[Bioc-devel] Classes to be supported by ggraph

Paul Shannon pshannon at systemsbiology.org
Sun Feb 7 17:57:23 CET 2016

Possibly of interest on this topic, though it implements a different sort of (interactive) solution, are two Bioc packages:  RCyjs and RCy3.  

RCyjs renders to the browser, using the cytoscape.js javascript library and websockets:


RCy3 renders to Cytoscape, the mature and  popular network visualization desktop app:


Both bioc packages forgo the relatively non-interactive tradition of plotting in R, for a fully interactive approach.  Both R and the rendering platforms are simultaneously and reciprocally fully interactive.

The devel versions of each of these packages would be the ones to look at if you are interested.

RCyjs http://bioconductor.org/packages/3.3/bioc/html/RCyjs.html 
RCy3  http://bioconductor.org/packages/3.3/bioc/html/RCy3.html

RCyjs is currently a little bit more mature, but RCy3 is rapidly catching up.  

RCyjs is based upon the Bioc class “BrowserViz” and uses he httpuv package maintained by the Shiny project and nicely extended by Hector Corrado Bravo for http and web socket.

The goal of both of these packages is

1) use community standard network visualization tools (Cytoscape for the desktop, cytoscape.js in the browser)

2) preserve and extend the fully interactive nature of both R, and the Cytoscape* rendering and analysis platforms.

The unit tests for each package are extensive.  They, along with the package vignettes, are a good introduction to the capabilities and programming idioms of the packages.  They may be of interest to some.   Questions, bug reports, requests for new features are always welcome.


 - Paul

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