aPEAR (version 1.0.0)

plotPathClusters: aPEAR enrichment network

Description

Creates enrichment network plot.

Usage

plotPathClusters(
  enrichment,
  sim,
  clusters,
  theme = aPEAR.theme,
  verbose = FALSE,
  ...
)

Value

a ggplot2 object

Arguments

enrichment

a data.frame containing enrichment results

sim

similarity matrix of the enriched pathways

clusters

clusters of the enriched pathways

theme

object of class aPEAR.theme.config

verbose

enable / disable log messages

...

additional parameters (see ?aPEAR.theme)

Examples

# \donttest{
# 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')

# Obtain clusters within the enriched pathways using default parameters
data <- findPathClusters(enrich@result)

# Create the enrichment network visualization using default parameters
plotPathClusters(enrich@result, data$sim, data$clusters)

# Create the enrichment network visualization with repelled labels and elipses
plotPathClusters(enrich@result, data$sim, data$clusters, repelLabels = TRUE, drawEllipses = TRUE)
# }