[BioC] RCytoscape performance

Chad Burrus chburrus at indiana.edu
Wed Nov 10 22:29:41 CET 2010

Does anyone have any experience with the RCytoscape package and highly
connected graphs?  I've got a graph being built dynamically with R and
then pushed over to Cytoscape via the RCytoscape plugin.  However, the
communication between R and Cytoscape is taking an incredibly long
time--3-4 days for a graph with 362 nodes and 65703 edges, to be
precise.  I'm still working on figuring out exactly which of the
commands is taking so long (or if it's a combination of all of them,
as I'm coming to suspect), but I've reproduced the code I'm using to
interact with RCytoscape below.  It's basically just the tutorial
code, though (from

Some context:  I'm running R 2.11.1, Cytoscape 2.7.0, and CytoscapeRPC
1.2 on a Linux box with a manual install of the RCytoscape and XMLRPC
packages as described at
 I can get more information if you need it.

Thanks in advance for any help.

Chad Burrus
MS Bioinformatics, Candidate
School of Informatics and Computing
Indiana University, Bloomington
Phone: (812) 783-9127

  R Code
# graph is a graphAM object that's fully constructed except for the
attributes added below
graph = initNodeAttribute(graph, "sourceDataset", "char", "X")
nodeData(graph, xNames, "sourceDataset") = "X"
nodeData(graph, yNames, "sourceDataset") = "Y"
graph = initEdgeAttribute(graph, "dot", "numeric", 0)
# add the edgeData at the last minute to improve performance
edgeData(graph, from, to, "dot") = dotData

# from here on, things are really slow
cw = CytoscapeWindow(paste(prefix, "Network"), graph)

  End R Code

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