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Plot Combined GSEA Results

Source: R/plotCombinedGSEA.R
plotCombinedGSEA.Rd

This function creates a scatter plot visualizing multiple GSEA (Gene Set Enrichment Analysis) results across different contrasts. Each point represents a pathway, where:

  • The x-axis corresponds to the Normalized Enrichment Score (NES).

  • The y-axis corresponds to the significance level (-log10 adjusted p-value).

  • The color represents different pathways.

  • The shape represents different contrasts.

  • A dashed horizontal line marks the chosen significance threshold.

Usage

plotCombinedGSEA(
  GSEA_results,
  sig_threshold = 0.05,
  PointSize = 4,
  widthlegend = 16
)

Arguments

GSEA_results

A named list of data frames, where each data frame contains GSEA results for a contrast. Each data frame should have the columns: NES (Normalized Enrichment Score), padj (adjusted p-value), and pathway (pathway name). Output from runGSEA.

sig_threshold

Numeric, default = 0.05. Adjusted p-value threshold for significance. A dashed horizontal line is drawn at this threshold.

PointSize

Numeric, default = 4. Size of the plotted points.

widthlegend

Numeric, default = 16. Controls the width of pathway labels in the legend.

Value

A ggplot2 object displaying the combined GSEA results.

Examples

# Example GSEA results (mock data)
GSEA_results <- list(
"Contrast1" = data.frame(
NES = rnorm(3),
  padj = runif(3),
  pathway = paste("Pathway", 1:3),
  stat_used = c("t", "B", "B")
),
"Contrast2" = data.frame(
  NES = rnorm(3),
  padj = runif(3),
  pathway = paste("Pathway", 4:6),
  stat_used = c("t", "B", "B")
)
)


# Generate the plot
plotCombinedGSEA(GSEA_results, sig_threshold = 0.05, PointSize = 4)