plot_gatai_results: Plot Comprehensive GATAI Results

Description

Create a suite of plots summarizing the effects of GATAI gene removal on phylotranscriptomic patterns.

Usage

plot_gatai_results(
  phyex_set,
  gatai_result,
  conservation_test = stat_flatline_test,
  runs_threshold = 0.5,
  signature_plot_type = c("separate", "combined")
)

Value

A named list of ggplot/patchwork objects and results:

signature_plots: Signature plots before/after GATAI and top variance removal
heatmap_plot: Heatmap of GATAI-removed genes
profiles_plot: Gene expression profiles of GATAI-removed genes
profiles_plot_facet: Faceted gene profiles by strata
gene_space_plot: Gene space plot of GATAI-removed genes
mean_var_plot: Mean-variance plot highlighting GATAI-removed genes
strata_plot: Phylostrata distribution plot (log obs/exp) for GATAI-removed genes
null_dist_plot: Null distribution plot with test statistics and p-values
convergence_plots: GATAI convergence plots (if available)

Arguments

phyex_set: A PhyloExpressionSet object containing the original gene expression data.
gatai_result: Result list from destroy_pattern(), containing GATAI analysis output.
conservation_test: Function for conservation test (default: stat_flatline_test).
runs_threshold: Threshold for gene removal consistency across runs (default: 0.5).
signature_plot_type: Type of signature plot: "separate" for individual plots, "combined" for overlay (default: both options).

Author

Filipa Martins Costa, Stefan Manolache

Details

This function provides a comprehensive visualization of the impact of GATAI gene removal, including transcriptomic signature plots, gene expression profiles, heatmaps, mean-variance relationships, phylostrata distributions, conservation test comparisons, and convergence diagnostics.