plotEnrichmentHeatmap: Heatmap of Feature Set Enrichment Analysis results

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

Description

This method generates a heatmap with the adjusted p.values that result from the the feature set enrichment analysis. Rows are feature sets and columns are factors.

Usage

plotEnrichmentHeatmap(fsea.results, alpha = 0.05, logScale = TRUE, ...)

Arguments

fsea.results	output of runEnrichmentAnalysis function
alpha	FDR threshold to filter out unsignificant feature sets which are not represented in the heatmap. Default is 0.05.
logScale	boolean indicating whether to plot the log of the p.values.
...	extra arguments to be passed to pheatmap function

Value

produces a heatmap

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)

# overview of enriched pathways per factor at an FDR of 1%
plotEnrichmentHeatmap(fsea.results, alpha=0.01)

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