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Plot Taxon Prevalence

Source: R/plot_microbiome_visualization.R
plot_prevalence.Rd

Draw a prevalence barplot for dominant taxa.

Usage

plot_prevalence(
  object,
  taxonomic_rank = c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species"),
  detection = 0,
  proportion = TRUE,
  top_n = 20
)

Arguments

object

A microbiome_dataset object.

taxonomic_rank

Taxonomic rank used for aggregation.

detection

Detection threshold used in prevalence calculation.

proportion

Whether prevalence should be shown as a proportion.

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_prevalence(
  object = x,
  taxonomic_rank = "Phylum",
  top_n = 10
)