[BioC] Quick questions about RCytoscape
pshannon at fhcrc.org
Thu Mar 14 16:56:40 CET 2013
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:
> 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.
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.
> Sorry if it is too basic or unreasonable.
> [[alternative HTML version deleted]]
> Bioconductor mailing list
> Bioconductor at r-project.org
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
More information about the Bioconductor