Alpha diversity boxplot — alpha_div_boxplot • animalcules

Alpha diversity boxplot

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