plotEnrichment {MOFA}R Documentation

Plot output of Feature Set Enrichment Analysis

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)
[Package MOFA version 1.4.0 Index]