, 10249.C025.13SD, 10249.C025.13SS, 10249.C025.14SD, 10249.C025.14SS, 10249.C025.15SS, 10249.C025.16SS, 10249.C025.17SS, 10249.C025.18SS, 10249.C025.19SD, 10249.C025.19SS, 10249.C025.20SS, 10249.C025.21SS, 10249.C027.02SS, 10249.C027.03SS, 10249.C027.04SS, 10249.C027.05SS, 10249.C027.06SS, 10249.C027.07SS, 10249.C027.08SS, 10249.C027.09SS, 10249.C027.10SS, 10249.C027.11SD, 10249.C027.12SD, 10249.C027.12SS, 10249.C027.13SS, 10249.C027.14SS, 10249.C027.15SS, 10249.C027.16SS, 10249.C027.17SD, 10249.C027.17SS, 10249.C027.18SS, 10249.C027.19SD, 10249.C027.19SS, 10249.C027.20SD, 10249.C027.20SS, 10249.C027.21SS, 10249.C027.22SS, 10249.C030.02SS, 10249.C030.03SS, 10249.C030.04SS, 10249.C030.05SS, 10249.C030.06SS, 10249.C030.07SS, 10249.C030.08SS, 10249.C030.09SS, 10249.C030.10SS, 10249.C030.11SD, 10249.C030.11SS, 10249.C030.12SS, 10249.C030.13SS, 10249.C030.14SS, 10249.C030.16SS, 10249.C030.17SD, 10249.C030.17SS, 10249.C030.18SS, 10249.C030.19SD, 10249.C030.19SS, 10249.C030.20SS, 10249.C031.02SS, 10249.C031.03SS, 10249.C031.04SS, 10249.C031.05SS, 10249.C031.06SS, 10249.C031.07SS, 10249.C031.08SS, 10249.C031.09SS, 10249.C031.10SS, 10249.C031.11SD, 10249.C031.11SS, 10249.C031.12SS, 10249.C031.13SS, 10249.C031.14SS, 10249.C031.16SS, 10249.C031.17SD, 10249.C031.17SS, 10249.C031.18SS, 10249.C031.19SD, 10249.C031.19SS, 10249.C031.20SS, 10249.C031.21SS, 10249.C032.02SS, 10249.C032.03SS, 10249.C032.04SS, 10249.C032.05SS, 10249.C032.06SS, 10249.C032.07SS, 10249.C032.09SS, 10249.C032.10SS, 10249.C032.11SD, 10249.C032.11SS, 10249.C032.12SD, 10249.C032.13SS, 10249.C032.14SS, 10249.C032.15SS, 10249.C032.16SS, 10249.C032.17SS, 10249.C032.19SD, 10249.C032.19SS, 10249.C032.20SD, 10249.C032.20SS, 10249.C032.21SS, 10249.C032.22SS, 10249.C033.02SS, 10249.C033.03SS, 10249.C033.04SS, 10249.C033.05SS, 10249.C033.06SS, 10249.C033.07SS, 10249.C033.08SS, 10249.C033.09SD, 10249.C033.09SS, 10249.C033.10SD, 10249.C033.10SS, 10249.C033.11SD, 10249.C033.11SS, 10249.C033.12SS, 10249.C033.13SS, 10249.C033.14SS, 10249.C033.15SS, 10249.C033.16SS, 10249.C033.17SD, 10249.C033.17SS, 10249.C033.18SD, 10249.C033.18SS, 10249.C033.19SS, 10249.C034.02SS, 10249.C034.03SS, 10249.C034.04SS, 10249.C034.05SS, 10249.C034.06SS, 10249.C034.07SS, 10249.C034.08SS, 10249.C034.09SS, 10249.C034.10SS, 10249.C034.11SS, 10249.C034.12SS, 10249.C034.13SS, 10249.C034.14SS, 10249.C034.15SD, 10249.C034.15SS, 10249.C034.16SS, 10249.C034.17SD, 10249.C034.17SS, 10249.C035.02SS, 10249.C035.03SS, 10249.C035.04SS, 10249.C035.05SS, 10249.C035.06SD, 10249.C035.06SS, 10249.C035.07SD, 10249.C035.07SS, 10249.C035.08SS, 10249.C035.09SS, 10249.C035.10SS, 10249.C035.11SS, 10249.C035.12SD, 10249.C035.12SS, 10249.C035.13SD, 10249.C035.13SS, 10249.C035.14SD, 10249.C035.14SS, 10249.C035.15SD, 10249.C035.15SS, 10249.C035.16SS, 10249.C035.17SS, 10249.C036.02SS, 10249.C036.03SS, 10249.C036.04SS, 10249.C036.05SD, 10249.C036.05SS, 10249.C036.07SS, 10249.C036.08SS, 10249.C036.09SS, 10249.C036.10SS, 10249.C036.11SS, 10249.C036.12SS, 10249.C036.13SS, 10249.C036.14SD, 10249.C036.14SS, 10249.C036.15SS, 10249.C036.16SS, 10249.C037.02SS, 10249.C037.04SS, 10249.C037.05SS, 10249.C037.06SS, 10249.C037.07SS, 10249.C037.08SS, 10249.C037.09SS, 10249.C037.10SS, 10249.C037.11SS, 10249.C037.12SD, 10249.C037.12SS, 10249.C037.13SD, 10249.C037.13SS, 10249.C037.14SS, 10249.C037.15SS, 10249.C037.16SS, 10249.C037.17SS, 10249.C037.18SS, 10249.C038.02SS, 10249.C038.04SS, 10249.C038.05SD, 10249.C038.05SS, 10249.C038.06SD, 10249.C038.06SS, 10249.C038.07SD, 10249.C038.07SS, 10249.C038.08SS, 10249.C038.09SS, 10249.C038.10SS, 10249.C038.11SS, 10249.C038.12SD, 10249.C038.12SS, 10249.C038.13SD, 10249.C038.13SS, 10249.C038.14SS, 10249.C038.15SD, 10249.C038.15SS, 10249.C038.16SD, 10249.C038.16SS, 10249.C038.18SS, 10249.C041.02SS, 10249.C041.03SS, 10249.C041.04SS, 10249.C041.05SD, 10249.C041.05SS, 10249.C041.06SD, 10249.C041.06SS, 10249.C041.08SS, 10249.C041.09SS, 10249.C041.10SS, 10249.C041.11SS, 10249.C041.12SS, 10249.C041.13SD, 10249.C041.13SS, 10249.C041.14SD, 10249.C041.14SS, 10249.C041.16SD, 10249.C041.16SS, 10249.C041.17SD, 10249.C041.17SS, 10249.C041.18SS, 10249.C041.19SS, 10249.C042.02SS, 10249.C042.03SS, 10249.C042.04SS, 10249.C042.05SS, 10249.C042.06SD, 10249.C042.06SS, 10249.C042.07SS, 10249.C042.08SS, 10249.C042.09SS, 10249.C042.10SS, 10249.C042.11SD, 10249.C042.11SS, 10249.C042.12SS, 10249.C042.13SS, 10249.C042.14SD, 10249.C042.14SS, 10249.C042.15SD, 10249.C042.15SS, 10249.C042.16SS, 10249.C042.17SS, 10249.C043.02SS, 10249.C043.03SS, 10249.C043.04SD, 10249.C043.04SS, 10249.C043.05SD, 10249.C043.05SS, 10249.C043.06SS, 10249.C043.07SS, 10249.C043.08SS, 10249.C043.09SS, 10249.C043.10SD, 10249.C043.10SS, 10249.C043.11SD, 10249.C043.11SS, 10249.C043.12SD, 10249.C043.12SS, 10249.C043.14SS, 10249.C043.15SD, 10249.C043.15SS, 10249.C043.16SS, 10249.C043.17SS, 10249.C043.18SS, 10249.C043.20SS, 10249.C044.02SS, 10249.C044.03SS, 10249.C044.04SS, 10249.C044.05SS, 10249.C044.06SS, 10249.C044.07SS, 10249.C044.08SS, 10249.C044.09SS, 10249.C044.10SS, 10249.C044.11SS, 10249.C044.12SD, 10249.C044.12SS, 10249.C044.13SD, 10249.C044.13SS, 10249.C044.15SD, 10249.C044.15SS, 10249.C044.16SS, 10249.C044.17SS, 10249.C045.02SS, 10249.C045.03SS, 10249.C045.04SS, 10249.C045.05SD, 10249.C045.05SS, 10249.C045.06SS, 10249.C045.08SD, 10249.C045.08SS, 10249.C045.09SD, 10249.C045.09SS, 10249.C045.10SD, 10249.C045.10SS, 10249.C045.11SS, 10249.C045.12SS, 10249.C045.13SS, 10249.C046.02SS, 10249.C046.03SS, 10249.C046.04SS, 10249.C046.05SS, 10249.C046.06SD, 10249.C046.06SS, 10249.C046.07SD, 10249.C046.07SS, 10249.C046.08SS, 10249.C046.09SD, 10249.C046.09SS, 10249.C046.10SD, 10249.C046.10SS, 10249.C046.11SD, 10249.C046.11SS, 10249.C046.12SS, 10249.C046.13SS, 10249.C046.14SS, 10249.C047.02SD, 10249.C047.02SS, 10249.C047.05SS, 10249.C047.06SD, 10249.C047.06SS, 10249.C047.07SD, 10249.C047.07SS, 10249.C047.08SD, 10249.C047.08SS, 10249.C047.09SS, 10249.C047.10SS, 10249.C047.11SS, 10249.C047.13SS, 10249.C049.03SD, 10249.C049.03SS, 10249.C049.04SS, 10249.C049.07SD, 10249.C049.07SS, 10249.C049.08SD, 10249.C049.08SS, 10249.C049.09SD, 10249.C049.09SS, 10249.C049.10SS, 10249.C049.11SS, 10249.C049.12SS, 10249.C049.13SS, 10249.C049.14SS, 10249.C052.03SD, 10249.C052.03SS, 10249.C052.04SD, 10249.C052.04SS, 10249.C052.05SD, 10249.C052.06SS, 10249.C052.07SS, 10249.C052.08SS, 10249.C052.09SS, 10249.C053.02SD, 10249.C053.02SS, 10249.C053.03SD, 10249.C053.03SS, 10249.C053.04SD, 10249.C053.04SS, 10249.C053.05SD, 10249.C053.05SS, 10249.C053.06SS, 10249.C053.07SS, 10249.C053.08SS, 10249.C053.09SS, 10249.C055.02SD, 10249.C055.02SS, 10249.C055.03SD, 10249.C055.03SS, 10249.C055.04SD, 10249.C055.04SS, 10249.C055.05SD, 10249.C055.05SS, 10249.C055.06SS, 10249.C055.07SS, 10249.C055.08SS, 10249.C055.09SS, 10249.C056.03SD, 10249.C056.03SS, 10249.C056.04SD, 10249.C056.04SS, 10249.C056.05SD, 10249.C056.05SS, 10249.C056.06SS, 10249.C056.07SS, 10249.C056.08SS, 10249.C056.09SS, 10249.C056.10SS, 10249.C057.02SS, 10249.C057.03SD, 10249.C057.03SS, 10249.C057.04SD, 10249.C057.04SS, 10249.C057.05SD, 10249.C057.05SS, 10249.C057.06SS, 10249.C057.08SS, 10249.C057.09SS, 10249.C057.10SS, 10249.C057.11SS
#> Updated feature table to match the subsetted data.
#> Updated feature annotation to match the subsetted data.
#> Data subsetting complete. Returning updated data object.
#> Rule 1 passed: data.obj is a list.
#> Rule 2 passed: meta.dat is a data.frame.
#> Rule 3 passed: The row names of feature.tab match the row names of feature.ann.
#> Rule 4 passed: The order of rows in meta.dat has been adjusted to match feature.tab.
#> Rule 5 passed: feature.tab is a matrix.
#> Rule 6 passed: feature.ann is a matrix.
#> Please note: The data components should follow base R data.frame and matrix structures, not phyloseq's formal class.
#> Validation passed.
#> Note: Passing validation does not guarantee the absence of all data issues. Further data exploration may be needed.
#> Data has been subsetted based on the provided condition.
#> Updated metadata to match the subsetted data.
#> The following samples were excluded: 10249.C001.02SS, 10249.C001.03SS, 10249.C001.04SS, 10249.C001.05SS, 10249.C001.06SS, 10249.C001.07SS, 10249.C001.08SS, 10249.C001.09SS, 10249.C001.10SS, 10249.C001.11SS, 10249.C001.12SS, 10249.C001.13SS, 10249.C001.14SS, 10249.C001.15SS, 10249.C001.16SS, 10249.C001.17SS, 10249.C001.18SS, 10249.C001.19SS, 10249.C001.20SS, 10249.C001.25SS, 10249.C001.26SS, 10249.C001.27SS, 10249.C001.29SS, 10249.C001.30SS, 10249.C001.31SS, 10249.C001.32SS, 10249.C001.34SD, 10249.C001.34SS, 10249.C001.35SS, 10249.C001.36SD, 10249.C001.36SS, 10249.C002.02SS, 10249.C002.03SS, 10249.C002.04SS, 10249.C002.05SS, 10249.C002.06SS, 10249.C002.07SS, 10249.C002.08SS, 10249.C002.09SS, 10249.C002.10SS, 10249.C002.11SS, 10249.C002.12SS, 10249.C002.13SS, 10249.C002.15SS, 10249.C002.16SS, 10249.C002.18SS, 10249.C002.19SD, 10249.C002.19SS, 10249.C002.20SS, 10249.C002.21SD, 10249.C002.21SS, 10249.C004.02SS, 10249.C004.03SS, 10249.C004.04SS, 10249.C004.05SS, 10249.C004.06SS, 10249.C004.07SS, 10249.C004.08SS, 10249.C004.09SS, 10249.C004.10SS, 10249.C004.11SS, 10249.C004.12SS, 10249.C004.13SS, 10249.C004.14SS, 10249.C004.15SS, 10249.C005.02SS, 10249.C005.03SS, 10249.C005.04SS, 10249.C005.05SS, 10249.C005.07SS, 10249.C005.08SS, 10249.C005.09SS, 10249.C005.10SS, 10249.C005.11SS, 10249.C005.12SS, 10249.C005.13SS, 10249.C005.14SS, 10249.C005.15SS, 10249.C005.16SS, 10249.C005.17SS, 10249.C005.18SS, 10249.C005.19SD, 10249.C005.19SS, 10249.C005.20SS, 10249.C005.21SD, 10249.C005.21SS, 10249.C005.22SS, 10249.C007.02SS, 10249.C007.03SS, 10249.C007.04SS, 10249.C007.05SS, 10249.C007.06SS, 10249.C007.07SS, 10249.C007.08SS, 10249.C007.09SS, 10249.C007.10SS, 10249.C007.11SS, 10249.C007.12SS, 10249.C007.13SS, 10249.C007.14SS, 10249.C007.15SS, 10249.C007.16SS, 10249.C007.17SS, 10249.C007.18SS, 10249.C007.19SS, 10249.C007.20SS, 10249.C007.21SS, 10249.C007.22SD, 10249.C007.22SS, 10249.C007.23SD, 10249.C007.23SS, 10249.C007.24SD, 10249.C007.24SS, 10249.C007.26SS, 10249.C008.02SS, 10249.C008.03SS, 10249.C008.04SS, 10249.C008.05SS, 10249.C008.06SS, 10249.C008.07SS, 10249.C008.08SS, 10249.C008.09SS, 10249.C008.10SS, 10249.C008.11SS, 10249.C008.12SS, 10249.C008.13SS, 10249.C008.14SS, 10249.C008.15SS, 10249.C008.16SD, 10249.C008.16SS, 10249.C008.18SS, 10249.C009.02SS, 10249.C009.03SS, 10249.C009.04SS, 10249.C009.05SS, 10249.C009.06SS, 10249.C009.07SS, 10249.C009.08SS, 10249.C009.09SS, 10249.C009.10SS, 10249.C009.11SS, 10249.C009.12SS, 10249.C009.13SS, 10249.C009.14SS, 10249.C009.16SS, 10249.C009.17SS, 10249.C009.18SD, 10249.C009.18SS, 10249.C009.19SS, 10249.C009.20SD, 10249.C009.20SS, 10249.C009.21SS, 10249.C010.02SS, 10249.C010.03SS, 10249.C010.04SS, 10249.C010.05SS, 10249.C010.06SS, 10249.C010.07SS, 10249.C010.08SS, 10249.C010.09SS, 10249.C010.10SS, 10249.C010.11SS, 10249.C010.12SS, 10249.C010.13SS, 10249.C010.14SS, 10249.C010.15SS, 10249.C010.16SS, 10249.C010.18SD, 10249.C010.18SS, 