Hi Paul,

thank you, sorry for the unfocused question again.

I was thinking in export graphs in .sif from R, like this one

http://metexplore.toulouse.inra.fr/metexploreJoomla/metexplore/tmp/graph_1584167971.sif

maybe some one already did that.
So exporting a file like this I could send to a collaborator.

I usually export as
cw <- new.CytoscapeWindow ('Pathway', graph=g)

and inside cytoscape I save as .sif. I will be nice save the graphs from R.
(by the way, today I tried to communicate with cytoscape and had this error:

cw <- existing.CytoscapeWindow ('human_BioCyc',
 copy.graph.from.cytoscape.to.R=TRUE)
Error in function (type, msg, asError = TRUE)  :
  Recv failure: Connection reset by peer
cw <- new.CytoscapeWindow ('vignette', graph=g)
Error in function (type, msg, asError = TRUE)  :
  Recv failure: Connection reset by peer

do you know this error?

About the plots, I know which plots I want from R, but, even working with
small networks (up to 60 nodes) one plot to each node will be very hard to
visualize at once. So, if we could "hide' them and show with one click,
will help a lot. In my case each node is a metabolite, and I have
intensities for various samples, with a scatter plot for all samples
together.

Thanks

Ricardo

2013/3/14 Paul Shannon <pshannon@fhcrc.org>

> 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:
>
>
> http://rcytoscape.systemsbiology.net/versions/current/cookbook/infoNodes-plots/
>
> 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.
>
> Cheers,
>
>  - Paul
>
>
>
> > Sorry if it is too basic or unreasonable.
> >
> > thks
> >
> > Ricardo
> >
> >       [[alternative HTML version deleted]]
> >
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>
>

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