Plot presence/absence heatmap — plot

Creates a heatmap visualization of the presence/absence matrix using ComplexHeatmap. Rows are orthogroups, columns are assemblies.

Usage

plot_heatmap(
  pa,
  cluster_rows = TRUE,
  cluster_cols = TRUE,
  show_row_names = FALSE,
  show_col_names = TRUE,
  color = NULL,
  row_annotation = NULL,
  col_annotation = NULL,
  distance_method = "binary",
  ...
)

Arguments

pa: A pa_matrix object.
cluster_rows: Logical. Whether to cluster rows (default: TRUE).
cluster_cols: Logical. Whether to cluster columns (default: TRUE).
show_row_names: Logical. Whether to show row names (default: FALSE).
show_col_names: Logical. Whether to show column names (default: TRUE).
color: Character vector or color function. Colors for the heatmap. If NULL, auto-detected based on pa$type.
row_annotation: A data.frame with row names matching orthogroup IDs. Columns become annotation tracks on the left side.
col_annotation: A data.frame with row names matching assembly names. Columns become annotation tracks on the top.
distance_method: Character. Distance metric for clustering: "binary" (default), "jaccard", or "bray-curtis".
...: Additional arguments passed to ComplexHeatmap::Heatmap().

Value

A ComplexHeatmap Heatmap object.

Examples

if (FALSE) { # \dontrun{
plot_heatmap(pa)
plot_heatmap(pa, cluster_rows = FALSE)
} # }