10249.C010.19SS, 10249.C010.20SD, 10249.C010.20SS, 10249.C010.21SS, 10249.C011.02SS, 10249.C011.03SS, 10249.C011.04SS, 10249.C011.05SS, 10249.C011.06SS, 10249.C011.07SS, 10249.C011.08SS, 10249.C011.09SS, 10249.C011.10SS, 10249.C011.11SS, 10249.C011.12SS, 10249.C011.13SD, 10249.C011.14SS, 10249.C011.16SS, 10249.C011.17SD, 10249.C011.17SS, 10249.C011.18SS, 10249.C011.19SD, 10249.C011.19SS, 10249.C011.20SS, 10249.C011.21SS, 10249.C012.02SS, 10249.C012.03SS, 10249.C012.04SS, 10249.C012.05SS, 10249.C012.06SS, 10249.C012.07SS, 10249.C012.08SS, 10249.C012.09SS, 10249.C012.10SS, 10249.C012.11SS, 10249.C012.12SS, 10249.C012.13SS, 10249.C012.14SS, 10249.C012.15SS, 10249.C012.16SS, 10249.C012.17SS, 10249.C012.18SS, 10249.C012.19SD, 10249.C012.19SS, 10249.C012.20SS, 10249.C012.21SD, 10249.C012.21SS, 10249.C012.22SD, 10249.C012.22SS, 10249.C014.02SS, 10249.C014.03SS, 10249.C014.04SS, 10249.C014.05SS, 10249.C014.06SS, 10249.C014.07SS, 10249.C014.08SS, 10249.C014.09SS, 10249.C014.10SS, 10249.C014.12SS, 10249.C014.13SS, 10249.C014.15SS, 10249.C014.16SS, 10249.C014.17SS, 10249.C014.18SS, 10249.C014.19SD, 10249.C014.19SS, 10249.C014.20SD, 10249.C014.20SS, 10249.C014.21SS, 10249.C014.22SS, 10249.C016.03SS, 10249.C016.04SS, 10249.C016.05SS, 10249.C016.06SS, 10249.C016.07SS, 10249.C016.08SS, 10249.C016.09SS, 10249.C016.10SS, 10249.C016.11SS, 10249.C016.12SS, 10249.C016.13SS, 10249.C016.14SS, 10249.C016.15SS, 10249.C016.17SS, 10249.C016.18SS, 10249.C016.19SS, 10249.C016.20SS, 10249.C016.21SD, 10249.C016.21SS, 10249.C016.22SD, 10249.C016.22SS, 10249.C016.23SS, 10249.C016.24SS, 10249.C017.04SS, 10249.C017.05SS, 10249.C017.06SS, 10249.C017.07SS, 10249.C017.08SS, 10249.C017.09SS, 10249.C017.10SS, 10249.C017.11SS, 10249.C017.12SS, 10249.C018.02SS, 10249.C018.03SS, 10249.C018.04SS, 10249.C018.05SS, 10249.C018.06SS, 10249.C018.07SS, 10249.C018.08SS, 10249.C018.09SS, 10249.C018.10SS, 10249.C018.11SD, 10249.C018.11SS, 10249.C018.12SD, 10249.C018.12SS, 10249.C018.13SS, 10249.C018.14SS, 10249.C018.15SS, 10249.C018.16SS, 10249.C018.17SS, 10249.C018.18SS, 10249.C018.19SS, 10249.C020.06SS, 10249.C020.07SS, 10249.C020.08SS, 10249.C020.09SS, 10249.C020.10SS, 10249.C020.11SS, 10249.C020.12SS, 10249.C020.13SS, 10249.C020.14SS, 10249.C020.15SS, 10249.C020.16SS, 10249.C020.17SS, 10249.C020.18SS, 10249.C020.19SS, 10249.C020.20SS, 10249.C020.21SS, 10249.C020.22SD, 10249.C020.22SS, 10249.C020.23SD, 10249.C020.23SS, 10249.C020.24SD, 10249.C020.24SS, 10249.C020.25SD, 10249.C020.25SS, 10249.C020.26SD, 10249.C020.26SS, 10249.C020.28SS, 10249.C020.29SS, 10249.C021.03SS, 10249.C021.04SS, 10249.C021.05SS, 10249.C021.06SS, 10249.C021.07SS, 10249.C021.08SS, 10249.C021.09SS, 10249.C021.10SS, 10249.C021.12SS, 10249.C021.13SS, 10249.C022.02SS, 10249.C022.03SS, 10249.C022.04SS, 10249.C022.05SS, 10249.C022.06SS, 10249.C022.07SS, 10249.C022.08SS, 10249.C022.09SS, 10249.C022.10SS, 10249.C022.11SS, 10249.C022.12SS, 10249.C022.13SS, 10249.C022.15SS, 10249.C022.16SS, 10249.C022.18SD, 10249.C022.18SS, 10249.C022.19SS, 10249.C022.20SS, 10249.C022.21SS, 10249.C024.02SS, 10249.C024.03SS, 10249.C024.04SS, 10249.C024.05SS, 10249.C024.06SS, 10249.C024.07SS, 10249.C024.08SS, 10249.C024.09SS, 10249.C024.10SS, 10249.C024.12SS, 10249.C024.13SS, 10249.C024.14SS, 10249.C024.15SS, 10249.C024.16SS, 10249.C024.17SS, 10249.C024.18SS, 10249.C024.19SD, 10249.C024.19SS, 10249.C024.20SD, 10249.C024.20SS, 10249.C024.21SS, 10249.C024.22SS, 10249.C025.02SS, 10249.C025.03SS, 10249.C025.04SS, 10249.C025.05SS, 10249.C025.06SS, 10249.C025.07SS, 10249.C025.08SS, 10249.C025.09SS, 10249.C025.10SS, 10249.C025.11SS, 10249.C025.12SS, 10249.C025.13SD, 10249.C025.13SS, 10249.C025.14SD, 10249.C025.14SS, 10249.C025.15SS, 10249.C025.16SS, 10249.C025.17SS, 10249.C025.18SS, 10249.C025.19SD, 10249.C025.19SS, 10249.C025.20SS, 10249.C025.21SS, 10249.C027.02SS, 10249.C027.03SS, 10249.C027.04SS, 10249.C027.05SS, 10249.C027.06SS, 10249.C027.07SS, 10249.C027.08SS, 10249.C027.09SS, 10249.C027.10SS, 10249.C027.11SD, 10249.C027.12SD, 10249.C027.12SS, 10249.C027.13SS, 10249.C027.14SS, 10249.C027.15SS, 10249.C027.16SS, 10249.C027.17SD, 10249.C027.17SS, 10249.C027.18SS, 10249.C027.19SD, 10249.C027.19SS, 10249.C027.20SD, 10249.C027.20SS, 10249.C027.21SS, 10249.C027.22SS, 10249.C030.02SS, 10249.C030.03SS, 10249.C030.04SS, 10249.C030.05SS, 10249.C030.06SS, 10249.C030.07SS, 10249.C030.08SS, 10249.C030.09SS, 10249.C030.10SS, 10249.C030.11SD, 10249.C030.11SS, 10249.C030.12SS, 10249.C030.13SS, 10249.C030.14SS, 10249.C030.16SS, 10249.C030.17SD, 10249.C030.17SS, 10249.C030.18SS, 10249.C030.19SD, 10249.C030.19SS, 10249.C030.20SS, 10249.C031.02SS, 10249.C031.03SS, 10249.C031.04SS, 10249.C031.05SS, 10249.C031.06SS, 10249.C031.07SS, 10249.C031.08SS, 10249.C031.09SS, 10249.C031.10SS, 10249.C031.11SD, 10249.C031.11SS, 10249.C031.12SS, 10249.C031.13SS, 10249.C031.14SS, 10249.C031.16SS, 10249.C031.17SD, 10249.C031.17SS, 10249.C031.18SS, 10249.C031.19SD, 10249.C031.19SS, 10249.C031.20SS, 10249.C031.21SS, 10249.C032.02SS, 10249.C032.03SS, 10249.C032.04SS, 10249.C032.05SS, 10249.C032.06SS, 10249.C032.07SS, 10249.C032.09SS, 10249.C032.10SS, 10249.C032.11SD, 10249.C032.11SS, 10249.C032.12SD, 10249.C032.13SS, 10249.C032.14SS, 10249.C032.15SS, 10249.C032.16SS, 10249.C032.17SS, 10249.C032.19SD, 10249.C032.19SS, 10249.C032.20SD, 10249.C032.20SS, 10249.C032.21SS, 10249.C032.22SS, 10249.C033.02SS, 10249.C033.03SS, 10249.C033.04SS, 10249.C033.05SS, 10249.C033.06SS, 10249.C033.07SS, 10249.C033.08SS, 10249.C033.09SD, 10249.C033.09SS, 10249.C033.10SD, 10249.C033.10SS, 10249.C033.11SD, 10249.C033.11SS, 10249.C033.12SS, 10249.C033.13SS, 10249.C033.14SS, 10249.C033.15SS, 10249.C033.16SS, 10249.C033.17SD, 10249.C033.17SS, 10249.C033.18SD, 10249.C033.18SS, 10249.C033.19SS, 10249.C034.02SS, 10249.C034.03SS, 10249.C034.04SS, 10249.C034.05SS, 10249.C034.06SS, 10249.C034.07SS, 10249.C034.08SS, 10249.C034.09SS, 10249.C034.10SS, 10249.C034.11SS, 10249.C034.12SS, 10249.C034.13SS, 10249.C034.14SS, 10249.C034.15SD, 10249.C034.15SS, 10249.C034.16SS, 10249.C034.17SD, 10249.C034.17SS, 10249.C035.02SS, 10249.C035.03SS, 10249.C035.04SS, 10249.C035.05SS, 10249.C035.06SD, 10249.C035.06SS, 10249.C035.07SD, 10249.C035.07SS, 10249.C035.08SS, 10249.C035.09SS, 10249.C035.10SS, 10249.C035.11SS, 10249.C035.12SD, 10249.C035.12SS, 10249.C035.13SD, 10249.C035.13SS, 10249.C035.14SD, 10249.C035.14SS, 10249.C035.15SD, 10249.C035.15SS, 10249.C035.16SS, 10249.C035.17SS, 10249.C036.02SS, 10249.C036.03SS, 10249.C036.04SS, 10249.C036.05SD, 10249.C036.05SS, 10249.C036.07SS, 10249.C036.08SS, 10249.C036.09SS, 10249.C036.10SS, 10249.C036.11SS, 10249.C036.12SS, 10249.C036.13SS, 10249.C036.14SD, 10249.C036.14SS, 10249.C036.15SS, 10249.C036.16SS, 10249.C037.02SS, 10249.C037.04SS, 10249.C037.05SS, 10249.C037.06SS, 10249.C037.07SS, 10249.C037.08SS, 10249.C037.09SS, 10249.C037.10SS, 10249.C037.11SS, 10249.C037.12SD, 10249.C037.12SS, 10249.C037.13SD, 10249.C037.13SS, 10249.C037.14SS, 10249.C037.15SS, 10249.C037.16SS, 10249.C037.17SS, 10249.C037.18SS, 10249.C038.02SS, 10249.C038.04SS, 10249.C038.05SD, 10249.C038.05SS, 10249.C038.06SD, 10249.C038.06SS, 10249.C038.07SD, 10249.C038.07SS, 10249.C038.08SS, 10249.C038.09SS, 10249.C038.10SS, 10249.C038.11SS, 10249.C038.12SD, 10249.C038.12SS, 10249.C038.13SD, 10249.C038.13SS, 10249.C038.14SS, 10249.C038.15SD, 10249.C038.15SS, 10249.C038.16SD, 10249.C038.16SS, 10249.C038.18SS, 10249.C041.02SS, 10249.C041.03SS, 10249.C041.04SS, 10249.C041.05SD, 10249.C041.05SS, 10249.C041.06SD, 10249.C041.06SS, 10249.C041.08SS, 10249.C041.09SS, 10249.C041.10SS, 10249.C041.11SS, 10249.C041.12SS, 10249.C041.13SD, 10249.C041.13SS, 10249.C041.14SD, 10249.C041.14SS, 10249.C041.16SD, 10249.C041.16SS, 10249.C041.17SD, 10249.C041.17SS, 10249.C041.18SS, 10249.C041.19SS, 10249.C042.02SS, 10249.C042.03SS, 10249.C042.04SS, 10249.C042.05SS, 10249.C042.06SD, 10249.C042.06SS, 10249.C042.07SS, 10249.C042.08SS, 10249.C042.09SS, 10249.C042.10SS, 10249.C042.11SD, 10249.C042.11SS, 10249.C042.12SS, 10249.C042.13SS, 10249.C042.14SD, 10249.C042.14SS, 10249.C042.15SD, 10249.C042.15SS, 10249.C042.16SS, 10249.C042.17SS, 10249.C043.02SS, 10249.C043.03SS, 10249.C043.04SD, 10249.C043.04SS, 10249.C043.05SD, 10249.C043.05SS, 10249.C043.06SS, 10249.C043.07SS, 10249.C043.08SS, 10249.C043.09SS, 10249.C043.10SD, 10249.C043.10SS, 10249.C043.11SD, 10249.C043.11SS, 10249.C043.12SD, 10249.C043.12SS, 10249.C043.14SS, 10249.C043.15SD, 10249.C043.15SS, 10249.C043.16SS, 10249.C043.17SS, 10249.C043.18SS, 10249.C043.20SS, 10249.C044.02SS, 10249.C044.03SS, 10249.C044.04SS, 10249.C044.05SS, 10249.C044.06SS, 10249.C044.07SS, 10249.C044.08SS, 10249.C044.09SS, 10249.C044.10SS, 10249.C044.11SS, 10249.C044.12SD, 10249.C044.12SS, 10249.C044.13SD, 10249.C044.13SS, 10249.C044.15SD, 10249.C044.15SS, 10249.C044.16SS, 10249.C044.17SS, 10249.C045.02SS, 10249.C045.03SS, 10249.C045.04SS, 10249.C045.05SD, 10249.C045.05SS, 10249.C045.06SS, 10249.C045.08SD, 10249.C045.08SS, 10249.C045.09SD, 10249.C045.09SS, 10249.C045.10SD, 10249.C045.10SS, 10249.C045.11SS, 10249.C045.12SS, 10249.C045.13SS, 10249.C046.02SS, 10249.C046.03SS, 10249.C046.04SS, 10249.C046.05SS, 10249.C046.06SD, 10249.C046.06SS, 10249.C046.07SD, 10249.C046.07SS, 10249.C046.08SS, 10249.C046.09SD, 10249.C046.09SS, 10249.C046.10SD, 10249.C046.10SS, 10249.C046.11SD, 10249.C046.11SS, 10249.C046.12SS, 10249.C046.13SS, 10249.C046.14SS, 10249.C047.02SD, 10249.C047.02SS, 10249.C047.05SS, 10249.C047.06SD, 10249.C047.06SS, 10249.C047.07SD, 10249.C047.07SS, 10249.C047.08SD, 10249.C047.08SS, 10249.C047.09SS, 10249.C047.10SS, 10249.C047.11SS, 10249.C047.13SS, 10249.C049.03SD, 10249.C049.03SS, 10249.C049.04SS, 10249.C049.07SD, 10249.C049.07SS, 10249.C049.08SD, 10249.C049.08SS, 10249.C049.09SD, 10249.C049.09SS, 10249.C049.10SS, 10249.C049.11SS, 10249.C049.12SS, 10249.C049.13SS, 10249.C049.14SS, 10249.C052.03SD, 10249.C052.03SS, 10249.C052.04SD, 10249.C052.04SS, 10249.C052.05SD, 10249.C052.06SS, 10249.C052.07SS, 10249.C052.08SS, 10249.C052.09SS, 10249.C053.02SD, 10249.C053.02SS, 10249.C053.03SD, 10249.C053.03SS, 10249.C053.04SD, 10249.C053.04SS, 10249.C053.05SD, 10249.C053.05SS, 10249.C053.06SS, 10249.C053.07SS, 10249.C053.08SS, 10249.C053.09SS, 10249.C055.02SD, 10249.C055.02SS, 10249.C055.03SD, 10249.C055.03SS, 10249.C055.04SD, 10249.C055.04SS, 10249.C055.05SD, 10249.C055.05SS, 10249.C055.06SS, 10249.C055.07SS, 10249.C055.08SS, 10249.C055.09SS, 10249.C056.03SD, 10249.C056.03SS, 10249.C056.04SD, 10249.C056.04SS, 10249.C056.05SD, 10249.C056.05SS, 10249.C056.06SS, 10249.C056.07SS, 10249.C056.08SS, 10249.C056.09SS, 10249.C056.10SS, 10249.C057.02SS, 10249.C057.03SD, 10249.C057.03SS, 10249.C057.04SD, 10249.C057.04SS, 10249.C057.05SD, 10249.C057.05SS, 10249.C057.06SS, 10249.C057.08SS, 10249.C057.09SS, 10249.C057.10SS, 10249.C057.11SS
#> Updated feature table to match the subsetted data.
#> Updated feature annotation to match the subsetted data.
#> Data subsetting complete. Returning updated data object.
#> $Phylum
#> $Phylum$Phylum

