taxa.mean.plot: Plot mean taxa abundance

In metamicrobiomeR: Microbiome Data Analysis & Meta-Analysis with GAMLSS-BEZI & Random Effects

Description

This function visualize mean relative abundance by group as stacked plots.

Usage

taxa.mean.plot(
  tabmean,
  sumvar = "taxa",
  tax.select = "none",
  tax.lev = "l2",
  comvar,
  groupvar,
  mean.filter = 0.005,
  pallete.by.phylum = FALSE,
  show.taxname = "full",
  legend.position = "right",
  xlab = "",
  ylab = "Relative abundance"
)

Arguments

tabmean	table of mean abundance generated from taxa.meansdn.
sumvar	variable to be plotted. Options are c("taxa","path"). Default is "taxa"
tax.select	list of selected taxa/pathways to be plotted. Default is "none" or plot all taxa/pathways.
tax.lev	taxa level to be visualized. Options are from "l2" (phylum) to "l7" (species). Default is "l2". If sumvar="path", all pathways will be visualized.
comvar	main variable for comparison.
groupvar	variable for stratifying.
mean.filter	mean abundance filtering threshold (only plot those with mean abundance>threshold and plot all those with mean abundance <threshold as "other").
pallete.by.phylum	whether each pallete of color for each phylum. Default is FALSE (plot distinc colors).
show.taxname	whether show "full" taxa name or "short" name. Default is "full".
legend.position	position of legend. Options are c("right", "left","bottom","top","none") as in ggplot2. Default is "right".
xlab	label for x-axis. Default is "Chronological age (month)".
ylab	label for y-axis. Default is "Relative abundance".

Value

a list of ggplot2 object and list of taxa/pathways plotted (those with mean abundance >mean.filter).

Examples

#Load summary tables of bacterial taxa relative abundance from Bangladesh data
data(taxtab6)
taxlist.rm<-taxa.filter(taxtab=taxtab6, percent.filter = 0.05, relabund.filter = 0.00005)
taxa.meansdn.rm<-taxa.meansdn(taxtab=taxtab6,sumvar="bf",groupvar="age.sample")
taxa.meansdn.rm<-taxa.meansdn.rm[taxa.meansdn.rm$bf!="No_BF",]
taxa.meansdn.rm$bf<-gdata::drop.levels(taxa.meansdn.rm$bf,reorder=FALSE)
#phylum
p.bf.l2<-taxa.mean.plot(tabmean=taxa.meansdn.rm, tax.lev="l2",
comvar="bf", groupvar="age.sample",mean.filter=0.005, show.taxname="short")
p.bf.l2$p

metamicrobiomeR documentation built on Nov. 9, 2020, 5:06 p.m.