myTAI (version 2.3.4)

plot_distribution_strata: Plot Distribution of Genes Across Phylostrata

Description

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
)

Value

A ggplot2 object showing the phylostratum distribution

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)

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)