Plot bayesian network inferred from expression data based on the enrichment analysis results from libraries including clusterProfiler and ReactomePA using bnlearn.

BiocManager::install("CBNplot")

library(devtools)
install_github("noriakis/CBNplot")

• Documentation: https://noriakis.github.io/software/CBNplot/
• Web server: https://cbnplot.com
  • Currently moving to the new server (2024/04/07)

• The gene-to-gene relationship compared with the reference network.

• The plot is customizable highliting edges and nodes like hub genes.

• The example using MicrobiomeProfiler, thanks to the fix by @xiangpin.

library(MicrobiomeProfiler)
data(Rat_data)
ko.res <- enrichKO(Rat_data)
exp.dat <- matrix(abs(rnorm(910)), 91, 10) %>% magrittr::set_rownames(value=Rat_data) %>% magrittr::set_colnames(value=paste0('S', seq_len(ncol(.))))
exp.dat %>% head
library(CBNplot)
bngeneplot(ko.res, exp=exp.dat, pathNum=1, orgDb=NULL)

• Another customized plot.