plotEnrichmentHeatmap {MOFA} | R Documentation |
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.
plotEnrichmentHeatmap(fsea.results, alpha = 0.05, logScale = TRUE, ...)
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 |
produces a heatmap
# 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)