enrichmentNetwork {aPEAR}

aPEAR enrichment network

Description

Creates an enrichment network plot. This function internally calls findPathClusters to obtain pathway clusters and then plotPathClusters to create the enrichment network visualization.

Usage

enrichmentNetwork(
  enrichment,
  methods = aPEAR.methods,
  theme = aPEAR.theme,
  verbose = FALSE,
  ...
)

Arguments

enrichment

a data.frame containing enrichment results

methods

object of class aPEAR.methods.config

theme

object of class aPEAR.theme.config

verbose

enable / disable log messages

...

additional parameters (see ?aPEAR.methods and ?aPEAR.theme)

Value

a ggplot2 object

See Also

?findPathClusters, ?plotPathClusters

Examples

# Load libraries
library(clusterProfiler)
library(DOSE)
library(org.Hs.eg.db)
data(geneList)

# Perform enrichment using clusterProfiler
enrich <- gseGO(geneList, OrgDb = org.Hs.eg.db, ont = 'CC')

# Create enrichment network visualization with default parameters
enrichmentNetwork(enrich@result)

# Create enrichment network visualization with repelled labels and elipses
enrichmentNetwork(enrich@result, repelLabels = TRUE, drawEllipses = TRUE)