plot_taxa: Plots relative distribution for taxa across samples.

In Gibbons-Lab/mbtools: Provides helper functions for microbiome preprocessing and analysis

Plots relative distribution for taxa across samples.

Description

Plots relative distribution for taxa across samples.

Usage

plot_taxa(
  ps,
  level = "Phylum",
  show_samples = TRUE,
  sort = TRUE,
  max_taxa = 12,
  only_data = FALSE,
  ...
)

Arguments

ps	A phyloseq data set.
level	The taxonomy level to use. Defaults to phylum.
show_samples	Whether to show sample names.
sort	Whether to sort taxa by abundance across all samples.
max_taxa	Maximum number of different taxa to plot. If more than 12 there is probably no color scale that can visualize them.
only_data	Only get the raw data for the plot as a data table.
...	Addditional arguments passed to geom_bar.

Value

Nothing or a data.table containing the relative abundances.

Examples

 NULL

Gibbons-Lab/mbtools documentation built on Jan. 28, 2024, 11:08 a.m.