visualize_gsea: Visualize GSEA results

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

Visualize GSEA results

Description

This function creates various visualizations for Gene Set Enrichment Analysis (GSEA) results.

Usage

visualize_gsea(
  gsea_results,
  plot_type = "enrichment_plot",
  n_pathways = 20,
  sort_by = "p.adjust",
  colors = NULL,
  abundance = NULL,
  metadata = NULL,
  group = NULL,
  network_params = list(),
  heatmap_params = list()
)

Arguments

gsea_results	A data frame containing GSEA results from the pathway_gsea function
plot_type	A character string specifying the visualization type: "enrichment_plot", "dotplot", "barplot", "network", or "heatmap"
n_pathways	An integer specifying the number of pathways to display
sort_by	A character string specifying the sorting criterion: "NES", "pvalue", or "p.adjust"
colors	A vector of colors for the visualization
abundance	A data frame containing the original abundance data (required for heatmap visualization)
metadata	A data frame containing sample metadata (required for heatmap visualization)
group	A character string specifying the column name in metadata that contains the grouping variable (required for heatmap visualization)
network_params	A list of parameters for network visualization
heatmap_params	A list of parameters for heatmap visualization

Value

A ggplot2 object or ComplexHeatmap object

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"
)

# Create enrichment plot
visualize_gsea(gsea_results, plot_type = "enrichment_plot", n_pathways = 10)

# Create dotplot
visualize_gsea(gsea_results, plot_type = "dotplot", n_pathways = 20)

# Create barplot
visualize_gsea(gsea_results, plot_type = "barplot", n_pathways = 15)

# Create network plot
visualize_gsea(gsea_results, plot_type = "network", n_pathways = 15)

# Create heatmap
visualize_gsea(
  gsea_results,
  plot_type = "heatmap",
  n_pathways = 15,
  abundance = abundance_data,
  metadata = metadata,
  group = "Environment"
)

## End(Not run)

ggpicrust2 documentation built on April 13, 2025, 9:08 a.m.