#> 
#> 
#> $Family
#> $Family$Family

#> 
#> 
#> $Genus
#> $Genus$Genus

#> 
#> 

plot_feature_diversity(
data.obj = ecam.obj,
group.var = "antiexposedall",
strata.var = "delivery",
time.var = "month",
time.point.plot = unique(ecam.obj$meta.dat$month)[1],
is.plot.change = TRUE,
feature.level = c("Phylum", "Family", "Genus"),
feature.dat.type = "proportion",
features.plot = NULL,
prop.to.lump = 0.0001,
top.k.plot = NULL,
top.k.func = NULL,
renormalize = FALSE,
plot.other = TRUE,
plot.scheme = "individual",
plot.type = "boxplot"
)
#> Rule 1 passed: data.obj is a list.
#> Rule 2 passed: meta.dat is a data.frame.
#> Rule 3 passed: The row names of feature.tab match the row names of feature.ann.
#> Rule 4 passed: The order of rows in meta.dat has been adjusted to match feature.tab.
#> Rule 5 passed: feature.tab is a matrix.
#> Rule 6 passed: feature.ann is a matrix.
#> Please note: The data components should follow base R data.frame and matrix structures, not phyloseq's formal class.
#> Validation passed.
#> Note: Passing validation does not guarantee the absence of all data issues. Further data exploration may be needed.
#> Data has been subsetted based on the provided condition.
#> Updated metadata to match the subsetted data.
#> The following samples were excluded: 10249.C001.02SS, 10249.C001.03SS, 10249.C001.04SS, 10249.C001.05SS, 10249.C001.06SS, 10249.C001.07SS, 10249.C001.08SS, 10249.C001.09SS, 10249.C001.10SS, 10249.C001.11SS, 10249.C001.12SS, 10249.C001.13SS, 10249.C001.14SS, 10249.C001.15SS, 10249.C001.16SS, 10249.C001.17SS, 10249.C001.18SS, 10249.C001.19SS, 10249.C001.20SS, 10249.C001.25SS, 10249.C001.26SS, 10249.C001.27SS, 10249.C001.29SS, 10249.C001.30SS, 10249.C001.31SS, 10249.C001.32SS, 10249.C001.34SD, 10249.C001.34SS, 10249.C001.35SS, 10249.C001.36SD, 10249.C001.36SS, 10249.C002.02SS, 10249.C002.03SS, 10249.C002.04SS, 10249.C002.05SS, 10249.C002.06SS, 10249.C002.07SS, 10249.C002.08SS, 10249.C002.09SS, 10249.C002.10SS, 10249.C002.11SS, 10249.C002.12SS, 10249.C002.13SS, 10249.C002.15SS, 10249.C002.16SS, 10249.C002.18SS, 10249.C002.19SD, 10249.C002.19SS, 10249.C002.20SS, 10249.C002.21SD, 10249.C002.21SS, 10249.C004.02SS, 10249.C004.03SS, 10249.C004.04SS, 10249.C004.05SS, 10249.C004.06SS, 10249.C004.07SS, 10249.C004.08SS, 10249.C004.09SS, 10249.C004.10SS, 10249.C004.11SS, 10249.C004.12SS, 10249.C004.13SS, 10249.C004.14SS, 10249.C004.15SS, 10249.C005.02SS, 10249.C005.03SS, 10249.C005.04SS, 10249.C005.05SS, 10249.C005.07SS, 10249.C005.08SS, 10249.C005.09SS, 10249.C005.10SS, 10249.C005.11SS, 10249.C005.12SS, 10249.C005.13SS, 10249.C005.14SS, 10249.C005.15SS, 10249.C005.16SS, 10249.C005.17SS, 10249.C005.18SS, 10249.C005.19SD, 10249.C005.19SS, 10249.C005.20SS, 10249.C005.21SD, 10249.C005.21SS, 10249.C005.22SS, 10249.C007.02SS, 10249.C007.03SS, 10249.C007.04SS, 10249.C007.05SS, 10249.C007.06SS, 10249.C007.07SS, 10249.C007.08SS, 10249.C007.09SS, 10249.C007.10SS, 10249.C007.11SS, 10249.C007.12SS, 10249.C007.13SS, 10249.C007.14SS, 10249.C007.15SS, 10249.C007.16SS, 10249.C007.17SS, 10249.C007.18SS, 10249.C007.19SS, 10249.C007.20SS, 10249.C007.21SS, 10249.C007.22SD, 10249.C007.22SS, 10249.C007.23SD, 10249.C007.23SS, 10249.C007.24SD, 10249.C007.24SS, 10249.C007.26SS, 10249.C008.02SS, 10249.C008.03SS, 10249.C008.04SS, 10249.C008.05SS, 10249.C008.06SS, 10249.C008.07SS, 10249.C008.08SS, 10249.C008.09SS, 10249.C008.10SS, 10249.C008.11SS, 10249.C008.12SS, 10249.C008.13SS, 10249.C008.14SS, 10249.C008.15SS, 10249.C008.16SD, 10249.C008.16SS, 10249.C008.18SS, 10249.C009.02SS, 10249.C009.03SS, 10249.C009.04SS, 10249.C009.05SS, 10249.C009.06SS, 10249.C009.07SS, 10249.C009.08SS, 10249.C009.09SS, 10249.C009.10SS, 10249.C009.11SS, 10249.C009.12SS, 10249.C009.13SS, 10249.C009.14SS, 10249.C009.16SS, 10249.C009.17SS, 10249.C009.18SD, 10249.C009.18SS, 10249.C009.19SS, 10249.C009.20SD, 10249.C009.20SS, 10249.C009.21SS, 10249.C010.02SS, 10249.C010.03SS, 10249.C010.04SS, 10249.C010.05SS, 10249.C010.06SS, 10249.C010.07SS, 10249.C010.08SS, 10249.C010.09SS, 10249.C010.10SS, 10249.C010.11SS, 10249.C010.12SS, 10249.C010.13SS, 10249.C010.14SS, 10249.C010.15SS, 10249.C010.16SS, 10249.C010.18SD, 10249.C010.18SS, 10249.C010.19SS, 10249.C010.20SD, 10249.C010.20SS, 10249.C010.21SS, 10249.C011.02SS, 10249.C011.03SS, 10249.C011.04SS, 10249.C011.05SS, 10249.C011.06SS, 10249.C011.07SS, 10249.C011.08SS, 10249.C011.09SS, 10249.C011.10SS, 10249.C011.11SS, 10249.C011.12SS, 10249.C011.13SD, 10249.C011.14SS, 10249.C011.16SS, 10249.C011.17SD, 10249.C011.17SS, 10249.C011.18SS, 10249.C011.19SD, 10249.C011.19SS, 10249.C011.20SS, 10249.C011.21SS, 10249.C012.02SS, 10249.C012.03SS, 10249.C012.04SS, 10249.C012.05SS, 10249.C012.06SS, 10249.C012.07SS, 10249.C012.08SS, 10249.C012.09SS, 10249.C012.10SS, 10249.C012.11SS, 10249.C012.12SS, 10249.C012.13SS, 10249.C012.14SS, 10249.C012.15SS, 10249.C012.16SS, 10249.C012.17SS, 10249.C012.18SS, 10249.C012.19SD, 10249.C012.19SS, 10249.C012.20SS, 10249.C012.21SD, 10249.C012.21SS, 10249.C012.22SD, 10249.C012.22SS, 10249.C014.02SS, 10249.C014.03SS, 10249.C014.04SS, 10249.C014.05SS, 10249.C014.06SS, 10249.C014.07SS, 10249.C014.08SS, 10249.C014.09SS, 10249.C014.10SS, 10249.C014.12SS, 10249.C014.13SS, 10249.C014.15SS, 10249.C014.16SS, 10249.C014.17SS, 10249.C014.18SS, 10249.C014.19SD, 10249.C014.19SS, 10249.C014.20SD, 10249.C014.20SS, 10249.C014.21SS, 10249.C014.22SS, 10249.C016.03SS, 10249.C016.04SS, 10249.C016.05SS, 10249.C016.06SS, 10249.C016.07SS, 10249.C016.08SS, 10249.C016.09SS, 10249.C016.10SS, 10249.C016.11SS, 10249.C016.12SS, 10249.C016.13SS, 10249.C016.14SS, 10249.C016.15SS, 10249.C016.17SS, 10249.C016.18SS, 10249.C016.19SS, 10249.C016.20SS, 10249.C016.21SD, 10249.C016.21SS, 10249.C016.22SD, 10249.C016.22SS, 10249.C016.23SS, 10249.C016.24SS, 10249.C017.04SS, 10249.C017.05SS, 10249.C017.06SS, 10249.C017.07SS, 10249.C017.08SS, 10249.C017.09SS, 10249.C017.10SS, 10249.C017.11SS, 10249.C017.12SS, 10249.C018.02SS, 10249.C018.03SS, 10249.C018.04SS, 10249.C018.05SS, 10249.C018.06SS, 10249.C018.07SS, 10249.C018.08SS, 10249.C018.09SS, 10249.C018.10SS, 10249.C018.11SD, 10249.C018.11SS, 10249.C018.12SD, 10249.C018.12SS, 10249.C018.13SS, 10249.C018.14SS, 10249.C018.15SS, 10249.C018.16SS, 10249.C018.17SS, 10249.C018.18SS, 10249.C018.19SS, 10249.C020.06SS, 10249.C020.07SS, 10249.C020.08SS, 10249.C020.09SS, 10249.C020.10SS, 10249.C020.11SS, 10249.C020.12SS, 10249.C020.13SS, 10249.C020.14SS, 10249.C020.15SS, 10249.C020.16SS, 10249.C020.17SS, 10249.C020.18SS, 10249.C020.19SS, 10249.C020.20SS, 10249.C020.21SS, 10249.C020.22SD, 10249.C020.22SS, 10249.C020.23SD, 10249.C020.23SS, 10249.C020.24SD, 10249.C020.24SS, 10249.C020.25SD, 10249.C020.25SS, 10249.C020.26SD, 10249.C020.26SS, 10249.C020.28SS, 10249.C020.29SS, 10249.C021.03SS, 10249.C021.04SS, 10249.C021.05SS, 10249.C021.06SS, 10249.C021.07SS, 10249.C021.08SS, 10249.C021.09SS, 10249.C021.10SS, 10249.C021.12SS, 10249.C021.13SS, 10249.C022.02SS, 10249.C022.03SS, 10249.C022.04SS, 10249.C022.05SS, 10249.C022.06SS, 10249.C022.07SS, 10249.C022.08SS, 10249.C022.09SS, 10249.C022.10SS, 10249.C022.11SS, 10249.C022.12SS, 10249.C022.13SS, 10249.C022.15SS, 10249.C022.16SS, 10249.C022.18SD, 10249.C022.18SS, 10249.C022.19SS, 10249.C022.20SS, 10249.C022.21SS, 10249.C024.02SS, 10249.C024.03SS, 10249.C024.04SS, 10249.C024.05SS, 10249.C024.06SS, 10249.C024.07SS, 10249.C024.08SS, 10249.C024.09SS, 10249.C024.10SS, 10249.C024.12SS, 10249.C024.13SS, 10249.C024.14SS, 10249.C024.15SS, 10249.C024.16SS, 10249.C024.17SS, 10249.C024.18SS, 10249.C024.19SD, 10249.C024.19SS, 10249.C024.20SD, 10249.C024.20SS, 10249.C024.21SS, 10249.C024.22SS, 10249.C025.02SS, 10249.C025.03SS, 10249.C025.04SS, 10249.C025.05SS, 10249.C025.06SS, 10249.C025.07SS, 10249.C025.08SS, 10249.C025.09SS, 10249.C025.10SS, 10249.C025.11SS, 10249.C025.12SS, 10249.C025.13SD, 10249.C025.13SS, 10249.C025.14SD, 10249.C025.14SS, 10249.C025.15SS, 10249.C025.16SS, 10249.C025.17SS, 10249.C025.18SS, 10249.C025.19SD, 10249.C025.19SS, 10249.C025.20SS, 10249.C025.21SS, 10249.C027.02SS, 10249.C027.03SS, 10249.C027.04SS, 10249.C027.05SS, 10249.C027.06SS, 10249.C027.07SS, 10249.C027.08SS, 10249.C027.09SS, 10249.C027.10SS, 10249.C027.11SD, 10249.C027.12SD, 10249.C027.12SS, 10249.C027.13SS, 10249.C027.14SS, 10249.C027.15SS, 10249.C027.16SS, 10249.C027.17SD, 10249.C027.17SS, 10249.C027.18SS, 10249.C027.19SD, 10249.C027.19SS, 10249.C027.20SD, 10249.C027.20SS, 10249.C027.21SS, 10249.C027.22SS, 10249.C030.02SS, 10249.C030.03SS, 10249.C030.04SS, 10249.C030.05SS, 10249.C030.06SS, 10249.C030.07SS, 10249.C030.08SS, 10249.C030.09SS, 10249.C030.10SS, 10249.C030.11SD, 10249.C030.11SS, 10249.C030.12SS, 10249.C030.13SS, 10249.C030.14SS, 10249.C030.16SS, 10249.C030.17SD, 10249.C030.17SS, 10249.C030.18SS, 10249.C030.19SD, 10249.C030.19SS, 10249.C030.20SS, 10249.C031.02SS, 10249.C031.03SS, 10249.C031.04SS, 10249.C031.05SS, 10249.C031.06SS, 10249.C031.07SS, 10249.C031.08SS, 10249.C031.09SS, 10249.C031.10SS, 10249.C031.11SD, 10249.C031.11SS, 10249.C031.12SS, 10249.C031.13SS, 10249.C031.14SS, 10249.C031.16SS, 10249.C031.17SD, 10249.C031.17SS, 10249.C031.18SS, 10249.C031.19SD, 10249.C031.19SS, 10249.C031.20SS, 10249.C031.21SS, 10249.C032.02SS, 10249.C032.03SS, 10249.C032.04SS, 10249.C032.05SS, 10249.C032.06SS, 10249.C032.07SS, 10249.C032.09SS, 10249.C032.10SS, 10249.C032.11SD, 10249.C032.11SS, 10249.C032.12SD, 10249.C032.13SS, 10249.C032.14SS, 10249.C032.15SS, 10249.C032.16SS, 10249.C032.17SS, 10249.C032.19SD, 10249.C032.19SS, 10249.C032.20SD, 10249.C032.20SS, 10249.C032.21SS, 10249.C032.22SS, 10249.C033.02SS, 10249.C033.03SS, 10249.C033.04SS, 10249.C033.05SS, 10249.C033.06SS, 10249.C033.07SS, 10249.C033.08SS, 10249.C033.09SD, 10249.C033.09SS, 10249.C033.10SD, 10249.C033.10SS, 10249.C033.11SD, 10249.C033.11SS, 10249.C033.12SS, 10249.C033.13SS, 10249.C033.14SS, 10249.C033.15SS, 10249.C033.16SS, 10249.C033.17SD, 10249.C033.17SS, 10249.C033.18SD, 10249.C033.18SS, 10249.C033.19SS, 10249.C034.02SS, 10249.C034.03SS, 10249.C034.04SS, 10249.C034.05SS, 10249.C034.06SS, 10249.C034.07SS, 10249.C034.08SS, 10249.C034.09SS, 10249.C034.10SS, 10249.C034.11SS, 10249.C034.12SS, 10249.C034.13SS, 10249.C034.14SS, 10249.C034.15SD, 10249.C034.15SS, 10249.C034.16SS, 10249.C034.17SD, 10249.C034.17SS, 10249.C035.02SS, 10249.C035.03SS, 10249.C035.04SS, 10249.C035.05SS, 10249.C035.06SD, 10249.C035.06SS, 10249.C035.07SD, 10249.C035.07SS, 10249.C035.08SS, 10249.C035.09SS, 10249.C035.10SS, 10249.C035.11SS, 10249.C035.12SD, 10249.C035.12SS, 10249.C035.13SD, 10249.C035.13SS, 10249.C035.14SD, 10249.C035.14SS, 10249.C035.15SD, 10249.C035.15SS, 10249.C035.16SS, 10249.C035.17SS, 10249.C036.02SS, 10249.C036.03SS, 10249.C036.04SS, 10249.C036.05SD, 10249.C036.05SS, 10249.C036.07SS, 10249.C036.08SS, 10249.C036.09SS, 10249.C036.10SS, 10249.C036.11SS, 10249.C036.12SS, 10249.C036.13SS, 10249.C036.14SD, 10249.C036.14SS, 10249.C036.15SS, 10249.C036.16SS, 10249.C037.02SS, 10249.C037.04SS, 10249.C037.05SS, 10249.C037.06SS, 10249.C037.07SS, 10249.C037.08SS, 10249.C037.09SS, 10249.C037.10SS, 10249.C037.11SS, 10249.C037.12SD, 10249.C037.12SS, 10249.C037.13SD, 10249.C037.13SS, 10249.C037.14SS, 10249.C037.15SS, 10249.C037.16SS, 10249.C037.17SS, 10249.C037.18SS, 10249.C038.02SS, 10249.C038.04SS, 10249.C038.05SD, 10249.C038.05SS, 10249.C038.06SD, 10249.C038.06SS, 10249.C038.07SD, 10249.C038.07SS, 10249.C038.08SS, 10249.C038.09SS, 10249.C038.10SS, 10249.C038.11SS, 10249.C038.12SD, 10249.C038.12SS, 10249.C038.13SD, 10249.C038.13SS, 10249.C038.14SS, 10249.C038.15SD, 10249.C038.15SS, 10249.C038.16SD, 10249.C038.16SS, 10249.C038.18SS, 10249.C041.02SS, 10249.C041.03SS, 10249.C041.04SS, 10249.C041.05SD, 10249.C041.05SS, 10249.C041.06SD, 10249.C041.06SS, 10249.C041.08SS, 10249.C041.09SS, 10249.C041.10SS, 10249.C041.11SS, 10249.C041.12SS, 10249.C041.13SD, 10249.C041.13SS, 10249.C041.14SD, 10249.C041.14SS, 10249.C041.16SD, 10249.C041.16SS, 10249.C041.17SD, 10249.C041.17SS, 10249.C041.18SS, 10249.C041.19SS, 10249.C042.02SS, 10249.C042.03SS, 10249.C042.04SS, 10249.C042.05SS, 10249.C042.06SD, 10249.C042.06SS, 10249.C042.07SS, 10249.C042.08SS, 10249.C042.09SS, 10249.C042.10SS, 10249.C042.11SD, 10249.C042.11SS, 10249.C042.12SS, 10249.C042.13SS, 10249.C042.14SD, 10249.C042.14SS, 10249.C042.15SD, 10249.C042.15SS, 10249.C042.16SS, 10249.C042.17SS, 10249.C043.02SS, 10249.C043.03SS, 10249.C043.04SD, 10249.C043.04SS, 10249.C043.05SD, 10249.C043.05SS, 10249.C043.06SS, 10249.C043.07SS, 10249.C043.08SS, 10249.C043.09SS, 10249.C043.10SD, 10249.C043.10SS, 10249.C043.11SD, 10249.C043.11SS, 10249.C043.12SD, 10249.C043.12SS, 10249.C043.14SS, 10249.C043.15SD, 10249.C043.15SS, 10249.C043.16SS, 10249.C043.17SS, 10249.C043.18SS, 10249.C043.20SS, 10249.C044.02SS, 10249.C044.03SS, 10249.C044.04SS, 10249.C044.05SS, 10249.C044.06SS, 10249.C044.07SS, 10249.C044.08SS, 10249.C044.09SS, 10249.C044.10SS, 10249.C044.11SS, 10249.C044.12SD, 10249.C044.12SS, 10249.C044.13SD, 10249.C044.13SS, 10249.C044.15SD, 10249.C044.15SS, 10249.C044.16SS, 10249.C044.17SS, 10249.C045.02SS, 10249.C045.03SS, 10249.C045.04SS, 10249.C045.05SD, 10249.C045.05SS, 10249.C045.06SS, 10249.C045.08SD, 10249.C045.08SS, 10249.C045.09SD, 10249.C045.09SS, 10249.C045.10SD, 10249.C045.10SS, 10249.C045.11SS, 10249.C045.12SS, 10249.C045.13SS, 10249.C046.02SS, 10249.C046.03SS, 10249.C046.04SS, 10249.C046.05SS, 10249.C046.06SD, 10249.C046.06SS, 10249.C046.07SD, 10249.C046.07SS, 10249.C046.08SS, 10249.C046.09SD, 10249.C046.09SS, 10249.C046.10SD, 10249.C046.10SS, 10249.C046.11SD, 10249.C046.11SS, 10249.C046.12SS, 10249.C046.13SS, 10249.C046.14SS, 10249.C047.02SD, 10249.C047.02SS, 10249.C047.05SS, 10249.C047.06SD, 10249.C047.06SS, 10249.C047.07SD, 10249.C047.07SS, 10249.C047.08SD, 10249.C047.08SS, 10249.C047.09SS, 10249.C047.10SS, 10249.C047.11SS, 10249.C047.13SS, 10249.C049.03SD, 10249.C049.03SS, 10249.C049.04SS, 10249.C049.07SD, 10249.C049.07SS, 10249.C049.08SD, 10249.C049.08SS, 10249.C049.09SD, 10249.C049.09SS, 10249.C049.10SS, 10249.C049.11SS, 10249.C049.12SS, 10249.C049.13SS, 10249.C049.14SS, 10249.C052.03SD, 10249.C052.03SS, 10249.C052.04SD, 10249.C052.04SS, 10249.C052.05SD, 10249.C052.06SS, 10249.C052.07SS, 10249.C052.08SS, 10249.C052.09SS, 10249.C053.02SD, 10249.C053.02SS, 10249.C053.03SD, 10249.C053.03SS, 10249.C053.04SD, 10249.C053.04SS, 10249.C053.05SD, 10249.C053.05SS, 10249.C053.06SS, 10249.C053.07SS, 10249.C053.08SS, 10249.C053.09SS, 10249.C055.02SD, 10249.C055.02SS, 10249.C055.03SD, 10249.C055.03SS, 10249.C055.04SD, 10249.C055.04SS, 10249.C055.05SD, 10249.C055.05SS, 10249.C055.06SS, 10249.C055.07SS, 10249.C055.08SS, 10249.C055.09SS, 10249.C056.03SD, 10249.C056.03SS, 10249.C056.04SD, 10249.C056.04SS, 10249.C056.05SD, 10249.C056.05SS, 10249.C056.06SS, 10249.C056.07SS, 10249.C056.08SS, 10249.C056.09SS, 10249.C056.10SS, 10249.C057.02SS, 10249.C057.03SD, 10249.C057.03SS, 10249.C057.04SD, 10249.C057.04SS, 10249.C057.05SD, 10249.C057.05SS, 10249.C057.06SS, 10249.C057.08SS, 10249.C057.09SS, 10249.C057.10SS, 10249.C057.11SS
