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Generate Beta Diversity Ordination Plot

Source: R/generate_beta_ordination_single.R
generate_beta_ordination_single.Rd

This function generates ordination plots (Principal Component Analysis) based on beta-diversity distances. It also allows for stratification and grouping of samples, and calculation of distances at a specific time point.

Usage

generate_beta_ordination_single(
  data.obj,
  subject.var,
  time.var = NULL,
  t.level = NULL,
  group.var = NULL,
  adj.vars = NULL,
  strata.var = NULL,
  dist.obj = NULL,
  dist.name = c("BC", "Jaccard"),
  pc.obj = NULL,
  base.size = 16,
  theme.choice = "bw",
  custom.theme = NULL,
  palette = NULL,
  pdf = TRUE,
  file.ann = NULL,
  pdf.wid = 11,
  pdf.hei = 8.5,
  ...
)

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.

subject.var

String. Variable to be used as subject.

time.var

String. Variable to be used for time. Default is NULL.

t.level

Character string specifying the time level/value to subset data to, if a time variable is provided. Default NULL does not subset data.

group.var

String. Variable to be used for grouping. Default is NULL.

adj.vars

A character vector of variable names to be used for adjustment.

strata.var

String. Variable to be used for stratification. Default is NULL.

dist.obj

Distance matrix between samples, usually calculated using mStat_calculate_beta_diversity function. If NULL, beta diversity will be automatically computed from data.obj using mStat_calculate_beta_diversity.

dist.name

A character vector specifying which beta diversity indices to calculate. Supported indices are "BC" (Bray-Curtis), "Jaccard", "UniFrac" (unweighted UniFrac), "GUniFrac" (generalized UniFrac), "WUniFrac" (weighted UniFrac), and "JS" (Jensen-Shannon divergence). If a name is provided but the corresponding object does not exist within dist.obj, it will be computed internally. If the specific index is not supported, an error message will be returned. Default is c('BC', 'Jaccard').

pc.obj

A list containing the results of dimension reduction/Principal Component Analysis. This should be the output from functions like mStat_calculate_PC, containing the PC coordinates and other metadata. If NULL (default), dimension reduction will be automatically performed using metric multidimensional scaling (MDS) via mStat_calculate_PC. The pc.obj list structure should contain:

points

A matrix with samples as rows and PCs as columns containing the coordinates.

eig

Eigenvalues for each PC dimension.

vectors

Loadings vectors for features onto each PC.

Other metadata

like method, dist.name, etc.

See mStat_calculate_PC function for details on output format.

base.size

Numeric. Base size for plot elements. Default is 16.

theme.choice

Plot theme choice. Specifies the visual style of the plot. Can be one of the following pre-defined themes: - "prism": Utilizes the ggprism::theme_prism() function from the ggprism package, offering a polished and visually appealing style. - "classic": Applies theme_classic() from ggplot2, providing a clean and traditional look with minimal styling. - "gray": Uses theme_gray() from ggplot2, which offers a simple and modern look with a light gray background. - "bw": Employs theme_bw() from ggplot2, creating a classic black and white plot, ideal for formal publications and situations where color is best minimized. - "light": Implements theme_light() from ggplot2, featuring a light theme with subtle grey lines and axes, suitable for a fresh, modern look. - "dark": Uses theme_dark() from ggplot2, offering a dark background, ideal for presentations or situations where a high-contrast theme is desired. - "minimal": Applies theme_minimal() from ggplot2, providing a minimalist theme with the least amount of background annotations and colors. - "void": Employs theme_void() from ggplot2, creating a blank canvas with no axes, gridlines, or background, ideal for custom, creative plots. Each theme option adjusts various elements like background color, grid lines, and font styles to match the specified aesthetic. Default is "bw", offering a universally compatible black and white theme suitable for a wide range of applications.

custom.theme

A custom ggplot theme provided as a ggplot2 theme object. This allows users to override the default theme and provide their own theme for plotting. Custom themes are useful for creating publication-ready figures with specific formatting requirements.

