View source: R/enrichmentNetwork.R
plotPathClusters | R Documentation |
Creates enrichment network plot.
plotPathClusters(
enrichment,
sim,
clusters,
theme = aPEAR.theme,
verbose = FALSE,
...
)
enrichment |
a data.frame containing enrichment results |
sim |
similarity matrix of the enriched pathways |
clusters |
clusters of the enriched pathways |
theme |
object of class |
verbose |
enable / disable log messages |
... |
additional parameters (see |
a ggplot2
object
# 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)
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