Plot Prevalence UpSet — plot_prevalence_upset • microbiomedataset

Draw an UpSet plot of taxa shared across groups.

Usage

plot_prevalence_upset(
  object,
  group_by,
  taxonomic_rank = c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species"),
  prevalence_cutoff = 0.3,
  relative = TRUE
)

Arguments

object: A microbiome_dataset object.
group_by: Sample metadata column defining the groups.
taxonomic_rank: Taxonomic rank used for aggregation.
prevalence_cutoff: Prevalence cutoff within each group.
relative: Whether to use relative abundance.

Value

A CombinationMatrix-based UpSet plot object.

Examples

data("global_patterns", package = "microbiomedataset")
plot_prevalence_upset(global_patterns, group_by = "SampleType", taxonomic_rank = "Phylum")