plot_counts: Plots counts for several taxa across a co-variable

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

Plots counts for several taxa across a co-variable

Description

Plots counts for several taxa across a co-variable

Usage

plot_counts(
  ps,
  variable,
  tax_level = "genus",
  taxa = NULL,
  normalized = TRUE,
  pc = 0.5,
  only_data = FALSE
)

Arguments

ps	A phyloseq data set.
variable	The name of the co-variable.
tax_level	The taxonomy level to use. Defaults to genus.
taxa	A character vector denoting the taxa to be plotted. Defaults to plotting all taxa.
normalized	Whether to normalize the counts using the DESeq2 size factors.
pc	The pseudo count to add.
only_data	Only get the raw data for the plot.

Value

Nothing.

Examples

 NULL

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