Plot Comprehensive GATAI Results

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")
)

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).

Value

A named list of ggplot/cowplot 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)

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.

Author

Filipa Martins Costa, Stefan Manolache

Examples

# Run GATAI analysis
# gatai_result <- destroy_pattern(phyex_set, num_runs = 20)
# Plot results
# plots <- plot_gatai_results(phyex_set, gatai_result)
# Print signature plots
# print(plots$signature_plots)