plotEnrichment {MOFA} | R Documentation |
Method to plot the results of the Feature Set Enrichment Analyisis (FSEA)
plotEnrichment(object, fsea.results, factor, alpha = 0.1, max.pathways = 25, adjust = TRUE)
object |
|
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? |
a ggplot2
object
# 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)