Plot Distribution of Genes Across Phylostrata — plot_distribution

Create a bar plot showing the distribution of genes across phylostrata, with options for showing observed vs. expected ratios.

Usage

plot_distribution_strata(
  strata,
  selected_gene_ids = names(strata),
  as_log_obs_exp = FALSE
)

Arguments

strata: Named factor vector of phylostratum assignments (names are gene IDs)
selected_gene_ids: Character vector of gene IDs to include in the plot (default: all genes in strata)
as_log_obs_exp: Logical indicating whether to show log2(observed/expected) ratios instead of raw counts (default: FALSE)

Value

A ggplot2 object showing the phylostratum distribution

Details

This function visualizes how genes are distributed across different phylostrata. When as_log_obs_exp=FALSE, it shows raw gene counts per stratum. When TRUE, it shows log2 ratios of observed vs. expected gene counts, useful for identifying enrichment or depletion of specific strata in gene sets.

Examples

# Plot raw gene counts by strata
p1 <- plot_distribution_strata(example_phyex_set@strata)

# Plot observed vs expected ratios for selected genes
p2 <- plot_distribution_strata(example_phyex_set@strata, 
                               selected_gene_ids = example_phyex_set@gene_ids[5:20],
                               as_log_obs_exp = TRUE)
#> Warning: Ignoring unknown parameters: `size`