#> Updated feature table to match the subsetted data.
#> Updated feature annotation to match the subsetted data.
#> Data subsetting complete. Returning updated data object.
#> Rule 1 passed: data.obj is a list.
#> Rule 2 passed: meta.dat is a data.frame.
#> Rule 3 passed: The row names of feature.tab match the row names of feature.ann.
#> Rule 4 passed: The order of rows in meta.dat has been adjusted to match feature.tab.
#> Rule 5 passed: feature.tab is a matrix.
#> Rule 6 passed: feature.ann is a matrix.
#> Please note: The data components should follow base R data.frame and matrix structures, not phyloseq's formal class.
#> Validation passed.
#> Note: Passing validation does not guarantee the absence of all data issues. Further data exploration may be needed.
#> Data has been subsetted based on the provided condition.
#> Updated metadata to match the subsetted data.
#> The following samples were excluded: 10249.C001.02SS, 10249.C001.03SS, 10249.C001.04SS, 10249.C001.05SS, 10249.C001.06SS, 10249.C001.07SS, 10249.C001.08SS, 10249.C001.09SS, 10249.C001.10SS, 10249.C001.11SS, 10249.C001.12SS, 10249.C001.13SS, 10249.C001.14SS, 10249.C001.15SS, 10249.C001.16SS, 10249.C001.17SS, 10249.C001.18SS, 10249.C001.19SS, 10249.C001.20SS, 10249.C001.25SS, 10249.C001.26SS, 10249.C001.27SS, 10249.C001.29SS, 10249.C001.30SS, 10249.C001.31SS, 10249.C001.32SS, 10249.C001.34SD, 10249.C001.34SS, 10249.C001.35SS, 10249.C001.36SD, 10249.C001.36SS, 10249.C002.02SS, 10249.C002.03SS, 10249.C002.04SS, 10249.C002.05SS, 10249.C002.06SS, 10249.C002.07SS, 10249.C002.08SS, 10249.C002.09SS, 10249.C002.10SS, 10249.C002.11SS, 10249.C002.12SS, 10249.C002.13SS, 10249.C002.15SS, 10249.C002.16SS, 10249.C002.18SS, 10249.C002.19SD, 10249.C002.19SS, 10249.C002.20SS, 10249.C002.21SD, 10249.C002.21SS, 10249.C004.02SS, 10249.C004.03SS, 10249.C004.04SS, 10249.C004.05SS, 10249.C004.06SS, 10249.C004.07SS, 10249.C004.08SS, 10249.C004.09SS, 10249.C004.10SS, 10249.C004.11SS, 10249.C004.12SS, 10249.C004.13SS, 10249.C004.14SS, 10249.C004.15SS, 10249.C005.02SS, 10249.C005.03SS, 10249.C005.04SS, 10249.C005.05SS, 10249.C005.07SS, 10249.C005.08SS, 10249.C005.09SS, 10249.C005.10SS, 10249.C005.11SS, 10249.C005.12SS, 10249.C005.13SS, 10249.C005.14SS, 10249.C005.15SS, 10249.C005.16SS, 10249.C005.17SS, 10249.C005.18SS, 10249.C005.19SD, 10249.C005.19SS, 10249.C005.20SS, 10249.C005.21SD, 10249.C005.21SS, 10249.C005.22SS, 10249.C007.02SS, 10249.C007.03SS, 10249.C007.04SS, 10249.C007.05SS, 10249.C007.06SS, 10249.C007.07SS, 10249.C007.08SS, 10249.C007.09SS, 10249.C007.10SS, 10249.C007.11SS, 10249.C007.12SS, 10249.C007.13SS, 10249.C007.14SS, 10249.C007.15SS, 10249.C007.16SS, 10249.C007.17SS, 10249.C007.18SS, 10249.C007.19SS, 10249.C007.20SS, 10249.C007.21SS, 10249.C007.22SD, 10249.C007.22SS, 10249.C007.23SD, 10249.C007.23SS, 10249.C007.24SD, 10249.C007.24SS, 10249.C007.26SS, 10249.C008.02SS, 10249.C008.03SS, 10249.C008.04SS, 10249.C008.05SS, 10249.C008.06SS, 10249.C008.07SS, 10249.C008.08SS, 10249.C008.09SS, 10249.C008.10SS, 10249.C008.11SS, 10249.C008.12SS, 10249.C008.13SS, 10249.C008.14SS, 10249.C008.15SS, 10249.C008.16SD, 10249.C008.16SS, 10249.C008.18SS, 10249.C009.02SS, 10249.C009.03SS, 10249.C009.04SS, 10249.C009.05SS, 10249.C009.06SS, 10249.C009.07SS, 10249.C009.08SS, 10249.C009.09SS, 10249.C009.10SS, 10249.C009.11SS, 10249.C009.12SS, 10249.C009.13SS, 10249.C009.14SS, 10249.C009.16SS, 10249.C009.17SS, 10249.C009.18SD, 10249.C009.18SS, 10249.C009.19SS, 10249.C009.20SD, 10249.C009.20SS, 10249.C009.21SS, 10249.C010.02SS, 10249.C010.03SS, 10249.C010.04SS, 10249.C010.05SS, 10249.C010.06SS, 10249.C010.07SS, 10249.C010.08SS, 10249.C010.09SS, 10249.C010.10SS, 10249.C010.11SS, 10249.C010.12SS, 10249.C010.13SS, 10249.C010.14SS, 10249.C010.15SS, 10249.C010.16SS, 10249.C010.18SD, 10249.C010.18SS, 10249.C010.19SS, 10249.C010.20SD, 10249.C010.20SS, 10249.C010.21SS, 10249.C011.02SS, 10249.C011.03SS, 10249.C011.04SS, 10249.C011.05SS, 10249.C011.06SS, 10249.C011.07SS, 10249.C011.08SS, 10249.C011.09SS, 10249.C011.10SS, 10249.C011.11SS, 10249.C011.12SS, 10249.C011.13SD, 10249.C011.14SS, 10249.C011.16SS, 10249.C011.17SD, 10249.C011.17SS, 10249.C011.18SS, 10249.C011.19SD, 10249.C011.19SS, 10249.C011.20SS, 10249.C011.21SS, 10249.C012.02SS, 10249.C012.03SS, 10249.C012.04SS, 10249.C012.05SS, 10249.C012.06SS, 10249.C012.07SS, 10249.C012.08SS, 10249.C012.09SS, 10249.C012.10SS, 10249.C012.11SS, 10249.C012.12SS, 10249.C012.13SS, 10249.C012.14SS, 10249.C012.15SS, 10249.C012.16SS, 10249.C012.17SS, 10249.C012.18SS, 10249.C012.19SD, 10249.C012.19SS, 10249.C012.20SS, 10249.C012.21SD, 10249.C012.21SS, 10249.C012.22SD, 10249.C012.22SS, 10249.C014.02SS, 10249.C014.03SS, 10249.C014.04SS, 10249.C014.05SS, 10249.C014.06SS, 10249.C014.07SS, 10249.C014.08SS, 10249.C014.09SS, 10249.C014.10SS, 10249.C014.12SS, 10249.C014.13SS, 10249.C014.15SS, 10249.C014.16SS, 10249.C014.17SS, 10249.C014.18SS, 10249.C014.19SD, 10249.C014.19SS, 10249.C014.20SD, 10249.C014.20SS, 10249.C014.21SS, 10249.C014.22SS, 10249.C016.03SS, 10249.C016.04SS, 10249.C016.05SS, 10249.C016.06SS, 10249.C016.07SS, 10249.C016.08SS, 10249.C016.09SS, 10249.C016.10SS, 10249.C016.11SS, 10249.C016.12SS, 10249.C016.13SS, 10249.C016.14SS, 10249.C016.15SS, 10249.C016.17SS, 10249.C016.18SS, 10249.C016.19SS, 10249.C016.20SS, 10249.C016.21SD, 10249.C016.21SS, 10249.C016.22SD, 10249.C016.22SS, 10249.C016.23SS, 10249.C016.24SS, 10249.C017.04SS, 10249.C017.05SS, 10249.C017.06SS, 10249.C017.07SS, 10249.C017.08SS, 10249.C017.09SS, 10249.C017.10SS, 10249.C017.11SS, 10249.C017.12SS, 10249.C018.02SS, 10249.C018.03SS, 10249.C018.04SS, 10249.C018.05SS, 10249.C018.06SS, 10249.C018.07SS, 10249.C018.08SS, 10249.C018.09SS, 10249.C018.10SS, 10249.C018.11SD, 10249.C018.11SS, 10249.C018.12SD, 10249.C018.12SS, 10249.C018.13SS, 10249.C018.14SS, 10249.C018.15SS, 10249.C018.16SS, 10249.C018.17SS, 10249.C018.18SS, 10249.C018.19SS, 10249.C020.06SS, 10249.C020.07SS, 10249.C020.08SS, 10249.C020.09SS, 10249.C020.10SS, 10249.C020.11SS, 10249.C020.12SS, 10249.C020.13SS, 10249.C020.14SS, 10249.C020.15SS, 10249.C020.16SS, 10249.C020.17SS, 10249.C020.18SS, 10249.C020.19SS, 10249.C020.20SS, 10249.C020.21SS, 10249.C020.22SD, 10249.C020.22SS, 10249.C020.23SD, 10249.C020.23SS, 10249.C020.24SD, 10249.C020.24SS, 10249.C020.25SD, 10249.C020.25SS, 10249.C020.26SD, 10249.C020.26SS, 10249.C020.28SS, 10249.C020.29SS, 10249.C021.03SS, 10249.C021.04SS, 10249.C021.05SS, 10249.C021.06SS, 10249.C021.07SS, 10249.C021.08SS, 10249.C021.09SS, 10249.C021.10SS, 10249.C021.12SS, 10249.C021.13SS, 10249.C022.02SS, 10249.C022.03SS, 10249.C022.04SS, 10249.C022.05SS, 10249.C022.06SS, 10249.C022.07SS, 10249.C022.08SS, 10249.C022.09SS, 10249.C022.10SS, 10249.C022.11SS, 10249.C022.12SS, 10249.C022.13SS, 10249.C022.15SS, 10249.C022.16SS, 10249.C022.18SD, 10249.C022.18SS, 10249.C022.19SS, 10249.C022.20SS, 10249.C022.21SS, 10249.C024.02SS, 10249.C024.03SS, 10249.C024.04SS, 10249.C024.05SS, 10249.C024.06SS, 10249.C024.07SS, 10249.C024.08SS, 10249.C024.09SS, 10249.C024.10SS, 10249.C024.12SS, 10249.C024.13SS, 10249.C024.14SS, 10249.C024.15SS, 10249.C024.16SS, 10249.C024.17SS, 10249.C024.18SS, 10249.C024.19SD, 10249.C024.19SS, 10249.C024.20SD, 10249.C024.20SS, 10249.C024.21SS, 10249.C024.22SS, 10249.C025.02SS, 10249.C025.03SS, 10249.C025.04SS, 10249.C025.05SS, 10249.C025.06SS, 10249.C025.07SS, 10249.C025.08SS, 10249.C025.09SS, 10249.C025.10SS, 10249.C025.11SS, 10249.C025.12SS, 10249.C025.13SD, 10249.C025.13SS, 10249.C025.14SD, 10249.C025.14SS, 10249.C025.15SS, 10249.C025.16SS, 10249.C025.17SS, 10249.C025.18SS, 10249.C025.19SD, 10249.C025.19SS, 10249.C025.20SS, 10249.C025.21SS, 10249.C027.02SS, 10249.C027.03SS, 10249.C027.04SS, 10249.C027.05SS, 10249.C027.06SS, 10249.C027.07SS, 10249.C027.08SS, 10249.C027.09SS, 10249.C027.10SS, 10249.C027.11SD, 10249.C027.12SD, 10249.C027.12SS, 10249.C027.13SS, 10249.C027.14SS, 10249.C027.15SS, 10249.C027.16SS, 10249.C027.17SD, 10249.C027.17SS, 10249.C027.18SS, 10249.C027.19SD, 10249.C027.19SS, 10249.C027.20SD, 10249.C027.20SS, 10249.C027.21SS, 10249.C027.22SS, 10249.C030.02SS, 10249.C030.03SS, 10249.C030.04SS, 10249.C030.05SS, 10249.C030.06SS, 10249.C030.07SS, 10249.C030.08SS, 10249.C030.09SS, 10249.C030.10SS, 10249.C030.11SD, 10249.C030.11SS, 10249.C030.12SS, 10249.C030.13SS, 10249.C030.14SS, 10249.C030.16SS, 10249.C030.17SD, 10249.C030.17SS, 10249.C030.18SS, 10249.C030.19SD, 10249.C030.19SS, 10249.C030.20SS, 10249.C031.02SS, 10249.C031.03SS, 10249.C031.04SS, 10249.C031.05SS, 10249.C031.06SS, 10249.C031.07SS, 10249.C031.08SS, 10249.C031.09SS, 10249.C031.10SS, 10249.C031.11SD, 10249.C031.11SS, 10249.C031.12SS, 10249.C031.13SS, 10249.C031.14SS, 10249.C031.16SS, 10249.C031.17SD, 10249.C031.17SS, 10249.C031.18SS, 10249.C031.19SD, 10249.C031.19SS, 10249.C031.20SS, 10249.C031.21SS, 10249.C032.02SS, 10249.C032.03SS, 10249.C032.04SS, 10249.C032.05SS, 10249.C032.06SS, 10249.C032.07SS, 10249.C032.09SS, 10249.C032.10SS, 10249.C032.11SD, 10249.C032.11SS, 10249.C032.12SD, 10249.C032.13SS, 10249.C032.14SS, 10249.C032.15SS, 10249.C032.16SS, 10249.C032.17SS, 10249.C032.19SD, 10249.C032.19SS, 10249.C032.20SD, 10249.C032.20SS, 10249.C032.21SS, 10249.C032.22SS, 10249.C033.02SS, 10249.C033.03SS, 10249.C033.04SS, 10249.C033.05SS, 10249.C033.06SS, 10249.C033.07SS, 10249.C033.08SS, 10249.C033.09SD, 10249.C033.09SS, 10249.C033.10SD, 10249.C033.10SS, 10249.C033.11SD, 10249.C033.11SS, 10249.C033.12SS, 10249.C033.13SS, 10249.C033.14SS, 10249.C033.15SS, 10249.C033.16SS, 10249.C033.17SD, 10249.C033.17SS, 10249.C033.18SD, 10249.C033.18SS, 10249.C033.19SS, 10249.C034.02SS, 10249.C034.03SS, 10249.C034.04SS, 10249.C034.05SS, 10249.C034.06SS, 10249.C034.07SS, 10249.C034.08SS, 10249.C034.09SS, 10249.C034.10SS, 10249.C034.11SS, 10249.C034.12SS, 10249.C034.13SS, 10249.C034.14SS, 10249.C034.15SD, 10249.C034.15SS, 10249.C034.16SS, 10249.C034.17SD, 10249.C034.17SS, 10249.C035.02SS, 10249.C035.03SS, 10249.C035.04SS, 10249.C035.05SS, 10249.C035.06SD, 10249.C035.06SS, 10249.C035.07SD, 10249.C035.07SS, 10249.C035.08SS, 10249.C035.09SS, 10249.C035.10SS, 10249.C035.11SS, 10249.C035.12SD, 10249.C035.12SS, 10249.C035.13SD, 10249.C035.13SS, 10249.C035.14SD, 10249.C035.14SS, 10249.C035.15SD, 10249.C035.15SS, 10249.C035.16SS, 10249.C035.17SS, 10249.C036.02SS, 10249.C036.03SS, 10249.C036.04SS, 10249.C036.05SD, 10249.C036.05SS, 10249.C036.07SS, 10249.C036.08SS, 10249.C036.09SS, 10249.C036.10SS, 10249.C036.11SS, 10249.C036.12SS, 10249.C036.13SS, 10249.C036.14SD, 10249.C036.14SS, 10249.C036.15SS, 10249.C036.16SS, 10249.C037.02SS, 10249.C037.04SS, 10249.C037.05SS, 10249.C037.06SS, 10249.C037.07SS, 10249.C037.08SS, 10249.C037.09SS, 10249.C037.10SS, 10249.C037.11SS, 10249.C037.12SD, 10249.C037.12SS, 10249.C037.13SD, 10249.C037.13SS, 10249.C037.14SS, 10249.C037.15SS, 10249.C037.16SS, 10249.C037.17SS, 10249.C037.18SS, 10249.C038.02SS, 10249.C038.04SS, 10249.C038.05SD, 10249.C038.05SS, 10249.C038.06SD, 10249.C038.06SS, 10249.C038.07SD, 10249.C038.07SS, 10249.C038.08SS, 10249.C038.09SS, 10249.C038.10SS, 10249.C038.11SS, 10249.C038.12SD, 10249.C038.12SS, 10249.C038.13SD, 10249.C038.13SS, 10249.C038.14SS, 10249.C038.15SD, 10249.C038.15SS, 10249.C038.16SD, 10249.C038.16SS, 10249.C038.18SS, 10249.C041.02SS, 10249.C041.03SS, 10249.C041.04SS, 10249.C041.05SD, 10249.C041.05SS, 10249.C041.06SD, 10249.C041.06SS, 10249.C041.08SS, 10249.C041.09SS, 10249.C041.10SS, 10249.C041.11SS, 10249.C041.12SS, 10249.C041.13SD, 10249.C041.13SS, 10249.C041.14SD, 10249.C041.14SS, 10249.C041.16SD, 10249.C041.16SS, 10249.C041.17SD, 10249.C041.17SS, 10249.C041.18SS, 10249.C041.19SS, 10249.C042.02SS, 10249.C042.03SS, 10249.C042.04SS, 10249.C042.05SS, 10249.C042.06SD, 10249.C042.06SS, 10249.C042.07SS, 10249.C042.08SS, 10249.C042.09SS, 10249.C042.10SS, 10249.C042.11SD, 10249.C042.11SS, 10249.C042.12SS, 10249.C042.13SS, 10249.C042.14SD, 10249.C042.14SS, 10249.C042.15SD, 10249.C042.15SS, 10249.C042.16SS, 10249.C042.17SS, 10249.C043.02SS, 10249.C043.03SS, 10249.C043.04SD, 10249.C043.04SS, 10249.C043.05SD, 10249.C043.05SS, 10249.C043.06SS, 10249.C043.07SS, 10249.C043.08SS, 10249.C043.09SS, 10249.C043.10SD, 10249.C043.10SS, 10249.C043.11SD, 10249.C043.11SS, 10249.C043.12SD, 10249.C043.12SS, 10249.C043.14SS, 10249.C043.15SD, 10249.C043.15SS, 10249.C043.16SS, 10249.C043.17SS, 10249.C043.18SS, 10249.C043.20SS, 10249.C044.02SS, 10249.C044.03SS, 10249.C044.04SS, 10249.C044.05SS, 10249.C044.06SS, 10249.C044.07SS, 10249.C044.08SS, 10249.C044.09SS, 10249.C044.10SS, 10249.C044.11SS, 10249.C044.12SD, 10249.C044.12SS, 10249.C044.13SD, 10249.C044.13SS, 10249.C044.15SD, 10249.C044.15SS, 10249.C044.16SS, 10249.C044.17SS, 10249.C045.02SS, 10249.C045.03SS, 10249.C045.04SS, 10249.C045.05SD, 10249.C045.05SS, 10249.C045.06SS, 10249.C045.08SD, 10249.C045.08SS, 10249.C045.09SD, 10249.C045.09SS, 10249.C045.10SD, 10249.C045.10SS, 10249.C045.11SS, 10249.C045.12SS, 10249.C045.13SS, 10249.C046.02SS, 10249.C046.03SS, 10249.C046.04SS, 10249.C046.05SS, 10249.C046.06SD, 10249.C046.06SS, 10249.C046.07SD, 10249.C046.07SS, 10249.C046.08SS, 10249.C046.09SD, 10249.C046.09SS, 10249.C046.10SD, 10249.C046.10SS, 10249.C046.11SD, 10249.C046.11SS, 10249.C046.12SS, 10249.C046.13SS, 10249.C046.14SS, 10249.C047.02SD, 10249.C047.02SS, 10249.C047.05SS, 10249.C047.06SD, 10249.C047.06SS, 10249.C047.07SD, 10249.C047.07SS, 10249.C047.08SD, 10249.C047.08SS, 10249.C047.09SS, 10249.C047.10SS, 10249.C047.11SS, 10249.C047.13SS, 10249.C049.03SD, 10249.C049.03SS, 10249.C049.04SS, 10249.C049.07SD, 10249.C049.07SS, 10249.C049.08SD, 10249.C049.08SS, 10249.C049.09SD, 10249.C049.09SS, 10249.C049.10SS, 10249.C049.11SS, 10249.C049.12SS, 10249.C049.13SS, 10249.C049.14SS, 10249.C052.03SD, 10249.C052.03SS, 10249.C052.04SD, 10249.C052.04SS, 10249.C052.05SD, 10249.C052.06SS, 10249.C052.07SS, 10249.C052.08SS, 10249.C052.09SS, 10249.C053.02SD, 10249.C053.02SS, 10249.C053.03SD, 10249.C053.03SS, 10249.C053.04SD, 10249.C053.04SS, 10249.C053.05SD, 10249.C053.05SS, 10249.C053.06SS, 10249.C053.07SS, 10249.C053.08SS, 10249.C053.09SS, 10249.C055.02SD, 10249.C055.02SS, 10249.C055.03SD, 10249.C055.03SS, 10249.C055.04SD, 10249.C055.04SS, 10249.C055.05SD, 10249.C055.05SS, 10249.C055.06SS, 10249.C055.07SS, 10249.C055.08SS, 10249.C055.09SS, 10249.C056.03SD, 10249.C056.03SS, 10249.C056.04SD, 10249.C056.04SS, 10249.C056.05SD, 10249.C056.05SS, 10249.C056.06SS, 10249.C056.07SS, 10249.C056.08SS, 10249.C056.09SS, 10249.C056.10SS, 10249.C057.02SS, 10249.C057.03SD, 10249.C057.03SS, 10249.C057.04SD, 10249.C057.04SS, 10249.C057.05SD, 10249.C057.05SS, 10249.C057.06SS, 10249.C057.08SS, 10249.C057.09SS, 10249.C057.10SS, 10249.C057.11SS
#> Updated feature table to match the subsetted data.
