This vignette will show you how to convert networks between graphNEL and Cytoscape.
The whole point of RCy3 is to connect with Cytoscape. You will need to install and launch Cytoscape:
The graph package is a popular network tool among R users. With RCy3, you can easily translate graphNEL networks to Cytoscape networks!
Create a simple GraphNEL object
g <- makeSimpleGraph()
Now pass it along to Cytoscape:
Inversely, you can use createGraphFromNetwork() in RCy3 to retreive vertex (node) and edge data.frames to construct a GraphNEL object.
g2 <- createGraphFromNetwork("myGraph")
Compare the round-trip result for yourself…