[BioC] 5000 nodes RCytoscape

[Paul Shannon]

(Summarizing to the bioc list so the record will be complete.)

Your 5000-node, 6000-edge graph transmits from R to Cytoscape in less than 20 seconds.  Layout takes a bit longer.  All this works reliably up-to-date versions of the packages -- yours are quite old!  This crucially includes Duncan Temple Lang's XMLRPC_0.3.0.  which just reached Duncan's OmegaHat website.

   http://www.omegahat.org/XMLRPC/

It should be picked up soon, and automatically, along with everything else you need, via our standard mechanism:

   biocLite("RCytoscape")

A slightly condensed and somewhat improved version of your application code (creating the graph, sending it via RCytoscape) is included below.

Please let us know how this works.

Cheers!

  - Paul

On Mar 21, 2013, at 5:02 PM, Paul Shannon wrote:

> Hi Ruben,
> 
> Your difficulties should disappear with the update of a few packages.
> 
> (In addition, a slightly updated version of the code is pasted in below.)
> 
> You need to update many of your packages -- there are seriously out of date!  RCytoscape, graph, XMLRPC, XML all need to be updated.  See below for how to do this quick and easy with "biocLite".  
> 
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base     
> 
> other attached packages:
> [1] RCytoscape_1.9.7    XMLRPC_0.3-0        graph_1.37.7        BiocInstaller_1.9.8
> 
> loaded via a namespace (and not attached):
> [1] BiocGenerics_0.5.6 RCurl_1.95-3       XML_3.95-0.1       compiler_3.0.0     parallel_3.0.0     stats4_3.0.0       tools_3.0.0       
> 
> The preferred way to update -- since it picks up all dependencies -- is
> 
> source("http://bioconductor.org/biocLite.R")
> biocLite("RCytoscape")
> 
> I am doing my best to encourage Duncan Temple Lang, author of XMLRPC, to update his public offering to the version which has his speedup fixes, XMLRPC_0.3-0.  In the absence of that, I attach the package here:
> 
> <XMLRPC_0.3-0.tar.gz>
> 
> 
> Let me know how this works.
> 
> - Paul
> 
> 
> ---- graph creation and display code
> 
> filename <- "adj.txt"
> adj<-read.table(filename,sep=",")
> rownames(adj)=1:5000
> colnames(adj)=1:5000
> p=as.matrix(adj)
> 
> library (RCytoscape)
> 
>  # if you want to remove self-loops, enable this line
> diag (p) = 0   # remove any self-loops
> 
>  # now create a Bioconductor graph of subclass 'graphAM'
> g = new ('graphAM', adjMat=p, edgemode='directed')
> 
>  # these next few lines are useful if you run this script repetetively, since RCy requires that all window names are unique,
>  # these lines allows you to detect and then delete any pre-existing window with the same name
> 
> if (!exists('cy'))   # get access to application-level Cytoscape operations.
>  cy = CytoscapeConnection ()
> 
> window.name = 'adjacency matrix graph '
> 
>  # now create a window, send the graph, render it, lay it out
> 
> cw = CytoscapeWindow(window.name, g, overwriteWindow=TRUE)
> system.time(displayGraph (cw))   # 19 seconds elapsed time for me
> redraw (cw)
> 
> # I suggest you do layout from the Cytoscape menu (Layout->yFiles->Organic)
> # It is faster and better than jgraph-spring
> # layoutNetwork (cw, 'jgraph-spring')
> 
> 
> 
> 
> 
> 
> 
> On Mar 20, 2013, at 1:47 PM, rubens at andrew.cmu.edu wrote:
> 
>> Hi Paul,
>> 
>> I attach you all the required information:
>> 
>> a) The exact R code I used is in a txt file call coderuben.txt (attached)
>> b) I made a zip file with the adjacency matrix adj.txt.zip (attached)
>> c) the sessionInfo() and versions are:
>> 
>> 
>>> sessionInfo()
>> R version 2.14.0 (2011-10-31)
>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>> 
>> locale:
>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>> 
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>> 
>> other attached packages:
>> [1] RCytoscape_1.4.4 XMLRPC_0.2-4     graph_1.32.0
>> 
>> loaded via a namespace (and not attached):
>> [1] RCurl_1.91-1 tools_2.14.0 XML_3.9-4
>> 
>> Cytoscape version 2.8.3
>> CytoscapeRPC plugin version 1.8
>> 
>> 
>> 
>> Thanks
>> Ruben
>> <coderuben.txt><adj.txt.zip>
>