#> Updated feature annotation to match the subsetted data.
#> Data subsetting complete. Returning updated data object.
#> Rule 1 passed: data.obj is a list.
#> Rule 2 passed: meta.dat is a data.frame.
#> Rule 3 passed: The row names of feature.tab match the row names of feature.ann.
#> Rule 4 passed: The order of rows in meta.dat has been adjusted to match feature.tab.
#> Rule 5 passed: feature.tab is a matrix.
#> Rule 6 passed: feature.ann is a matrix.
#> Please note: The data components should follow base R data.frame and matrix structures, not phyloseq's formal class.
#> Validation passed.
#> Note: Passing validation does not guarantee the absence of all data issues. Further data exploration may be needed.
#> Data has been subsetted based on the provided condition.
#> Updated metadata to match the subsetted data.
#> The following samples were excluded: 10249.C001.02SS, 10249.C001.03SS, 10249.C001.04SS, 10249.C001.05SS, 10249.C001.06SS, 10249.C001.07SS, 10249.C001.08SS, 10249.C001.09SS, 10249.C001.10SS, 10249.C001.11SS, 10249.C001.12SS, 10249.C001.13SS, 10249.C001.14SS, 10249.C001.15SS, 10249.C001.16SS, 10249.C001.17SS, 10249.C001.18SS, 10249.C001.19SS, 10249.C001.20SS, 10249.C001.25SS, 10249.C001.26SS, 10249.C001.27SS, 10249.C001.29SS, 10249.C001.30SS, 10249.C001.31SS, 10249.C001.32SS, 10249.C001.34SD, 10249.C001.34SS, 10249.C001.35SS, 10249.C001.36SD, 10249.C001.36SS, 10249.C002.02SS, 10249.C002.03SS, 10249.C002.04SS, 10249.C002.05SS, 10249.C002.06SS, 10249.C002.07SS, 10249.C002.08SS, 10249.C002.09SS, 10249.C002.10SS, 10249.C002.11SS, 10249.C002.12SS, 10249.C002.13SS, 10249.C002.15SS, 10249.C002.16SS, 10249.C002.18SS, 10249.C002.19SD, 10249.C002.19SS, 10249.C002.20SS, 10249.C002.21SD, 10249.C002.21SS, 10249.C004.02SS, 10249.C004.03SS, 10249.C004.04SS, 10249.C004.05SS, 10249.C004.06SS, 10249.C004.07SS, 10249.C004.08SS, 10249.C004.09SS, 10249.C004.10SS, 10249.C004.11SS, 10249.C004.12SS, 10249.C004.13SS, 10249.C004.14SS, 10249.C004.15SS, 10249.C005.02SS, 10249.C005.03SS, 10249.C005.04SS, 10249.C005.05SS, 10249.C005.07SS, 10249.C005.08SS, 10249.C005.09SS, 10249.C005.10SS, 10249.C005.11SS, 10249.C005.12SS, 10249.C005.13SS, 10249.C005.14SS, 10249.C005.15SS, 10249.C005.16SS, 10249.C005.17SS, 10249.C005.18SS, 10249.C005.19SD, 10249.C005.19SS, 10249.C005.20SS, 10249.C005.21SD, 10249.C005.21SS, 10249.C005.22SS, 10249.C007.02SS, 10249.C007.03SS, 10249.C007.04SS, 10249.C007.05SS, 10249.C007.06SS, 10249.C007.07SS, 10249.C007.08SS, 10249.C007.09SS, 10249.C007.10SS, 10249.C007.11SS, 10249.C007.12SS, 10249.C007.13SS, 10249.C007.14SS, 10249.C007.15SS, 10249.C007.16SS, 10249.C007.17SS, 10249.C007.18SS, 10249.C007.19SS, 10249.C007.20SS, 10249.C007.21SS, 10249.C007.22SD, 10249.C007.22SS, 10249.C007.23SD, 10249.C007.23SS, 10249.C007.24SD, 10249.C007.24SS, 10249.C007.26SS, 10249.C008.02SS, 10249.C008.03SS, 10249.C008.04SS, 10249.C008.05SS, 10249.C008.06SS, 10249.C008.07SS, 10249.C008.08SS, 10249.C008.09SS, 10249.C008.10SS, 10249.C008.11SS, 10249.C008.12SS, 10249.C008.13SS, 10249.C008.14SS, 10249.C008.15SS, 10249.C008.16SD, 10249.C008.16SS, 10249.C008.18SS, 10249.C009.02SS, 10249.C009.03SS, 10249.C009.04SS, 10249.C009.05SS, 10249.C009.06SS, 10249.C009.07SS, 10249.C009.08SS, 10249.C009.09SS, 10249.C009.10SS, 10249.C009.11SS, 10249.C009.12SS, 10249.C009.13SS, 10249.C009.14SS, 10249.C009.16SS, 10249.C009.17SS, 10249.C009.18SD, 10249.C009.18SS, 10249.C009.19SS, 10249.C009.20SD, 10249.C009.20SS, 10249.C009.21SS, 10249.C010.02SS, 10249.C010.03SS, 10249.C010.04SS, 10249.C010.05SS, 10249.C010.06SS, 10249.C010.07SS, 10249.C010.08SS, 10249.C010.09SS, 10249.C010.10SS, 10249.C010.11SS, 10249.C010.12SS, 10249.C010.13SS, 10249.C010.14SS, 10249.C010.15SS, 10249.C010.16SS, 10249.C010.18SD, 10249.C010.18SS, 10249.C010.19SS, 10249.C010.20SD, 10249.C010.20SS, 10249.C010.21SS, 10249.C011.02SS, 10249.C011.03SS, 10249.C011.04SS, 10249.C011.05SS, 10249.C011.06SS, 10249.C011.07SS, 10249.C011.08SS, 10249.C011.09SS, 10249.C011.10SS, 10249.C011.11SS, 10249.C011.12SS, 10249.C011.13SD, 10249.C011.14SS, 10249.C011.16SS, 10249.C011.17SD, 10249.C011.17SS, 10249.C011.18SS, 10249.C011.19SD, 10249.C011.19SS, 10249.C011.20SS, 10249.C011.21SS, 10249.C012.02SS, 10249.C012.03SS, 10249.C012.04SS, 10249.C012.05SS, 10249.C012.06SS, 10249.C012.07SS, 10249.C012.08SS, 10249.C012.09SS, 10249.C012.10SS, 10249.C012.11SS, 10249.C012.12SS, 10249.C012.13SS, 10249.C012.14SS, 10249.C012.15SS, 10249.C012.16SS, 10249.C012.17SS, 10249.C012.18SS, 10249.C012.19SD, 10249.C012.19SS, 10249.C012.20SS, 10249.C012.21SD, 10249.C012.21SS, 10249.C012.22SD, 10249.C012.22SS, 10249.C014.02SS, 10249.C014.03SS, 10249.C014.04SS, 10249.C014.05SS, 10249.C014.06SS, 10249.C014.07SS, 10249.C014.08SS, 10249.C014.09SS, 10249.C014.10SS, 10249.C014.12SS, 10249.C014.13SS, 10249.C014.15SS, 10249.C014.16SS, 10249.C014.17SS, 10249.C014.18SS, 10249.C014.19SD, 10249.C014.19SS, 10249.C014.20SD, 10249.C014.20SS, 10249.C014.21SS, 10249.C014.22SS, 10249.C016.03SS, 10249.C016.04SS, 10249.C016.05SS, 10249.C016.06SS, 10249.C016.07SS, 10249.C016.08SS, 10249.C016.09SS, 10249.C016.10SS, 10249.C016.11SS, 10249.C016.12SS, 10249.C016.13SS, 10249.C016.14SS, 10249.C016.15SS, 10249.C016.17SS, 10249.C016.18SS, 10249.C016.19SS, 10249.C016.20SS, 10249.C016.21SD, 10249.C016.21SS, 10249.C016.22SD, 10249.C016.22SS, 10249.C016.23SS, 10249.C016.24SS, 10249.C017.04SS, 10249.C017.05SS, 10249.C017.06SS, 10249.C017.07SS, 10249.C017.08SS, 10249.C017.09SS, 10249.C017.10SS, 10249.C017.11SS, 10249.C017.12SS, 10249.C018.02SS, 10249.C018.03SS, 10249.C018.04SS, 10249.C018.05SS, 10249.C018.06SS, 10249.C018.07SS, 10249.C018.08SS, 10249.C018.09SS, 10249.C018.10SS, 10249.C018.11SD, 10249.C018.11SS, 10249.C018.12SD, 10249.C018.12SS, 10249.C018.13SS, 10249.C018.14SS, 10249.C018.15SS, 10249.C018.16SS, 10249.C018.17SS, 10249.C018.18SS, 10249.C018.19SS, 10249.C020.06SS, 10249.C020.07SS, 10249.C020.08SS, 10249.C020.09SS, 10249.C020.10SS, 10249.C020.11SS, 10249.C020.12SS, 10249.C020.13SS, 10249.C020.14SS, 10249.C020.15SS, 10249.C020.16SS, 10249.C020.17SS, 10249.C020.18SS, 10249.C020.19SS, 10249.C020.20SS, 10249.C020.21SS, 10249.C020.22SD, 10249.C020.22SS, 10249.C020.23SD, 10249.C020.23SS, 10249.C020.24SD, 10249.C020.24SS, 10249.C020.25SD, 10249.C020.25SS, 10249.C020.26SD, 10249.C020.26SS, 10249.C020.28SS, 10249.C020.29SS, 10249.C021.03SS, 10249.C021.04SS, 10249.C021.05SS, 10249.C021.06SS, 10249.C021.07SS, 10249.C021.08SS, 10249.C021.09SS, 10249.C021.10SS, 10249.C021.12SS, 10249.C021.13SS, 10249.C022.02SS, 10249.C022.03SS, 10249.C022.04SS, 10249.C022.05SS, 10249.C022.06SS, 10249.C022.07SS, 10249.C022.08SS, 10249.C022.09SS, 10249.C022.10SS, 10249.C022.11SS, 10249.C022.12SS, 10249.C022.13SS, 10249.C022.15SS, 10249.C022.16SS, 10249.C022.18SD, 10249.C022.18SS, 10249.C022.19SS, 10249.C022.20SS, 10249.C022.21SS, 10249.C024.02SS, 10249.C024.03SS, 10249.C024.04SS, 10249.C024.05SS, 10249.C024.06SS, 10249.C024.07SS, 10249.C024.08SS, 10249.C024.09SS, 10249.C024.10SS, 10249.C024.12SS, 10249.C024.13SS, 10249.C024.14SS, 10249.C024.15SS, 10249.C024.16SS, 10249.C024.17SS, 10249.C024.18SS, 10249.C024.19SD, 10249.C024.19SS, 10249.C024.20SD, 10249.C024.20SS, 10249.C024.21SS, 10249.C024.22SS, 10249.C025.02SS, 10249.C025.03SS, 10249.C025.04SS, 10249.C025.05SS, 10249.C025.06SS, 10249.C025.07SS, 10249.C025.08SS, 10249.C025.09SS, 10249.C025.10SS, 10249.C025.11SS, 10249.C025.12SS, 10249.C025.13SD, 10249.C025.13SS, 10249.C025.14SD, 10249.C025.14SS, 10249.C025.15SS, 10249.C025.16SS, 10249.C025.17SS, 10249.C025.18SS, 10249.C025.19SD, 10249.C025.19SS, 10249.C025.20SS, 10249.C025.21SS, 10249.C027.02SS, 10249.C027.03SS, 10249.C027.04SS, 10249.C027.05SS, 10249.C027.06SS, 10249.C027.07SS, 10249.C027.08SS, 10249.C027.09SS, 10249.C027.10SS, 10249.C027.11SD, 10249.C027.12SD, 10249.C027.12SS, 10249.C027.13SS, 10249.C027.14SS, 10249.C027.15SS, 10249.C027.16SS, 10249.C027.17SD, 10249.C027.17SS, 10249.C027.18SS, 10249.C027.19SD, 10249.C027.19SS, 10249.C027.20SD, 10249.C027.20SS, 10249.C027.21SS, 10249.C027.22SS, 10249.C030.02SS, 10249.C030.03SS, 10249.C030.04SS, 10249.C030.05SS, 10249.C030.06SS, 10249.C030.07SS, 10249.C030.08SS, 10249.C030.09SS, 10249.C030.10SS, 10249.C030.11SD, 10249.C030.11SS, 10249.C030.12SS, 10249.C030.13SS, 10249.C030.14SS, 10249.C030.16SS, 10249.C030.17SD, 10249.C030.17SS, 10249.C030.18SS, 10249.C030.19SD, 10249.C030.19SS, 10249.C030.20SS, 10249.C031.02SS, 10249.C031.03SS, 10249.C031.04SS, 10249.C031.05SS, 10249.C031.06SS, 10249.C031.07SS, 10249.C031.08SS, 10249.C031.09SS, 10249.C031.10SS, 10249.C031.11SD, 10249.C031.11SS, 10249.C031.12SS, 10249.C031.13SS, 10249.C031.14SS, 10249.C031.16SS, 10249.C031.17SD, 10249.C031.17SS, 10249.C031.18SS, 10249.C031.19SD, 10249.C031.19SS, 10249.C031.20SS, 10249.C031.21SS, 10249.C032.02SS, 10249.C032.03SS, 10249.C032.04SS, 10249.C032.05SS, 10249.C032.06SS, 10249.C032.07SS, 10249.C032.09SS, 10249.C032.10SS, 10249.C032.11SD, 10249.C032.11SS, 10249.C032.12SD, 10249.C032.13SS, 10249.C032.14SS, 10249.C032.15SS, 10249.C032.16SS, 10249.C032.17SS, 10249.C032.19SD, 10249.C032.19SS, 10249.C032.20SD, 10249.C032.20SS, 10249.C032.21SS, 10249.C032.22SS, 10249.C033.02SS, 10249.C033.03SS, 10249.C033.04SS, 10249.C033.05SS, 10249.C033.06SS, 10249.C033.07SS, 10249.C033.08SS, 10249.C033.09SD, 10249.C033.09SS, 10249.C033.10SD, 10249.C033.10SS, 10249.C033.11SD, 10249.C033.11SS, 10249.C033.12SS, 10249.C033.13SS, 10249.C033.14SS, 10249.C033.15SS, 10249.C033.16SS, 10249.C033.17SD, 10249.C033.17SS, 10249.C033.18SD, 10249.C033.18SS, 10249.C033.19SS, 10249.C034.02SS, 10249.C034.03SS, 10249.C034.04SS, 10249.C034.05SS, 10249.C034.06SS, 10249.C034.07SS, 10249.C034.08SS, 10249.C034.09SS, 10249.C034.10SS, 10249.C034.11SS, 10249.C034.12SS, 10249.C034.13SS, 10249.C034.14SS, 10249.C034.15SD, 10249.C034.15SS, 10249.C034.16SS, 10249.C034.17SD, 10249.C034.17SS, 10249.C035.02SS, 10249.C035.03SS, 10249.C035.04SS, 10249.C035.05SS, 10249.C035.06SD, 10249.C035.06SS, 10249.C035.07SD, 10249.C035.07SS, 10249.C035.08SS, 10249.C035.09SS, 10249.C035.10SS, 10249.C035.11SS, 10249.C035.12SD, 10249.C035.12SS, 10249.C035.13SD, 10249.C035.13SS, 10249.C035.14SD, 10249.C035.14SS, 10249.C035.15SD, 10249.C035.15SS, 10249.C035.16SS, 10249.C035.17SS, 10249.C036.02SS, 10249.C036.03SS, 10249.C036.04SS, 10249.C036.05SD, 10249.C036.05SS, 10249.C036.07SS, 10249.C036.08SS, 10249.C036.09SS, 10249.C036.10SS, 10249.C036.11SS, 10249.C036.12SS, 10249.C036.13SS, 10249.C036.14SD, 10249.C036.14SS, 10249.C036.15SS, 10249.C036.16SS, 10249.C037.02SS, 10249.C037.04SS, 10249.C037.05SS, 10249.C037.06SS, 10249.C037.07SS, 10249.C037.08SS, 10249.C037.09SS, 10249.C037.10SS, 10249.C037.11SS, 10249.C037.12SD, 10249.C037.12SS, 10249.C037.13SD, 10249.C037.13SS, 10249.C037.14SS, 10249.C037.15SS, 10249.C037.16SS, 10249.C037.17SS, 10249.C037.18SS, 10249.C038.02SS, 10249.C038.04SS, 10249.C038.05SD, 10249.C038.05SS, 10249.C038.06SD, 10249.C038.06SS, 10249.C038.07SD, 10249.C038.07SS, 10249.C038.08SS, 10249.C038.09SS, 10249.C038.10SS, 10249.C038.11SS, 10249.C038.12SD, 10249.C038.12SS, 10249.C038.13SD, 10249.C038.13SS, 10249.C038.14SS, 10249.C038.15SD, 10249.C038.15SS, 10249.C038.16SD, 10249.C038.16SS, 10249.C038.18SS, 10249.C041.02SS, 10249.C041.03SS, 10249.C041.04SS, 10249.C041.05SD, 10249.C041.05SS, 10249.C041.06SD, 10249.C041.06SS, 10249.C041.08SS, 10249.C041.09SS, 10249.C041.10SS, 10249.C041.11SS, 10249.C041.12SS, 10249.C041.13SD, 10249.C041.13SS, 10249.C041.14SD, 10249.C041.14SS, 10249.C041.16SD, 10249.C041.16SS, 10249.C041.17SD, 10249.C041.17SS, 10249.C041.18SS, 10249.C041.19SS, 10249.C042.02SS, 10249.C042.03SS, 10249.C042.04SS, 10249.C042.05SS, 10249.C042.06SD, 10249.C042.06SS, 10249.C042.07SS, 10249.C042.08SS, 10249.C042.09SS, 10249.C042.10SS, 10249.C042.11SD, 10249.C042.11SS, 10249.C042.12SS, 10249.C042.13SS, 10249.C042.14SD, 10249.C042.14SS, 10249.C042.15SD, 10249.C042.15SS, 10249.C042.16SS, 10249.C042.17SS, 10249.C043.02SS, 10249.C043.03SS, 10249.C043.04SD, 10249.C043.04SS, 10249.C043.05SD, 10249.C043.05SS, 10249.C043.06SS, 10249.C043.07SS, 10249.C043.08SS, 10249.C043.09SS, 10249.C043.10SD, 10249.C043.10SS, 10249.C043.11SD, 10249.C043.11SS, 10249.C043.12SD, 10249.C043.12SS, 10249.C043.14SS, 10249.C043.15SD, 10249.C043.15SS, 10249.C043.16SS, 10249.C043.17SS, 10249.C043.18SS, 10249.C043.20SS, 10249.C044.02SS, 10249.C044.03SS, 10249.C044.04SS, 10249.C044.05SS, 10249.C044.06SS, 10249.C044.07SS, 10249.C044.08SS, 10249.C044.09SS, 10249.C044.10SS, 10249.C044.11SS, 10249.C044.12SD, 10249.C044.12SS, 10249.C044.13SD, 10249.C044.13SS, 10249.C044.15SD, 10249.C044.15SS, 10249.C044.16SS, 10249.C044.17SS, 10249.C045.02SS, 10249.C045.03SS, 10249.C045.04SS, 10249.C045.05SD, 10249.C045.05SS, 10249.C045.06SS, 10249.C045.08SD, 10249.C045.08SS, 10249.C045.09SD, 10249.C045.09SS, 10249.C045.10SD, 10249.C045.10SS, 10249.C045.11SS, 10249.C045.12SS, 10249.C045.13SS, 10249.C046.02SS, 10249.C046.03SS, 10249.C046.04SS, 10249.C046.05SS, 10249.C046.06SD, 10249.C046.06SS, 10249.C046.07SD, 10249.C046.07SS, 10249.C046.08SS, 10249.C046.09SD, 10249.C046.09SS, 10249.C046.10SD, 10249.C046.10SS, 10249.C046.11SD, 10249.C046.11SS, 10249.C046.12SS, 10249.C046.13SS, 10249.C046.14SS, 10249.C047.02SD, 10249.C047.02SS, 10249.C047.05SS, 10249.C047.06SD, 10249.C047.06SS, 10249.C047.07SD, 10249.C047.07SS, 10249.C047.08SD, 10249.C047.08SS, 10249.C047.09SS, 10249.C047.10SS, 10249.C047.11SS, 10249.C047.13SS, 10249.C049.03SD, 10249.C049.03SS, 10249.C049.04SS, 10249.C049.07SD, 10249.C049.07SS, 10249.C049.08SD, 10249.C049.08SS, 10249.C049.09SD, 10249.C049.09SS, 10249.C049.10SS, 10249.C049.11SS, 10249.C049.12SS, 10249.C049.13SS, 10249.C049.14SS, 10249.C052.03SD, 10249.C052.03SS, 10249.C052.04SD, 10249.C052.04SS, 10249.C052.05SD, 10249.C052.06SS, 10249.C052.07SS, 10249.C052.08SS, 10249.C052.09SS, 10249.C053.02SD, 10249.C053.02SS, 10249.C053.03SD, 10249.C053.03SS, 10249.C053.04SD, 10249.C053.04SS, 10249.C053.05SD, 10249.C053.05SS, 10249.C053.06SS, 10249.C053.07SS, 10249.C053.08SS, 10249.C053.09SS, 10249.C055.02SD, 10249.C055.02SS, 10249.C055.03SD, 10249.C055.03SS, 10249.C055.04SD, 10249.C055.04SS, 10249.C055.05SD, 10249.C055.05SS, 10249.C055.06SS, 10249.C055.07SS, 10249.C055.08SS, 10249.C055.09SS, 10249.C056.03SD, 10249.C056.03SS, 10249.C056.04SD, 10249.C056.04SS, 10249.C056.05SD, 10249.C056.05SS, 10249.C056.06SS, 10249.C056.07SS, 10249.C056.08SS, 10249.C056.09SS, 10249.C056.10SS, 10249.C057.02SS, 10249.C057.03SD, 10249.C057.03SS, 10249.C057.04SD, 10249.C057.04SS, 10249.C057.05SD, 10249.C057.05SS, 10249.C057.06SS, 10249.C057.08SS, 10249.C057.09SS, 10249.C057.10SS, 10249.C057.11SS
#> Updated feature table to match the subsetted data.
#> Updated feature annotation to match the subsetted data.
#> Data subsetting complete. Returning updated data object.
#> $Phylum
#> $Phylum$Phylum
#> $Phylum$Phylum$p__Actinobacteria

