/aPEAR

Enrichment Networks for Pathway Enrichment Analysis

Primary LanguageRMIT LicenseMIT

aPEAR: an R package for enrichment network visualisation

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Installation

Install latest stable version

library(devtools)
install_github('ievaKer/aPEAR')

Install latest beta version

library(devtools)
install_github('ievaKer/aPEAR@development')

Run an example

library(aPEAR)
library(clusterProfiler)
library(org.Hs.eg.db)
library(DOSE)
data(geneList)

enrich <- gseGO(geneList, OrgDb = org.Hs.eg.db, ont = 'CC')
p <- enrichmentNetwork(enrich@result, drawEllipses = TRUE, fontSize = 2.5)

p

Plotly integration

To create interactive plots, use plotly:

library(plotly)

ggplotly(p, tooltip=c('ID', 'Cluster', 'Cluster size'))

You may find example plots in results directory of this repository.