R Reactome FI Cytoscape plugin wrapper. This package currently implements a limited interface to ReactomeFI functionality including network construction, network clustering, and Pathway/GO term enrichment. It also implements some network plotting capabilities using either sna/ggplot2 or RCytoscape.
- plyr
- ggplot2
- sna
- RCurl
- XML
The easiest way to install reactomefi is through devtools:
devtools::install_github("funnell/reactomefi")
network <- ReactomeFINetwork("2012", genes)
annotate(network, "Pathway")
plot(network)
network <- ReactomeFINetwork("2012", genes, cluster=TRUE)
annotateModules(network, "Pathway")
plot(network)