#> 
#> $Phylum$Phylum$p__Bacteroidetes

#> 
#> $Phylum$Phylum$p__Firmicutes

#> 
#> $Phylum$Phylum$p__Proteobacteria

#> 
#> 
#> 
#> $Family
#> $Family$Family
#> $Family$Family$f__Bacteroidaceae

#> 
#> $Family$Family$f__Bifidobacteriaceae

#> 
#> $Family$Family$f__Clostridiaceae

#> 
#> $Family$Family$f__Enterobacteriaceae

#> 
#> $Family$Family$f__Erysipelotrichaceae

#> 
#> $Family$Family$f__Lachnospiraceae

#> 
#> $Family$Family$f__Pseudomonadaceae

#> 
#> $Family$Family$f__Ruminococcaceae

#> 
#> $Family$Family$f__Staphylococcaceae

#> 
#> $Family$Family$f__Streptococcaceae

#> 
#> $Family$Family$f__Veillonellaceae

#> 
#> 
#> 
#> $Genus
#> $Genus$Genus
#> $Genus$Genus$`__`

#> 
#> $Genus$Genus$g__

#> 
#> $Genus$Genus$g__Bacteroides

#> 
#> $Genus$Genus$g__Bifidobacterium

#> 
#> $Genus$Genus$g__Clostridium

#> 
#> $Genus$Genus$g__Faecalibacterium

#> 
#> $Genus$Genus$g__Pseudomonas

#> 
#> $Genus$Genus$g__Staphylococcus

#> 
#> $Genus$Genus$g__Streptococcus

#> 
#> $Genus$Genus$g__Veillonella

#> 
#> $Genus$Genus$`g__[Ruminococcus]`

#> 
#> 
#> 

data(peerj32.obj)
plot_feature_diversity(
data.obj = peerj32.obj,
group.var = "group",
strata.var = "sex",
subject.var = "subject",
time.var = "time",
time.point.plot = c("1", "2"),
is.plot.change = TRUE,
feature.change.func = "relative change",
feature.level = c("Phylum", "Family", "Genus"),
prop.to.lump = 0.0001,
top.k.plot = NULL,
top.k.func = NULL,
renormalize = FALSE,
plot.other = TRUE,
plot.scheme = "combined",
plot.type = "boxplot"
)
#> Rule 1 passed: data.obj is a list.
#> Rule 2 passed: meta.dat is a data.frame.
#> Rule 3 passed: The row names of feature.tab match the row names of feature.ann.
#> Rule 4 passed: The column names of feature.tab match the row names of meta.dat.
#> Rule 5 passed: feature.tab is a matrix.
#> Rule 6 passed: feature.ann is a matrix.
#> Please note: The data components should follow base R data.frame and matrix structures, not phyloseq's formal class.
#> Validation passed.
#> Note: Passing validation does not guarantee the absence of all data issues. Further data exploration may be needed.
#> Your data is in raw format ('Raw'). Normalization is crucial for further analyses. Now, 'mStat_normalize_data' function is automatically applying 'Rarefy-TSS' transformation.
#> Data has been successfully normalized using TSS method.
#> Rule 1 passed: data.obj is a list.
#> Rule 2 passed: meta.dat is a data.frame.
#> Rule 3 passed: The row names of feature.tab match the row names of feature.ann.
#> Rule 4 passed: The column names of feature.tab match the row names of meta.dat.
#> Rule 5 passed: feature.tab is a matrix.
#> Rule 6 passed: feature.ann is a matrix.
#> Please note: The data components should follow base R data.frame and matrix structures, not phyloseq's formal class.
#> Validation passed.
#> Note: Passing validation does not guarantee the absence of all data issues. Further data exploration may be needed.
#> Your data is in raw format ('Raw'). Normalization is crucial for further analyses. Now, 'mStat_normalize_data' function is automatically applying 'Rarefy-TSS' transformation.
#> Data has been successfully normalized using TSS method.
#> Rule 1 passed: data.obj is a list.
#> Rule 2 passed: meta.dat is a data.frame.
#> Rule 3 passed: The row names of feature.tab match the row names of feature.ann.
#> Rule 4 passed: The column names of feature.tab match the row names of meta.dat.
#> Rule 5 passed: feature.tab is a matrix.
#> Rule 6 passed: feature.ann is a matrix.
#> Please note: The data components should follow base R data.frame and matrix structures, not phyloseq's formal class.
#> Validation passed.
#> Note: Passing validation does not guarantee the absence of all data issues. Further data exploration may be needed.
#> Your data is in raw format ('Raw'). Normalization is crucial for further analyses. Now, 'mStat_normalize_data' function is automatically applying 'Rarefy-TSS' transformation.
#> Data has been successfully normalized using TSS method.
#> $Phylum
#> $Phylum$Phylum

#> 
#> 
#> $Family
#> $Family$Family

#> 
#> 
#> $Genus
#> $Genus$Genus

#> 
#> 

plot_feature_diversity(
data.obj = peerj32.obj,
group.var = "group",
strata.var = "sex",
subject.var = "subject",
time.var = "time",
time.point.plot = c("1", "2"),
is.plot.change = TRUE,
feature.change.func = "relative change",
feature.level = c("Phylum", "Family", "Genus"),
prop.to.lump = 0.0001,
top.k.plot = NULL,
top.k.func = NULL,
renormalize = FALSE,
plot.other = TRUE,
plot.scheme = "individual",
plot.type = "boxplot"
)
#> Rule 1 passed: data.obj is a list.
#> Rule 2 passed: meta.dat is a data.frame.
#> Rule 3 passed: The row names of feature.tab match the row names of feature.ann.
#> Rule 4 passed: The column names of feature.tab match the row names of meta.dat.
#> Rule 5 passed: feature.tab is a matrix.
#> Rule 6 passed: feature.ann is a matrix.
#> Please note: The data components should follow base R data.frame and matrix structures, not phyloseq's formal class.
#> Validation passed.
#> Note: Passing validation does not guarantee the absence of all data issues. Further data exploration may be needed.
#> Your data is in raw format ('Raw'). Normalization is crucial for further analyses. Now, 'mStat_normalize_data' function is automatically applying 'Rarefy-TSS' transformation.
#> Data has been successfully normalized using TSS method.
#> Rule 1 passed: data.obj is a list.
#> Rule 2 passed: meta.dat is a data.frame.
#> Rule 3 passed: The row names of feature.tab match the row names of feature.ann.
#> Rule 4 passed: The column names of feature.tab match the row names of meta.dat.
#> Rule 5 passed: feature.tab is a matrix.
#> Rule 6 passed: feature.ann is a matrix.
#> Please note: The data components should follow base R data.frame and matrix structures, not phyloseq's formal class.
#> Validation passed.
#> Note: Passing validation does not guarantee the absence of all data issues. Further data exploration may be needed.
#> Your data is in raw format ('Raw'). Normalization is crucial for further analyses. Now, 'mStat_normalize_data' function is automatically applying 'Rarefy-TSS' transformation.
#> Data has been successfully normalized using TSS method.
#> Rule 1 passed: data.obj is a list.
#> Rule 2 passed: meta.dat is a data.frame.
#> Rule 3 passed: The row names of feature.tab match the row names of feature.ann.
#> Rule 4 passed: The column names of feature.tab match the row names of meta.dat.
#> Rule 5 passed: feature.tab is a matrix.
#> Rule 6 passed: feature.ann is a matrix.
#> Please note: The data components should follow base R data.frame and matrix structures, not phyloseq's formal class.
#> Validation passed.
#> Note: Passing validation does not guarantee the absence of all data issues. Further data exploration may be needed.
#> Your data is in raw format ('Raw'). Normalization is crucial for further analyses. Now, 'mStat_normalize_data' function is automatically applying 'Rarefy-TSS' transformation.
#> Data has been successfully normalized using TSS method.
#> $Phylum
#> $Phylum$Phylum
#> $Phylum$Phylum$Actinobacteria

