alpha_div_boxplot: Alpha diversity boxplot

In compbiomed/animalcules: Interactive microbiome analysis toolkit

Alpha diversity boxplot

Description

Alpha diversity boxplot

Usage

alpha_div_boxplot(
  MAE,
  tax_level,
  condition,
  alpha_metric = c("inverse_simpson", "gini_simpson", "shannon", "fisher", "coverage",
    "unit")
)

Arguments

MAE	A multi-assay experiment object. Required.
tax_level	The taxon level used for organisms. Required.
condition	Which condition to group samples. Required.
alpha_metric	Which alpha diversity metric to use. Required. Can be one of:"inverse_simpson", "gini_simpson", "shannon", "fisher", "coverage", "unit"

Value

A plotly object

Examples

data_dir <- system.file("extdata/MAE.rds", package = "animalcules")
toy_data <- readRDS(data_dir)
p <- alpha_div_boxplot(toy_data,
  tax_level = "genus",
  condition = "DISEASE",
  alpha_metric = "shannon"
)
p

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