relabu_boxplot: Plot boxplots comparing different organism prevalence across...

In compbiomed/animalcules: Interactive microbiome analysis toolkit

Plot boxplots comparing different organism prevalence across conditions

Description

Plot boxplots comparing different organism prevalence across conditions

Usage

relabu_boxplot(
  MAE,
  tax_level,
  condition,
  organisms = c(),
  datatype = c("counts", "relative abundance", "logcpm")
)

Arguments

MAE	A multi-assay experiment object
tax_level	The taxon level used for organisms
condition	Compare groups by condition e.g. 'SEX'
organisms	Include organisms for plotting.
datatype	counts, relative abundance,logcpm

Value

A plotly object

Examples

data_dir <- system.file("extdata/MAE.rds", package = "animalcules")
toy_data <- readRDS(data_dir)
p <- relabu_boxplot(toy_data,
  tax_level = "genus",
  organisms = c("Escherichia", "Actinomyces"),
  condition = "SEX",
  datatype = "logcpm"
)
p

compbiomed/animalcules documentation built on Feb. 7, 2024, 12:13 p.m.