[BioC] Quick questions about RCytoscape

Paul Shannon pshannon at fhcrc.org
Thu Mar 14 16:56:40 CET 2013

Hi Ricardo,

I believe there are three strategies to explore:  

   1) CyRFace: http://www.ebi.ac.uk/saezrodriguez/cno/cyrface/
   2) RCytoscape:  the Bioconductor package
   3) Write appropriate cytoscape files from R (interactions, node & edge attributes)

Some specifics below.

On Mar 13, 2013, at 2:40 PM, Ricardo Silva wrote:

> Hi,
> Anyone knows if there is a way to include R plots as node attributes, so
> that we can click and see the plots for each node in cytoscape?

RCytoscape offers something vaguely like this, in which the nodes ARE plots.   See:


More flexibly, still using RCytoscape, you could write an R function which

  1) queried Cytoscape for currently selected node/s
  2) marshalled appropriate data in R and created the plot you want.

   plotExpression(getSelectedNodes(cw, list.of.conditions))

I have not tried it, but by attaching an instance of RServe to Cytoscape, CyRFace perhaps permits you to issue an R plotting command from Cytoscape.

> Additionally, is it possible to export a cytoscape format from R, so that
> can produce graphs automatically and send to someone without opening
> cytoscape myself?

Do you want to send
   a) Cytoscape session files?
   b) a jpeg or png of the resulting network?
   c) input files your intended user could interactively load into Cytoscape?
   d) R code which creates a graph and displays it in Cytoscape?

All of these are possible.  I'd be glad to give you specifics.


 - Paul

> Sorry if it is too basic or unreasonable.
> thks
> Ricardo
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