README.md

In noriakis/CBNplotTest: 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

From Bioconductor:

BiocManager::install("CBNplot")

From GitHub:

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

Usage

• Documentation: https://noriakis.github.io/software/CBNplot/
• Web server: https://cbnplot.com

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/CBNplotTest documentation built on Nov. 18, 2022, 8:05 a.m.