Plot pan-genome structure — plot_pan

Creates a bar chart showing the composition of the pan-genome by category: Core (present in all assemblies), Accessory, Rare, Unique (present in one assembly), and optionally Singletons (proteins not in any orthogroup).

Usage

plot_pan_structure(
  clusters,
  pa = NULL,
  rare_threshold = 0.1,
  accessory_threshold = 0.6,
  exclude_singletons = FALSE,
  colors = NULL,
  show_counts = TRUE,
  title = NULL
)

Arguments

clusters: An orthogroup_result object.
pa: Optional pre-built pa_matrix. If NULL, built internally.
rare_threshold: Proportion threshold for "Rare" category (default 0.10). Orthogroups present in <= this proportion of assemblies (but > 1) are "Rare".
accessory_threshold: Proportion threshold for "Accessory" category (default 0.60). Orthogroups present in > rare_threshold and <= this proportion are "Accessory".
exclude_singletons: Logical. If TRUE, singletons are not shown (default FALSE).
colors: Named vector of colors for each category. If NULL, uses default palette.
show_counts: Logical. If TRUE, display count labels on bars (default TRUE).
title: Plot title. If NULL, uses default.

Value

A ggplot object.

Examples

if (FALSE) { # \dontrun{
# Basic usage
plot_pan_structure(clusters)

# Custom thresholds
plot_pan_structure(clusters, rare_threshold = 0.15, accessory_threshold = 0.50)

# Without singletons
plot_pan_structure(clusters, exclude_singletons = TRUE)
} # }