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", "scatter", or "heatmap"
p_threshold	A numeric value specifying the significance threshold

Value

A ggplot2 object or a list containing the plot and comparison results

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
gsea_results <- pathway_gsea(
  abundance = abundance_data,
  metadata = metadata,
  group = "Environment",
  pathway_type = "KEGG",
  method = "fgsea"
)

# 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 13, 2025, 9:08 a.m.