README.md

In noriakis/CBNplot: plot bayesian network inferred from gene expression data based on enrichment analysis results

CBNplot: Bayesian network plot for the enrichment analysis results

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

Installation

BiocManager::install("CBNplot")

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

Usage

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

Plot examples

• 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.

noriakis/CBNplot documentation built on Oct. 10, 2024, 12:21 p.m.