plot_enrichment_detailed: Plot detailed output of the Feature Set Enrichment Analysis

In bioFAM/MOFA2: Multi-Omics Factor Analysis v2

Plot detailed output of the Feature Set Enrichment Analysis

Description

Method to plot a detailed output of the Feature Set Enrichment Analyisis (FSEA).
Each row corresponds to a significant pathway, sorted by statistical significance, and each dot corresponds to a gene.
For each pathway, we display the top genes of the pathway sorted by the corresponding feature statistic (by default, the absolute value of the weight) The top genes with the highest statistic (max.genes argument) are displayed and labeled in black. The remaining genes are colored in grey.

Usage

plot_enrichment_detailed(
  enrichment.results,
  factor,
  alpha = 0.1,
  max.genes = 5,
  max.pathways = 10,
  text_size = 3
)

Arguments

enrichment.results	output of run_enrichment function
factor	string with factor name or numeric with factor index
alpha	p.value threshold to filter out feature sets
max.genes	maximum number of genes to display, per pathway
max.pathways	maximum number of enriched pathways to display
text_size	size of the text to label the top genes

Value

a ggplot2 object

bioFAM/MOFA2 documentation built on June 12, 2024, 3:57 p.m.