compare_gsea_daa: Compare GSEA and DAA results

In ggpicrust2: Make 'PICRUSt2' Output Analysis and Visualization Easier

Compare GSEA and DAA results

Description

This function compares the results from Gene Set Enrichment Analysis (GSEA) and Differential Abundance Analysis (DAA) to identify similarities and differences.

Usage

compare_gsea_daa(
  gsea_results,
  daa_results,
  plot_type = "venn",
  p_threshold = 0.05
)

Arguments

gsea_results	A data frame containing GSEA results from the pathway_gsea function
daa_results	A data frame containing DAA results from the pathway_daa function
plot_type	A character string specifying the visualization type: "venn", "upset", or "scatter"
p_threshold	A numeric value specifying the significance threshold

Value

A list with two elements: plot (a ggplot2 object, or an UpSetR object when plot_type = "upset" and UpSetR is installed) and results (a named list with the overlap, GSEA-only, and DAA-only pathway sets plus their counts).

Examples

## Not run: 
# Load example data
data(ko_abundance)
data(metadata)

# Prepare abundance data
abundance_data <- as.data.frame(ko_abundance)
rownames(abundance_data) <- abundance_data[, "#NAME"]
abundance_data <- abundance_data[, -1]

# Run GSEA analysis (using camera method - recommended)
gsea_results <- pathway_gsea(
  abundance = abundance_data,
  metadata = metadata,
  group = "Environment",
  pathway_type = "KEGG",
  method = "camera"
)

# Run DAA analysis
daa_results <- pathway_daa(
  abundance = abundance_data,
  metadata = metadata,
  group = "Environment"
)

# Compare results
comparison <- compare_gsea_daa(
  gsea_results = gsea_results,
  daa_results = daa_results,
  plot_type = "venn"
)

## End(Not run)

ggpicrust2 documentation built on April 30, 2026, 1:06 a.m.