Plot Core Taxa — plot_core_taxa • microbiomedataset

Highlight taxa that satisfy prevalence and abundance thresholds.

Usage

plot_core_taxa(
  object,
  taxonomic_rank = c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species"),
  detection = 0,
  prevalence_cutoff = 0.5,
  abundance_cutoff = NULL,
  relative = TRUE,
  top_n = 20
)

Arguments

object: A microbiome_dataset object.
taxonomic_rank: Taxonomic rank used for aggregation.
detection: Detection threshold used for prevalence.
prevalence_cutoff: Core prevalence cutoff.
abundance_cutoff: Core mean abundance cutoff.
relative: Whether to use relative abundance.
top_n: Number of taxa displayed.

Value

A ggplot object.

Examples

data("global_patterns", package = "microbiomedataset")
x <- prune_taxa(global_patterns, variable_id = global_patterns@variable_info$variable_id[1:200])
plot_core_taxa(x, taxonomic_rank = "Phylum", top_n = 8)