[BioC] cytoscapePlot() from graphite package

[Paul Shannon]

Hi John,

To install the CytoscapeRPC plugin:

  1) make sure that you have Cytoscape 2.8.3 installed
  2) start Cytoscape
  3) from the "Plugins" menu, choose "Manage Plugins"
  4) Under "Communication/Scripting" (or maybe just "Scripting") locate CytoscapeRPC
  5) Install, restart Cytoscape, then 
  6) From the plugins menu, choose CytoscapeRPC->Activate
  7) You can also set CytoscapeRPC->Setting->Autostart

Let me know if this works.

 - Paul

On Jan 21, 2013, at 3:13 PM, array chip wrote:

> Thank you Paul! Can you please show me how to enable/install CytoscapeRPC? I am new to bioconductor, I simply installed graphite package with:
> 
> source("http://bioconductor.org/biocLite.R")
> biocLite("graphite")
> 
> 
> Thanks,
> 
> John
> 
> 
> 
> From: Paul Shannon <pshannon at fhcrc.org>
> To: array chip <arrayprofile at yahoo.com> 
> Cc: Paul Shannon <pshannon at fhcrc.org>; Bioconductor Mailing List <bioconductor at r-project.org> 
> Sent: Monday, January 21, 2013 3:02 PM
> Subject: Re: [BioC] cytoscapePlot() from graphite package
> 
> Hi John,
> 
> This usually means that Cytoscape is not running, or that the CytoscapeRPC plugin is not enabled, or not enabled on the correct port. 
> 
> Let us know if you still have trouble after these things are set up.
> 
> - Paul
> 
> 
> 
> On Jan 21, 2013, at 2:58 PM, array chip wrote:
> 
> > Hi, I was trying to use cytoscapePlot() from the graphite package, but got the error message below:
> > 
> >> library(graphite)
> >> cytoscapePlot(convertIdentifiers(reactome$`Unwinding of DNA`, "symbol"))
> > Loading required package: RCytoscape
> > Loading required package: XMLRPC
> > Error in function (type, msg, asError = TRUE)  : couldn't connect to host
> > In addition: Warning messages:
> > 1: package ‘RCytoscape’ was built under R version 2.15.2 
> > 2: package ‘XMLRPC’ was built under R version 2.15.2
> > 
> > 
> > What's the problem here?
> > 
> > thanks!
> > 
> > John
> >     [[alternative HTML version deleted]]
> > 
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