plot_alpha_by: Alpha and beta diversity plots stratified by sample variables

In waldronlab/nychanesmicrobiome: Analysis of the NYC-HANES Microbiome Specimens

Alpha and beta diversity plots stratified by sample variables

Description

Alpha and beta diversity plots stratified by sample variables

Usage

plot_alpha_by(
  pseq,
  vars,
  metadata = sample_data(pseq)[, vars],
  notch = TRUE,
  adjust_formula,
  alpha_p
)

plot_beta_by(pseq, vars, dist_mtrx)

Arguments

pseq	An object of class phyloseq
vars	Character vector. Names of variables in sample_data to stratify by.
metadata	Data.frame. Defaults to sample_data(pseq)[,vars], but this allows the use of say, a calculated variable without having to modify the pseq.
notch	Logical. Whether or not to return notched boxplots.
dist_mtrx	Matrix. Matrix of between-group distances, e.g. as returned by phyloseq::distance().

waldronlab/nychanesmicrobiome documentation built on April 21, 2024, 8:52 a.m.