README.md

aPEAR: an R package for enrichment network visualisation

Citation

If you use this package in your research, please cite:

Kerseviciute I, Gordevicius J. aPEAR: an R package for autonomous visualisation of pathway enrichment networks. BioRxiv. 2023 Mar 29; doi: 10.1101/2023.03.28.534514

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'))