#> 
#> $Phylum$Phylum$Bacteroidetes

#> 
#> $Phylum$Phylum$Firmicutes

#> 
#> $Phylum$Phylum$Proteobacteria

#> 
#> $Phylum$Phylum$Verrucomicrobia

#> 
#> 
#> 
#> $Family
#> $Family$Family
#> $Family$Family$Actinobacteria

#> 
#> $Family$Family$Bacilli

#> 
#> $Family$Family$Bacteroidetes

#> 
#> $Family$Family$`Clostridium cluster IV`

#> 
#> $Family$Family$`Clostridium cluster XIVa`

#> 
#> $Family$Family$Proteobacteria

#> 
#> $Family$Family$Verrucomicrobia

#> 
#> 
#> 
#> $Genus
#> $Genus$Genus
#> $Genus$Genus$Akkermansia

#> 
#> $Genus$Genus$`Anaerostipes caccae et rel.`

#> 
#> $Genus$Genus$`Bacteroides intestinalis et rel.`

#> 
#> $Genus$Genus$`Bacteroides uniformis et rel.`

#> 
#> $Genus$Genus$`Bacteroides vulgatus et rel.`

#> 
#> $Genus$Genus$Bifidobacterium

#> 
#> $Genus$Genus$`Bryantella formatexigens et rel.`

#> 
#> $Genus$Genus$`Clostridium leptum et rel.`

#> 
#> $Genus$Genus$`Clostridium nexile et rel.`

#> 
#> $Genus$Genus$`Clostridium sphenoides et rel.`

#> 
#> $Genus$Genus$`Clostridium symbiosum et rel.`

#> 
#> $Genus$Genus$`Coprococcus eutactus et rel.`

#> 
#> $Genus$Genus$`Dorea formicigenerans et rel.`

#> 
#> $Genus$Genus$`Eubacterium hallii et rel.`

#> 
#> $Genus$Genus$`Eubacterium rectale et rel.`

#> 
#> $Genus$Genus$`Eubacterium ventriosum et rel.`

#> 
#> $Genus$Genus$`Faecalibacterium prausnitzii et rel.`

#> 
#> $Genus$Genus$`Lachnobacillus bovis et rel.`

#> 
#> $Genus$Genus$`Lachnospira pectinoschiza et rel.`

#> 
#> $Genus$Genus$`Oscillospira guillermondii et rel.`

#> 
#> $Genus$Genus$`Outgrouping clostridium cluster XIVa`

#> 
#> $Genus$Genus$`Papillibacter cinnamivorans et rel.`

#> 
#> $Genus$Genus$`Roseburia intestinalis et rel.`

#> 
#> $Genus$Genus$`Ruminococcus bromii et rel.`

#> 
#> $Genus$Genus$`Ruminococcus gnavus et rel.`

#> 
#> $Genus$Genus$`Ruminococcus lactaris et rel.`

#> 
#> $Genus$Genus$`Ruminococcus obeum et rel.`

#> 
#> $Genus$Genus$`Streptococcus bovis et rel.`

#> 
#> $Genus$Genus$`Streptococcus mitis et rel.`

#> 
#> $Genus$Genus$`Subdoligranulum variable at rel.`

#> 
#> 
#> 

plot_feature_diversity(
data.obj = peerj32.obj,
group.var = "group",
strata.var = "sex",
subject.var = "subject",
time.var = "time",
time.point.plot = c("1", "2"),
is.plot.change = TRUE,
feature.change.func = "relative change",
feature.level = c("Phylum", "Family", "Genus"),
prop.to.lump = 0.0001,
top.k.plot = NULL,
top.k.func = NULL,
renormalize = FALSE,
plot.other = TRUE,
plot.scheme = "combined",
plot.type = "heatmap"
)
#> Rule 1 passed: data.obj is a list.
#> Rule 2 passed: meta.dat is a data.frame.
#> Rule 3 passed: The row names of feature.tab match the row names of feature.ann.
#> Rule 4 passed: The column names of feature.tab match the row names of meta.dat.
#> Rule 5 passed: feature.tab is a matrix.
#> Rule 6 passed: feature.ann is a matrix.
#> Please note: The data components should follow base R data.frame and matrix structures, not phyloseq's formal class.
#> Validation passed.
#> Note: Passing validation does not guarantee the absence of all data issues. Further data exploration may be needed.
#> Your data is in raw format ('Raw'). Normalization is crucial for further analyses. Now, 'mStat_normalize_data' function is automatically applying 'TSS' transformation.
#> Data has been successfully normalized using TSS method.
#> Rule 1 passed: data.obj is a list.
#> Rule 2 passed: meta.dat is a data.frame.
#> Rule 3 passed: The row names of feature.tab match the row names of feature.ann.
#> Rule 4 passed: The column names of feature.tab match the row names of meta.dat.
#> Rule 5 passed: feature.tab is a matrix.
#> Rule 6 passed: feature.ann is a matrix.
#> Please note: The data components should follow base R data.frame and matrix structures, not phyloseq's formal class.
#> Validation passed.
#> Note: Passing validation does not guarantee the absence of all data issues. Further data exploration may be needed.
#> Your data is in raw format ('Raw'). Normalization is crucial for further analyses. Now, 'mStat_normalize_data' function is automatically applying 'TSS' transformation.
#> Data has been successfully normalized using TSS method.
#> Rule 1 passed: data.obj is a list.
#> Rule 2 passed: meta.dat is a data.frame.
#> Rule 3 passed: The row names of feature.tab match the row names of feature.ann.
#> Rule 4 passed: The column names of feature.tab match the row names of meta.dat.
#> Rule 5 passed: feature.tab is a matrix.
#> Rule 6 passed: feature.ann is a matrix.
#> Please note: The data components should follow base R data.frame and matrix structures, not phyloseq's formal class.
#> Validation passed.
#> Note: Passing validation does not guarantee the absence of all data issues. Further data exploration may be needed.
#> Your data is in raw format ('Raw'). Normalization is crucial for further analyses. Now, 'mStat_normalize_data' function is automatically applying 'TSS' transformation.
#> Data has been successfully normalized using TSS method.
#> $Phylum
#> $Phylum$Phylum
#> $Phylum$Phylum$average

#> 
#> $Phylum$Phylum$indiv

#> 
#> 
#> 
#> $Family
#> $Family$Family
#> $Family$Family$average

#> 
#> $Family$Family$indiv

#> 
#> 
#> 
#> $Genus
#> $Genus$Genus
#> $Genus$Genus$average

#> 
#> $Genus$Genus$indiv

#> 
#> 
#> 

plot_feature_diversity(
data.obj = peerj32.obj,
group.var = "group",
strata.var = "sex",
subject.var = "subject",
time.var = "time",
time.point.plot = c("1", "2"),
is.plot.change = FALSE,
feature.change.func = "relative change",
feature.level = c("Phylum", "Family", "Genus"),
prop.to.lump = 0.0001,
top.k.plot = NULL,
top.k.func = NULL,
renormalize = FALSE,
plot.other = TRUE,
plot.scheme = 'combined',
plot.type = "heatmap"
)
#> Rule 1 passed: data.obj is a list.
#> Rule 2 passed: meta.dat is a data.frame.
#> Rule 3 passed: The row names of feature.tab match the row names of feature.ann.
#> Rule 4 passed: The column names of feature.tab match the row names of meta.dat.
#> Rule 5 passed: feature.tab is a matrix.
#> Rule 6 passed: feature.ann is a matrix.
#> Please note: The data components should follow base R data.frame and matrix structures, not phyloseq's formal class.
#> Validation passed.
#> Note: Passing validation does not guarantee the absence of all data issues. Further data exploration may be needed.
#> Your data is in raw format ('Raw'). Normalization is crucial for further analyses. Now, 'mStat_normalize_data' function is automatically applying 'Rarefy-TSS' transformation.
#> Data has been successfully normalized using TSS method.
#> Rule 1 passed: data.obj is a list.
#> Rule 2 passed: meta.dat is a data.frame.
#> Rule 3 passed: The row names of feature.tab match the row names of feature.ann.
#> Rule 4 passed: The column names of feature.tab match the row names of meta.dat.
#> Rule 5 passed: feature.tab is a matrix.
#> Rule 6 passed: feature.ann is a matrix.
#> Please note: The data components should follow base R data.frame and matrix structures, not phyloseq's formal class.
#> Validation passed.
#> Note: Passing validation does not guarantee the absence of all data issues. Further data exploration may be needed.
#> Your data is in raw format ('Raw'). Normalization is crucial for further analyses. Now, 'mStat_normalize_data' function is automatically applying 'Rarefy-TSS' transformation.
#> Data has been successfully normalized using TSS method.
#> Rule 1 passed: data.obj is a list.
#> Rule 2 passed: meta.dat is a data.frame.
#> Rule 3 passed: The row names of feature.tab match the row names of feature.ann.
#> Rule 4 passed: The column names of feature.tab match the row names of meta.dat.
#> Rule 5 passed: feature.tab is a matrix.
#> Rule 6 passed: feature.ann is a matrix.
#> Please note: The data components should follow base R data.frame and matrix structures, not phyloseq's formal class.
#> Validation passed.
#> Note: Passing validation does not guarantee the absence of all data issues. Further data exploration may be needed.
#> Your data is in raw format ('Raw'). Normalization is crucial for further analyses. Now, 'mStat_normalize_data' function is automatically applying 'Rarefy-TSS' transformation.
#> Data has been successfully normalized using TSS method.
#> $Phylum
#> $Phylum$Phylum
#> $Phylum$Phylum$indiv

#> 
#> $Phylum$Phylum$average

#> 
#> 
#> 
#> $Family
#> $Family$Family
#> $Family$Family$indiv

#> 
#> $Family$Family$average

#> 
#> 
#> 
#> $Genus
#> $Genus$Genus
#> $Genus$Genus$indiv

#> 
#> $Genus$Genus$average

#> 
#> 
#> 

plot_feature_diversity(
data.obj = peerj32.obj,
group.var = "group",
strata.var = "sex",
subject.var = "subject",
time.var = "time",
time.point.plot = c("1", "2"),
is.plot.change = FALSE,
feature.level = c("Phylum", "Family", "Genus"),
prop.to.lump = 0.0001,
top.k.plot = NULL,
top.k.func = NULL,
renormalize = FALSE,
plot.other = TRUE,
plot.scheme = 'individual',
plot.type = "boxplot"
)
#> Rule 1 passed: data.obj is a list.
#> Rule 2 passed: meta.dat is a data.frame.
#> Rule 3 passed: The row names of feature.tab match the row names of feature.ann.
#> Rule 4 passed: The column names of feature.tab match the row names of meta.dat.
#> Rule 5 passed: feature.tab is a matrix.
#> Rule 6 passed: feature.ann is a matrix.
#> Please note: The data components should follow base R data.frame and matrix structures, not phyloseq's formal class.
#> Validation passed.
#> Note: Passing validation does not guarantee the absence of all data issues. Further data exploration may be needed.
#> Your data is in raw format ('Raw'). Normalization is crucial for further analyses. Now, 'mStat_normalize_data' function is automatically applying 'Rarefy-TSS' transformation.
#> Data has been successfully normalized using TSS method.
#> Rule 1 passed: data.obj is a list.
#> Rule 2 passed: meta.dat is a data.frame.
#> Rule 3 passed: The row names of feature.tab match the row names of feature.ann.
#> Rule 4 passed: The column names of feature.tab match the row names of meta.dat.
#> Rule 5 passed: feature.tab is a matrix.
#> Rule 6 passed: feature.ann is a matrix.
#> Please note: The data components should follow base R data.frame and matrix structures, not phyloseq's formal class.
#> Validation passed.
#> Note: Passing validation does not guarantee the absence of all data issues. Further data exploration may be needed.
#> Your data is in raw format ('Raw'). Normalization is crucial for further analyses. Now, 'mStat_normalize_data' function is automatically applying 'Rarefy-TSS' transformation.
#> Data has been successfully normalized using TSS method.
#> Rule 1 passed: data.obj is a list.
#> Rule 2 passed: meta.dat is a data.frame.
#> Rule 3 passed: The row names of feature.tab match the row names of feature.ann.
#> Rule 4 passed: The column names of feature.tab match the row names of meta.dat.
#> Rule 5 passed: feature.tab is a matrix.
#> Rule 6 passed: feature.ann is a matrix.
#> Please note: The data components should follow base R data.frame and matrix structures, not phyloseq's formal class.
#> Validation passed.
#> Note: Passing validation does not guarantee the absence of all data issues. Further data exploration may be needed.
#> Your data is in raw format ('Raw'). Normalization is crucial for further analyses. Now, 'mStat_normalize_data' function is automatically applying 'Rarefy-TSS' transformation.
#> Data has been successfully normalized using TSS method.
#> $Phylum
#> $Phylum$Phylum
#> $Phylum$Phylum$Actinobacteria

#> 
#> $Phylum$Phylum$Bacteroidetes

#> 
#> $Phylum$Phylum$Firmicutes

#> 
#> $Phylum$Phylum$Proteobacteria

#> 
#> $Phylum$Phylum$Verrucomicrobia

#> 
#> 
#> 
#> $Family
#> $Family$Family
#> $Family$Family$Actinobacteria

#> 
#> $Family$Family$Bacilli

#> 
#> $Family$Family$Bacteroidetes

#> 
#> $Family$Family$`Clostridium cluster IV`

#> 
#> $Family$Family$`Clostridium cluster XIVa`

#> 
#> $Family$Family$Proteobacteria

#> 
#> $Family$Family$Verrucomicrobia

#> 
#> 
#> 
#> $Genus
#> $Genus$Genus
#> $Genus$Genus$Akkermansia

#> 
#> $Genus$Genus$`Anaerostipes caccae et rel.`

#> 
#> $Genus$Genus$`Bacteroides intestinalis et rel.`

#> 
#> $Genus$Genus$`Bacteroides uniformis et rel.`

#> 
#> $Genus$Genus$`Bacteroides vulgatus et rel.`

#> 
#> $Genus$Genus$Bifidobacterium

#> 
#> $Genus$Genus$`Bryantella formatexigens et rel.`

#> 
#> $Genus$Genus$`Clostridium leptum et rel.`

#> 
#> $Genus$Genus$`Clostridium nexile et rel.`

#> 
#> $Genus$Genus$`Clostridium sphenoides et rel.`

#> 
#> $Genus$Genus$`Clostridium symbiosum et rel.`

#> 
#> $Genus$Genus$`Coprococcus eutactus et rel.`

#> 
#> $Genus$Genus$`Dorea formicigenerans et rel.`

#> 
#> $Genus$Genus$`Eubacterium hallii et rel.`

#> 
#> $Genus$Genus$`Eubacterium rectale et rel.`

#> 
#> $Genus$Genus$`Eubacterium ventriosum et rel.`

#> 
#> $Genus$Genus$`Faecalibacterium prausnitzii et rel.`

#> 
#> $Genus$Genus$`Lachnobacillus bovis et rel.`

#> 
#> $Genus$Genus$`Lachnospira pectinoschiza et rel.`

#> 
#> $Genus$Genus$`Oscillospira guillermondii et rel.`

#> 
#> $Genus$Genus$`Outgrouping clostridium cluster XIVa`

#> 
#> $Genus$Genus$`Papillibacter cinnamivorans et rel.`

#> 
#> $Genus$Genus$`Roseburia intestinalis et rel.`

#> 
#> $Genus$Genus$`Ruminococcus bromii et rel.`

#> 
#> $Genus$Genus$`Ruminococcus gnavus et rel.`

#> 
#> $Genus$Genus$`Ruminococcus lactaris et rel.`

#> 
#> $Genus$Genus$`Ruminococcus obeum et rel.`

#> 
#> $Genus$Genus$`Streptococcus bovis et rel.`

#> 
#> $Genus$Genus$`Streptococcus mitis et rel.`

#> 
#> $Genus$Genus$`Subdoligranulum variable at rel.`

#> 
#> 
#> 

plot_feature_diversity(
data.obj = peerj32.obj,
group.var = "group",
strata.var = "sex",
subject.var = "subject",
time.var = "time",
time.point.plot = c("1", "2"),
is.plot.change = FALSE,
feature.level = c("Phylum", "Family", "Genus"),
prop.to.lump = 0.0001,
top.k.plot = NULL,
top.k.func = NULL,
renormalize = FALSE,
plot.other = TRUE,
plot.scheme = 'combined',
plot.type = "barplot"
)
#> Rule 1 passed: data.obj is a list.
#> Rule 2 passed: meta.dat is a data.frame.
#> Rule 3 passed: The row names of feature.tab match the row names of feature.ann.
#> Rule 4 passed: The column names of feature.tab match the row names of meta.dat.
#> Rule 5 passed: feature.tab is a matrix.
#> Rule 6 passed: feature.ann is a matrix.
#> Please note: The data components should follow base R data.frame and matrix structures, not phyloseq's formal class.
#> Validation passed.
#> Note: Passing validation does not guarantee the absence of all data issues. Further data exploration may be needed.
#> Your data is in raw format ('Raw'). Normalization is crucial for further analyses. Now, 'mStat_normalize_data' function is automatically applying 'TSS' transformation.
#> Data has been successfully normalized using TSS method.
#> Warning: Removed 35 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 70 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 21 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 28 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 7 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 7 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 7 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 7 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Rule 1 passed: data.obj is a list.
#> Rule 2 passed: meta.dat is a data.frame.
#> Rule 3 passed: The row names of feature.tab match the row names of feature.ann.
#> Rule 4 passed: The column names of feature.tab match the row names of meta.dat.
#> Rule 5 passed: feature.tab is a matrix.
#> Rule 6 passed: feature.ann is a matrix.
#> Please note: The data components should follow base R data.frame and matrix structures, not phyloseq's formal class.
#> Validation passed.
#> Note: Passing validation does not guarantee the absence of all data issues. Further data exploration may be needed.
#> Your data is in raw format ('Raw'). Normalization is crucial for further analyses. Now, 'mStat_normalize_data' function is automatically applying 'TSS' transformation.
#> Data has been successfully normalized using TSS method.
#> Warning: Removed 95 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 190 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 57 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 76 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 19 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 19 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 19 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 19 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Rule 1 passed: data.obj is a list.
#> Rule 2 passed: meta.dat is a data.frame.
#> Rule 3 passed: The row names of feature.tab match the row names of feature.ann.
#> Rule 4 passed: The column names of feature.tab match the row names of meta.dat.
#> Rule 5 passed: feature.tab is a matrix.
#> Rule 6 passed: feature.ann is a matrix.
#> Please note: The data components should follow base R data.frame and matrix structures, not phyloseq's formal class.
#> Validation passed.
#> Note: Passing validation does not guarantee the absence of all data issues. Further data exploration may be needed.
#> Your data is in raw format ('Raw'). Normalization is crucial for further analyses. Now, 'mStat_normalize_data' function is automatically applying 'TSS' transformation.
#> Data has been successfully normalized using TSS method.
#> Warning: Removed 105 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 210 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 63 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 84 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 21 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 21 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 21 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 21 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> $Phylum
#> $Phylum$Phylum
#> $Phylum$Phylum$indiv
#> Warning: Removed 35 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 70 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 21 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 28 rows containing missing values or values outside the scale range
#> (`geom_segment()`).

#> 
#> $Phylum$Phylum$average
#> Warning: Removed 7 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 7 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 7 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 7 rows containing missing values or values outside the scale range
#> (`geom_segment()`).

#> 
#> 
#> 
#> $Family
#> $Family$Family
#> $Family$Family$indiv
#> Warning: Removed 95 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 190 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 57 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 76 rows containing missing values or values outside the scale range
#> (`geom_segment()`).

#> 
#> $Family$Family$average
#> Warning: Removed 19 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 19 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 19 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 19 rows containing missing values or values outside the scale range
#> (`geom_segment()`).

#> 
#> 
#> 
#> $Genus
#> $Genus$Genus
#> $Genus$Genus$indiv
#> Warning: Removed 105 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 210 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 63 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 84 rows containing missing values or values outside the scale range
#> (`geom_segment()`).

