revigoR

Quickstart

install.packages('remotes')
remotes::install_github('alexvpickering/revigoR')

library(revigoR)

# setup python virtualenv for scraping revigo (one time only)
setup_env()

# see ?add_path_genes for example workflow starting with limma differential expression
data(go_up1)

# submit goana result to revigo web app and download results to data_dir
data_dir <- tempdir()
scrape_revigo(data_dir, go_up1)

# forcegraph of revigo results (from cytoscape graph)
revigo_forcegraph(data_dir)

An interactive scatterplot using the MDS coordinate from revigo can also be generated:

revigo_scatterplot(data_dir)

Two GO Analyses

Visualize where revigo merges terms across two GO analyses (shades of purple) and doesn't (shades of orange and green for each analysis respectively):

# two analyses
data(go_up2)
go_up1$analysis <- 0
go_up2$analysis <- 1
go_up <- rbind(go_up1, go_up2)

data_dir <- tempdir()
scrape_revigo(data_dir, go_up)
revigo_forcegraph(data_dir)

revigo_scatterplot also supports two analysis results:

revigo_scatterplot(data_dir)