To use a custom theme, create a theme object with ggplot2::theme(), including any desired customizations. Common customizations for publication-ready figures might include adjusting text size for readability, altering line sizes for clarity, and repositioning or formatting the legend. For example:

“`r my_theme <- ggplot2::theme( axis.title = ggplot2::element_text(size=14, face="bold"), # Bold axis titles with larger font axis.text = ggplot2::element_text(size=12), # Slightly larger axis text legend.position = "top", # Move legend to the top legend.background = ggplot2::element_rect(fill="lightgray"), # Light gray background for legend panel.background = ggplot2::element_rect(fill="white", colour="black"), # White panel background with black border panel.grid.major = ggplot2::element_line(colour = "grey90"), # Lighter color for major grid lines panel.grid.minor = ggplot2::element_blank(), # Remove minor grid lines plot.title = ggplot2::element_text(size=16, hjust=0.5) # Centered plot title with larger font ) “`

Then pass `my_theme` to `custom.theme`. If `custom.theme` is NULL (the default), the theme is determined by `theme.choice`. This flexibility allows for both easy theme selection for general use and detailed customization for specific presentation or publication needs.

palette

An optional parameter specifying the color palette to be used for the plot. It can be either a character string specifying the name of a predefined palette or a vector of color codes in a format accepted by ggplot2 (e.g., hexadecimal color codes). Available predefined palettes include 'npg', 'aaas', 'nejm', 'lancet', 'jama', 'jco', and 'ucscgb', inspired by various scientific publications and the `ggsci` package. If `palette` is not provided or an unrecognized palette name is given, a default color palette will be used. Ensure the number of colors in the palette is at least as large as the number of groups being plotted.

pdf

Logical. If TRUE, the plots are saved as PDF files. Default is TRUE.

file.ann

File annotation. Default is NULL.

pdf.wid

Width of the PDF. Default is 11.

pdf.hei

Height of the PDF. Default is 8.5.

...

Additional arguments to be passed.

Value

A PCoA plot displaying the beta diversity ordination, stratified by the specified grouping and/or strata variables (if provided). The plot will be saved as a PDF if `pdf` is set to `TRUE`.

Details

The function is flexible and allows for various modifications, including the choice of distance measure and stratification factor, providing a comprehensive tool for microbiome beta diversity exploration. It integrates well with other MicrobiomeStat functions and takes their output as input.

See also

mStat_calculate_beta_diversity for creating the distance object, mStat_calculate_PC for computing the principal coordinates, and geom_point, geom_boxplot for the underlying plot functions used, and 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, mStat_import_biom_as_data_obj for data conversion.

Author

Caffery Yang cafferychen7850@gmail.com

Examples

if (FALSE) { # \dontrun{
library(aplot)
data(peerj32.obj)
dist.obj <- mStat_calculate_beta_diversity(peerj32.obj, dist.name = c('BC', 'Jaccard'))
pc.obj <- mStat_calculate_PC(dist.obj, method = c('mds'), k = 2, dist.name = c('BC','Jaccard'))
generate_beta_ordination_single(
  data.obj = peerj32.obj,
  dist.obj = NULL,
  pc.obj = NULL,
  subject.var = "subject",
  time.var = "time",
  t.level = "2",
  group.var = "group",
  strata.var = "sex",
  adj.vars = "sex",
  dist.name = c("BC"),
  base.size = 20,
  theme.choice = "bw",
  custom.theme = NULL,
  palette = NULL,
  pdf = TRUE,
  file.ann = NULL,
  pdf.wid = 11,
  pdf.hei = 8.5
)

data("subset_T2D.obj")
dist.obj <- mStat_calculate_beta_diversity(subset_T2D.obj, dist.name = c('BC', 'Jaccard'))
pc.obj <- mStat_calculate_PC(dist.obj, method = c('mds'), k = 2, dist.name = c('BC','Jaccard'))
generate_beta_ordination_single(
  data.obj = subset_T2D.obj,
  dist.obj = dist.obj,
  pc.obj = pc.obj,
  subject.var = "subject_id",
  time.var = "visit_number_num",
  t.level = NULL,
  group.var = "subject_race",
  strata.var = "subject_gender",
  adj.vars = "sample_body_site",
  dist.name = c("BC", 'Jaccard'),
  base.size = 20,
  theme.choice = "bw",
  custom.theme = NULL,
  palette = NULL,
  pdf = TRUE,
  file.ann = NULL,
  pdf.wid = 11,
  pdf.hei = 8.5
)
} # }