.plot_gene_heatmap_impl: Shared Gene Heatmap Implementation

Description

Internal helper function that contains the shared logic for creating gene heatmaps.

Usage

.plot_gene_heatmap_impl(
  expression_matrix,
  strata,
  gene_ids,
  num_strata,
  genes = NULL,
  top_p = NULL,
  top_k = 30,
  std = TRUE,
  cluster_rows = FALSE,
  cluster_cols = FALSE,
  show_gene_age = TRUE,
  show_gene_ids = FALSE,
  gene_annotation = NULL,
  gene_annotation_colors = NULL,
  annotation_col = NULL,
  annotation_col_colors = NULL,
  ...
)

Value

A ggplot object showing the gene expression heatmap

Arguments

expression_matrix: Matrix of expression values (genes x samples)
strata: Factor vector of gene phylostrata
gene_ids: Character vector of all gene IDs in the dataset (used for phylostratum mapping)
num_strata: Integer number of phylostrata
genes: Character vector of specific genes to plot. If NULL, uses top dynamic genes
top_p: Proportion of most dynamic genes to include (default: NULL). Ignored if top_k is specified.
top_k: Absolute number of top genes to select (default: 30). Takes precedence over top_p.
std: Logical indicating whether to use standardized expression values (default: TRUE)
cluster_rows: Logical indicating whether to cluster genes/rows (default: FALSE)
cluster_cols: Logical indicating whether to cluster identities/columns (default: FALSE)
show_gene_age: Logical indicating whether to show gene age as row annotation (default: TRUE)
show_gene_ids: Logical indicating whether to show gene names (default: FALSE)
gene_annotation: Data frame with custom gene annotations, rownames should match gene IDs (default: NULL)
gene_annotation_colors: Named list of color vectors for custom gene annotations (default: NULL)
annotation_col: Data frame with column annotations (default: NULL)
annotation_col_colors: List of colors for column annotations (default: NULL)
...: Additional arguments passed to pheatmap::pheatmap