Plot linda results

The function plots the effect size plot and volcano plot based on the output from linda.

Usage

linda.plot(
  linda.obj,
  variables.plot,
  titles = NULL,
  alpha = 0.05,
  lfc.cut = 1,
  legend = FALSE,
  directory = NULL,
  width = 11,
  height = 8
)

Arguments

linda.obj

return from function linda.

variables.plot

vector; variables whose results are to be plotted. For example, suppose the return value variables is equal to ('x1', 'x2', 'x3b', 'x3c', 'x1:x2'), then one could set variables.plot = c('x3b', 'x1:x2').

titles

vector; titles of the effect size plot and volcano plot for each variable in variables.plot. Default is NULL. If NULL, the titles will be set as variables.plot.

alpha

a real value between 0 and 1; cutoff for padj.

lfc.cut

a positive value; cutoff for log2FoldChange.

legend

TRUE or FALSE; whether to show the legends of the effect size plot and volcano plot.

directory

character; the directory to save the figures, e.g., getwd(). Default is NULL. If NULL, figures will not be saved.

width

the width of the graphics region in inches. See R function pdf.

height

the height of the graphics region in inches. See R function pdf.

Value

A list of ggplot2 objects.

plot.lfc

a list of effect size plots. Each plot corresponds to one variable in variables.plot.

plot.volcano

a list of volcano plots. Each plot corresponds to one variable in variables.plot.

References

Huijuan Zhou, Kejun He, Jun Chen, and Xianyang Zhang. LinDA: Linear Models for Differential Abundance Analysis of Microbiome Compositional Data.

Author

Huijuan Zhou huijuanzhou2019@gmail.com Jun Chen Chen.Jun2@mayo.edu Maintainer: Huijuan Zhou

Examples

if (FALSE) { # \dontrun{
library(ggrepel)
data(smokers)
ind <- smokers$meta$AIRWAYSITE == "Throat"
otu.tab <- as.data.frame(smokers$otu[, ind])
meta <- cbind.data.frame(
  Smoke = factor(smokers$meta$SMOKER[ind]),
  Sex = factor(smokers$meta$SEX[ind]),
  Site = factor(smokers$meta$SIDEOFBODY[ind]),
  SubjectID = factor(smokers$meta$HOST_SUBJECT_ID[ind])
)
ind1 <- which(meta$Site == "Left")
res.left <- linda(otu.tab[, ind1], meta[ind1, ],
  formula = "~Smoke+Sex"
)
ind2 <- which(meta$Site == "Right")
res.right <- linda(otu.tab[, ind2], meta[ind2, ],
  formula = "~Smoke+Sex"
)
rownames(res.left$output[[1]])[which(res.left$output[[1]]$reject)]
rownames(res.right$output[[1]])[which(res.right$output[[1]]$reject)]

linda.obj <- linda(otu.tab, meta,
  formula = "~Smoke+Sex+(1|SubjectID)"
)
} # }