Publication-Ready GSEA Results Barplot — do

Creates a horizontal barplot of top pathways from a Gene Set Enrichment Analysis (GSEA) result. Instead of the default dotplot, this function shows Normalized Enrichment Scores (NES) as bars with adjusted p-values as text labels and leading-edge gene annotations.

Usage

do_GseaPlot(
  gsea_object,
  analysis_name = "GSEA Analysis",
  simplify_go = TRUE,
  number_of_pathways = 10,
  selection = NULL,
  fill_scale = c("diverging", "viridis"),
  show_padj = TRUE,
  show_leading_edge = TRUE,
  title = NULL
)

Arguments

gsea_object: A gseaResult object from clusterProfiler::gseGO(), ReactomePA::gsePathway(), or similar, containing results in the @result slot.
analysis_name: Character. Subtitle for the plot. Defaults to "GSEA Analysis".
simplify_go: Logical. Whether to apply clusterProfiler::simplify() to GO terms (default: TRUE). Only applies when GO term IDs are detected; silently skipped otherwise.
number_of_pathways: Integer. Number of top upregulated and downregulated pathways to display (default: 10). Ignored when selection is provided.
selection: Character vector of pathway descriptions to plot. Overrides automatic top/bottom selection. Defaults to NULL.
fill_scale: Character. Color scale: "diverging" (RdBu, 0-centered) or "viridis" (sequential viridis-C, original style). Defaults to "diverging" to emphasize the signed nature of NES.
show_padj: Logical. Show adjusted p-value labels on bars. Defaults to TRUE.
show_leading_edge: Logical. Show leading-edge gene count and gene symbols in y-axis labels. Defaults to TRUE.
title: Character. Custom plot title. If NULL, auto-generated from analysis_name.

Value

A ggplot2 object.

Examples

if (FALSE) { # \dontrun{
data(gsea_pbmc3k)
do_GseaPlot(gsea_pbmc3k, analysis_name = "CD14+ Mono vs Others")

# Use viridis (original style)
do_GseaPlot(gsea_pbmc3k, fill_scale = "viridis")

# Plot specific pathways
do_GseaPlot(
  gsea_pbmc3k,
  selection = c("cell chemotaxis")
)
} # }