#> 
#> $Genus$Genus$average
#> Warning: Removed 21 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 21 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 21 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 21 rows containing missing values or values outside the scale range
#> (`geom_segment()`).

#> 
#> 
#> 

plot_feature_diversity(
data.obj = peerj32.obj,
group.var = "group",
strata.var = "sex",
subject.var = "subject",
time.var = "time",
time.point.plot = c("1", "2"),
is.plot.change = FALSE,
feature.level = c("Family"),
features.plot = unique(peerj32.obj$feature.ann[, "Family"])[11:20],
prop.to.lump = 0.0001,
top.k.plot = NULL,
top.k.func = NULL,
renormalize = FALSE,
plot.other = TRUE,
plot.scheme = 'combined',
plot.type = "barplot"
)
#> Rule 1 passed: data.obj is a list.
#> Rule 2 passed: meta.dat is a data.frame.
#> Rule 3 passed: The row names of feature.tab match the row names of feature.ann.
#> Rule 4 passed: The column names of feature.tab match the row names of meta.dat.
#> Rule 5 passed: feature.tab is a matrix.
#> Rule 6 passed: feature.ann is a matrix.
#> Please note: The data components should follow base R data.frame and matrix structures, not phyloseq's formal class.
#> Validation passed.
#> Note: Passing validation does not guarantee the absence of all data issues. Further data exploration may be needed.
#> Your data is in raw format ('Raw'). Normalization is crucial for further analyses. Now, 'mStat_normalize_data' function is automatically applying 'TSS' transformation.
#> Data has been successfully normalized using TSS method.
#> Warning: Removed 50 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 100 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 30 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 40 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 10 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 10 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 10 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 10 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> $Family
#> $Family$Family
#> $Family$Family$indiv
#> Warning: Removed 50 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 100 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 30 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 40 rows containing missing values or values outside the scale range
#> (`geom_segment()`).

#> 
#> $Family$Family$average
#> Warning: Removed 10 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 10 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 10 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 10 rows containing missing values or values outside the scale range
#> (`geom_segment()`).

#> 
#> 
#> 

plot_feature_diversity(
data.obj = peerj32.obj,
group.var = "group",
strata.var = "sex",
subject.var = "subject",
time.var = "time",
time.point.plot = c("1", "2"),
is.plot.change = FALSE,
feature.level = c("Family"),
prop.to.lump = 0.0001,
top.k.plot = NULL,
top.k.func = NULL,
renormalize = FALSE,
plot.other = TRUE,
plot.scheme = 'combined',
plot.type = "dotplot"
)
#> Rule 1 passed: data.obj is a list.
#> Rule 2 passed: meta.dat is a data.frame.
#> Rule 3 passed: The row names of feature.tab match the row names of feature.ann.
#> Rule 4 passed: The column names of feature.tab match the row names of meta.dat.
#> Rule 5 passed: feature.tab is a matrix.
#> Rule 6 passed: feature.ann is a matrix.
#> Please note: The data components should follow base R data.frame and matrix structures, not phyloseq's formal class.
#> Validation passed.
#> Note: Passing validation does not guarantee the absence of all data issues. Further data exploration may be needed.
#> Your data is in raw format ('Raw'). Normalization is crucial for further analyses. Now, 'mStat_normalize_data' function is automatically applying 'TSS' transformation.
#> Data has been successfully normalized using TSS method.
#> Adding missing grouping variables: `group`
#> $Family
#> $Family$Family

#> 
#> 

data(subset_T2D.obj)
plot_feature_diversity(
data.obj = subset_T2D.obj,
group.var = "sample_body_site",
strata.var = "subject_race",
subject.var = "subject_id",
time.var = "visit_number_num",
time.point.plot = unique(subset_T2D.obj$meta.dat$visit_number_num),
is.plot.change = FALSE,
feature.level = c("Family"),
prop.to.lump = 0.0001,
top.k.plot = NULL,
top.k.func = NULL,
renormalize = FALSE,
plot.other = TRUE,
plot.scheme = 'combined',
plot.type = "barplot"
)
#> Rule 1 passed: data.obj is a list.
#> Rule 2 passed: meta.dat is a data.frame.
#> Rule 3 passed: The row names of feature.tab match the row names of feature.ann.
#> Rule 4 passed: The column names of feature.tab match the row names of meta.dat.
#> Rule 5 passed: feature.tab is a matrix.
#> Rule 6 passed: feature.ann is a matrix.
#> Please note: The data components should follow base R data.frame and matrix structures, not phyloseq's formal class.
#> Validation passed.
#> Note: Passing validation does not guarantee the absence of all data issues. Further data exploration may be needed.
#> Your data is in raw format ('Raw'). Normalization is crucial for further analyses. Now, 'mStat_normalize_data' function is automatically applying 'TSS' transformation.
#> Data has been successfully normalized using TSS method.
#> Warning: Removed 20 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 20 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 20 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 20 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 20 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 20 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> $Family
#> $Family$Family
#> Warning: Removed 20 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 20 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 20 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 20 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 20 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 20 rows containing missing values or values outside the scale range
#> (`geom_segment()`).

#> 
#> 

plot_feature_diversity(
data.obj = subset_T2D.obj,
group.var = "sample_body_site",
strata.var = "subject_race",
subject.var = "subject_id",
time.var = "visit_number_num",
time.point.plot = unique(subset_T2D.obj$meta.dat$visit_number_num),
is.plot.change = FALSE,
feature.level = c("Family"),
features.plot = unique(subset_T2D.obj$feature.ann[, "Family"])[1:10],
prop.to.lump = 0.0001,
top.k.plot = NULL,
top.k.func = NULL,
renormalize = FALSE,
plot.other = TRUE,
plot.scheme = 'combined',
plot.type = "barplot"
)
#> Rule 1 passed: data.obj is a list.
#> Rule 2 passed: meta.dat is a data.frame.
#> Rule 3 passed: The row names of feature.tab match the row names of feature.ann.
#> Rule 4 passed: The column names of feature.tab match the row names of meta.dat.
#> Rule 5 passed: feature.tab is a matrix.
#> Rule 6 passed: feature.ann is a matrix.
#> Please note: The data components should follow base R data.frame and matrix structures, not phyloseq's formal class.
#> Validation passed.
#> Note: Passing validation does not guarantee the absence of all data issues. Further data exploration may be needed.
#> Your data is in raw format ('Raw'). Normalization is crucial for further analyses. Now, 'mStat_normalize_data' function is automatically applying 'TSS' transformation.
#> Data has been successfully normalized using TSS method.
#> Warning: Removed 27 rows containing missing values or values outside the scale range
#> (`geom_bar()`).
#> Warning: Removed 27 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 9 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 9 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 9 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 9 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 27 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 9 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> $Family
#> $Family$Family
#> Warning: Removed 27 rows containing missing values or values outside the scale range
#> (`geom_bar()`).
#> Warning: Removed 27 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 9 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 9 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 9 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 9 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 27 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 9 rows containing missing values or values outside the scale range
#> (`geom_segment()`).

#> 
#> 

plot_feature_diversity(
data.obj = subset_T2D.obj,
group.var = "sample_body_site",
strata.var = "subject_race",
subject.var = "subject_id",
time.var = "visit_number_num",
time.point.plot = unique(subset_T2D.obj$meta.dat$visit_number_num),
features.plot = unique(subset_T2D.obj$feature.ann[, "Family"])[1:10],
is.plot.change = FALSE,
feature.level = c("Family"),
prop.to.lump = 0.0001,
top.k.plot = NULL,
top.k.func = NULL,
renormalize = FALSE,
plot.other = TRUE,
plot.scheme = 'combined',
plot.type = "areaplot"
)
#> Rule 1 passed: data.obj is a list.
#> Rule 2 passed: meta.dat is a data.frame.
#> Rule 3 passed: The row names of feature.tab match the row names of feature.ann.
#> Rule 4 passed: The column names of feature.tab match the row names of meta.dat.
#> Rule 5 passed: feature.tab is a matrix.
#> Rule 6 passed: feature.ann is a matrix.
#> Please note: The data components should follow base R data.frame and matrix structures, not phyloseq's formal class.
#> Validation passed.
#> Note: Passing validation does not guarantee the absence of all data issues. Further data exploration may be needed.
#> Your data is in raw format ('Raw'). Normalization is crucial for further analyses. Now, 'mStat_normalize_data' function is automatically applying 'TSS' transformation.
#> Data has been successfully normalized using TSS method.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> $Family
#> $Family$Family
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.

#> 
#> 

plot_feature_diversity(
data.obj = subset_T2D.obj,
group.var = "sample_body_site",
strata.var = "subject_race",
subject.var = "subject_id",
time.var = "visit_number_num",
time.point.plot = unique(subset_T2D.obj$meta.dat$visit_number_num),
is.plot.change = FALSE,
feature.level = c("Family"),
prop.to.lump = 0.0001,
top.k.plot = NULL,
top.k.func = NULL,
renormalize = FALSE,
plot.other = TRUE,
plot.scheme = 'combined',
plot.type = "spaghettiplot"
)
#> Rule 1 passed: data.obj is a list.
#> Rule 2 passed: meta.dat is a data.frame.
#> Rule 3 passed: The row names of feature.tab match the row names of feature.ann.
#> Rule 4 passed: The column names of feature.tab match the row names of meta.dat.
#> Rule 5 passed: feature.tab is a matrix.
#> Rule 6 passed: feature.ann is a matrix.
#> Please note: The data components should follow base R data.frame and matrix structures, not phyloseq's formal class.
#> Validation passed.
#> Note: Passing validation does not guarantee the absence of all data issues. Further data exploration may be needed.
#> Your data is in raw format ('Raw'). Normalization is crucial for further analyses. Now, 'mStat_normalize_data' function is automatically applying 'Rarefy-TSS' transformation.
#> Data has been successfully normalized using TSS method.
#> $Family
#> $Family$Family

#> 
#> 

plot_feature_diversity(
data.obj = subset_T2D.obj,
group.var = "sample_body_site",
strata.var = "subject_race",
subject.var = "subject_id",
time.var = "visit_number_num",
time.point.plot = unique(subset_T2D.obj$meta.dat$visit_number_num),
is.plot.change = FALSE,
feature.level = c("Family"),
prop.to.lump = 0.0001,
top.k.plot = NULL,
top.k.func = NULL,
renormalize = FALSE,
plot.other = TRUE,
plot.scheme = 'individual',
plot.type = "spaghettiplot"
)
#> Rule 1 passed: data.obj is a list.
#> Rule 2 passed: meta.dat is a data.frame.
#> Rule 3 passed: The row names of feature.tab match the row names of feature.ann.
#> Rule 4 passed: The column names of feature.tab match the row names of meta.dat.
#> Rule 5 passed: feature.tab is a matrix.
#> Rule 6 passed: feature.ann is a matrix.
#> Please note: The data components should follow base R data.frame and matrix structures, not phyloseq's formal class.
#> Validation passed.
#> Note: Passing validation does not guarantee the absence of all data issues. Further data exploration may be needed.
#> Your data is in raw format ('Raw'). Normalization is crucial for further analyses. Now, 'mStat_normalize_data' function is automatically applying 'Rarefy-TSS' transformation.
#> Data has been successfully normalized using TSS method.
#> $Family
#> $Family$Family
#> $Family$Family$Aerococcaceae

#> 
#> $Family$Family$Bacteroidaceae

#> 
#> $Family$Family$Corynebacteriaceae

#> 
#> $Family$Family$Lachnospiraceae

#> 
#> $Family$Family$Neisseriaceae

#> 
#> $Family$Family$Other

#> 
#> $Family$Family$Porphyromonadaceae

#> 
#> $Family$Family$Prevotellaceae

#> 
#> $Family$Family$Propionibacteriaceae

#> 
#> $Family$Family$Rikenellaceae

#> 
#> $Family$Family$Ruminococcaceae

#> 
#> $Family$Family$Staphylococcaceae

#> 
#> $Family$Family$Streptococcaceae

#> 
#> $Family$Family$`[Tissierellaceae]`

#> 
#> $Family$Family$Unclassified

#> 
#> 
#> 

plot_feature_diversity(
data.obj = subset_T2D.obj,
group.var = "sample_body_site",
strata.var = "subject_race",
subject.var = "subject_id",
time.var = "visit_number_num",
time.point.plot = unique(subset_T2D.obj$meta.dat$visit_number_num),
is.plot.change = FALSE,
feature.level = c("Family"),
prop.to.lump = 0.0001,
top.k.plot = NULL,
top.k.func = NULL,
renormalize = FALSE,
plot.other = TRUE,
plot.scheme = 'combined',
plot.type = "heatmap"
)
#> Rule 1 passed: data.obj is a list.
#> Rule 2 passed: meta.dat is a data.frame.
#> Rule 3 passed: The row names of feature.tab match the row names of feature.ann.
#> Rule 4 passed: The column names of feature.tab match the row names of meta.dat.
#> Rule 5 passed: feature.tab is a matrix.
#> Rule 6 passed: feature.ann is a matrix.
#> Please note: The data components should follow base R data.frame and matrix structures, not phyloseq's formal class.
#> Validation passed.
#> Note: Passing validation does not guarantee the absence of all data issues. Further data exploration may be needed.
#> Your data is in raw format ('Raw'). Normalization is crucial for further analyses. Now, 'mStat_normalize_data' function is automatically applying 'TSS' transformation.
#> Data has been successfully normalized using TSS method.
#> $Family
#> $Family$Family
#> $Family$Family$indiv

#> 
#> $Family$Family$average

#> 
#> 
#> 

plot_feature_diversity(
data.obj = subset_T2D.obj,
group.var = "sample_body_site",
strata.var = "subject_race",
subject.var = "subject_id",
time.var = "visit_number_num",
time.point.plot = unique(subset_T2D.obj$meta.dat$visit_number_num),
is.plot.change = TRUE,
feature.level = c("Family"),
prop.to.lump = 0.0001,
top.k.plot = NULL,
top.k.func = NULL,
renormalize = FALSE,
plot.other = TRUE,
plot.scheme = 'combined',
plot.type = "heatmap"
)
#> Rule 1 passed: data.obj is a list.
#> Rule 2 passed: meta.dat is a data.frame.
#> Rule 3 passed: The row names of feature.tab match the row names of feature.ann.
#> Rule 4 passed: The column names of feature.tab match the row names of meta.dat.
#> Rule 5 passed: feature.tab is a matrix.
#> Rule 6 passed: feature.ann is a matrix.
#> Please note: The data components should follow base R data.frame and matrix structures, not phyloseq's formal class.
#> Validation passed.
#> Note: Passing validation does not guarantee the absence of all data issues. Further data exploration may be needed.
#> Your data is in raw format ('Raw'). Normalization is crucial for further analyses. Now, 'mStat_normalize_data' function is automatically applying 'TSS' transformation.
#> Data has been successfully normalized using TSS method.
#> No columns have been removed.
#> $Family
#> $Family$Family

#> 
#> 

plot_feature_diversity(
data.obj = subset_T2D.obj,
group.var = "sample_body_site",
strata.var = "subject_race",
subject.var = "subject_id",
time.var = "visit_number_num",
time.point.plot = unique(subset_T2D.obj$meta.dat$visit_number_num),
is.plot.change = FALSE,
feature.level = c("Family"),
prop.to.lump = 0.0001,
top.k.plot = NULL,
top.k.func = NULL,
renormalize = FALSE,
plot.other = TRUE,
plot.scheme = 'combined',
plot.type = "boxplot"
)
#> Rule 1 passed: data.obj is a list.
#> Rule 2 passed: meta.dat is a data.frame.
#> Rule 3 passed: The row names of feature.tab match the row names of feature.ann.
#> Rule 4 passed: The column names of feature.tab match the row names of meta.dat.
#> Rule 5 passed: feature.tab is a matrix.
#> Rule 6 passed: feature.ann is a matrix.
#> Please note: The data components should follow base R data.frame and matrix structures, not phyloseq's formal class.
#> Validation passed.
#> Note: Passing validation does not guarantee the absence of all data issues. Further data exploration may be needed.
#> Your data is in raw format ('Raw'). Normalization is crucial for further analyses. Now, 'mStat_normalize_data' function is automatically applying 'Rarefy-TSS' transformation.
#> Data has been successfully normalized using TSS method.
#> $Family
#> $Family$Family

#> 
#> 

plot_feature_diversity(
data.obj = subset_T2D.obj,
group.var = "sample_body_site",
strata.var = "subject_race",
subject.var = "subject_id",
time.var = "visit_number_num",
time.point.plot = unique(subset_T2D.obj$meta.dat$visit_number_num),
is.plot.change = FALSE,
feature.level = c("Family"),
prop.to.lump = 0.0001,
top.k.plot = NULL,
top.k.func = NULL,
renormalize = FALSE,
plot.other = TRUE,
plot.scheme = 'individual',
plot.type = "boxplot"
)
#> Rule 1 passed: data.obj is a list.
#> Rule 2 passed: meta.dat is a data.frame.
#> Rule 3 passed: The row names of feature.tab match the row names of feature.ann.
#> Rule 4 passed: The column names of feature.tab match the row names of meta.dat.
#> Rule 5 passed: feature.tab is a matrix.
#> Rule 6 passed: feature.ann is a matrix.
#> Please note: The data components should follow base R data.frame and matrix structures, not phyloseq's formal class.
#> Validation passed.
#> Note: Passing validation does not guarantee the absence of all data issues. Further data exploration may be needed.
#> Your data is in raw format ('Raw'). Normalization is crucial for further analyses. Now, 'mStat_normalize_data' function is automatically applying 'Rarefy-TSS' transformation.
#> Data has been successfully normalized using TSS method.
#> $Family
#> $Family$Family
#> $Family$Family$Aerococcaceae

#> 
#> $Family$Family$Bacteroidaceae

#> 
#> $Family$Family$Corynebacteriaceae

#> 
#> $Family$Family$Lachnospiraceae

#> 
#> $Family$Family$Neisseriaceae

#> 
#> $Family$Family$Other

#> 
#> $Family$Family$Porphyromonadaceae

#> 
#> $Family$Family$Prevotellaceae

#> 
#> $Family$Family$Propionibacteriaceae

#> 
#> $Family$Family$Rikenellaceae

#> 
#> $Family$Family$Ruminococcaceae

#> 
#> $Family$Family$Staphylococcaceae

#> 
#> $Family$Family$Streptococcaceae

#> 
#> $Family$Family$`[Tissierellaceae]`

#> 
#> $Family$Family$Unclassified

#> 
#> 
#>