plotEnrichmentHeatmap {MOFA} | R Documentation

## Heatmap of Feature Set Enrichment Analysis results

### 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)

[Package MOFA version 1.6.2 Index]