CBNplot
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Bayesian network plot for the 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)
![](https://github.com/noriakis/software/blob/main/images/CBNplot_readme_MP.png?raw=true)
- Another customized plot.