plotEnrichment: Plot output of Feature Set Enrichment Analysis

In bioFAM/MOFA: Multi-Omics Factor Analysis (MOFA)

Description

Method to plot the results of the Feature Set Enrichment Analyisis (FSEA)

Usage

plotEnrichment(object, fsea.results, factor, alpha = 0.1,
  max.pathways = 25, adjust = TRUE)

Arguments

object	MOFAmodel object on which FSEA was performed
fsea.results	output of runEnrichmentAnalysis function
factor	string with factor name or numeric with factor index
alpha	p.value threshold to filter out feature sets
max.pathways	maximum number of enriched pathways to display
adjust	use adjusted p-values?

Value

a ggplot2 object

Examples

# Example on the CLL data
filepath <- system.file("extdata", "CLL_model.hdf5", package = "MOFAdata")
MOFAobject <- loadModel(filepath)

# perform Enrichment Analysis on mRNA data using pre-build Reactome gene sets
data("reactomeGS", package = "MOFAdata")
fsea.results <- runEnrichmentAnalysis(MOFAobject, view="mRNA", feature.sets=reactomeGS)

# Plot top 10 enriched pathwyas on factor 5:
plotEnrichment(MOFAobject, fsea.results, factor=5,  max.pathways=10)

bioFAM/MOFA documentation built on Oct. 3, 2020, 12:53 a.m.