bartax: Taxonomic Composition Stacked Barcharts
In escamero/mirlyn: Multiple Iterations of Rarefying for Library Normalization

bartax

R Documentation

Taxonomic Composition Stacked Barcharts

Description

The bartax() function will create taxonomic composition barcharts. If desired, low-abundant taxonomic groups will be clustered into a single low abundant group.

Usage

bartax(
  x,
  xvar = "Sample",
  lowabun = 0.01,
  yvar = "Abundance",
  taxrank = "Genus",
  cols = NULL
)

Arguments

`x`	is a `phyloseq` object.
`xvar`	is a categorical variable selected from the metadata.
`lowabun`	is the cut off value for a low-abundant group. Set to `NULL` to not use.
`yvar`	is the relative abundance of reads.
`taxrank`	is the specified taxonomic rank.
`cols`	is a vector containing specified colour values (sufficient number for number of taxonomic groups).

Value

A ggplot object.

Examples

library(mirlyn)
data(example)
cols <- c("black","darkgoldenrod1","dodgerblue","deeppink4","chartreuse3",
   "burlywood4","navy","blueviolet", "tan2","lavenderblush3","cyan4")
bartax(example, "Sample", lowabun = 0.01, yvar = "Abundance", taxrank = "Phylum", cols)

escamero/mirlyn documentation built on Aug. 6, 2023, 9:30 p.m.