Given the similarity between these two packages, I decided to use my old R script ( plotNetworksRcytoscape.R) but with the RC圓 functions instead of those from RCytoscape, and with the new Cytoscape (v. Although the name is different, this package is actually a replacement for the old RCytoscape package and if you look at its reference manual, you will see that the majority of functions from the RCytoscape package are available under the same name in RC圓. If you have a new version of Cytoscape but don’t want to think about details of how R and Cytoscape communicate, then the RC圓 package is the tool you want. If you’re interested in network visualization with cyREST, I recommend you to check the cyRest R GitHub page that provides some code examples and required utility files. Instead, the recommended way to communicate with the new Cytoscape from R (and other scripting languages) is through the cyREST API. Starting with version 3, Cytoscape does not support CytoscapeRPC plugin. While some other network visualization tools may provide somewhat fancier network plots, the ability to see changes in visualization after running each command was a feature that made a difference for me and made me use Cytoscape more than other similar tools. I am a big fan of plotting networks in Cytoscape directly from R and I have to admit that I kept a copy of old Cytoscape version just to be able to use CytoscapeRPC and RCytoscape.
USING CYTOSCAPE UPDATE
Since then, some tools changed and some new tools appeared and I decided it is time to update my online notes.
USING CYTOSCAPE HOW TO
A few years ago I wrote a series of blogs about network visualization in R ( 1, 2, 3, and 4), as a mean of keeping organized notes on how to do it for myself but also for (hopefully) helping others to create their own plots efficiently.
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