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 1.6.2 Index]