[BioC] proposed: a bridge between R and Cytoscape

Steve Lianoglou mailinglist.honeypot at gmail.com
Tue Jun 22 18:37:56 CEST 2010

Hi Paul,

Your talk at the Adv. Bioc. workshop in May got me interested in this
topic, which somehow led me to stumble on this post on this Gephi


You can see my post (author "lianos") asking if this could let someone
drive Gephi from other languages. It seems there are two ways one
could go about that (using some toolkit, and also a "graph streaming"
project that is underway this summer).

Look at the reply from mbastian:


Perhaps this can help you in your endeavor. I'm not a big cytoscape
user, and haven't really compared cytoscape and Gephi, but some of the
videos I've seen of Gephi in action seem pretty cool:



On Mon, Jun 21, 2010 at 5:21 PM, Paul Shannon
<pshannon at systemsbiology.org> wrote:
> Many years ago, a couple of us wrote the first version of Cytoscape.  That project has subsequently, in the hands of others, developed into a fairly popular bioinformatics network exploration tool, with a variety of analytical and layout plugins.
> I, myself, have spent most of the intervening years analyzing data with R and Bioconductor, doing network visualization with an ad hoc, home-grown rJava & RMI connection I ginned up to an old version of cytoscape.
> I propose, now, to redo that, probably using sockets (a la the IGV/R bridge) from R, connecting to, and controlling Cytoscape 2.7 via a new plugin.
> I propose to provide a 'little language' in a bioconductor package, which allows graphs (nodes, edges, and arbitrary attributes) to be passed back and forth; to be laid out; rendered; animated (for example, with time course experimental data); along with some simple manipulations.  My little language is excerpted below.
> The Cytoscape community has expressed some enthusiasm for this idea, and offered some assistance.  I hope to find similar interest (and maybe occasional support) from the Bioc and general R communities as well.
> If you have any comments or suggestions on this idea, I'd love to hear them.  I want to do this in such a way that it will be useful to lots of people.
>  - Paul Shannon
>   Institute for Systems Biology
>   Seattle
> --- the existing R/cytoscape little language
> send (graph)
> get ()        # current subnetwork displayed in Cytoscape
> select (node.names)
> selectFirstNeighbors ()
> clear ()     # clears all current selections
> invert ()    # inverts the current selection
> hide ()      # hides selected nodes
> unhide ()    # reveals everything hidden
> deleteSelection ()
> destroy ()   # deletes the current graph
> layout ()    # asks that the current layout be applied;  actual
> write.gml (filename)  # save current graph to file
> render ()    # applies all visual mapping ('vizmap') rules, see below
> --- vizmap rules:  specify node and edge rendering, in which the specified attribute controls visual appearance
> nodeLabel (graph, nodeAttributeName)
> nodeFontSize (newSize)
> nodeShape (graph, nodeAttributeName, keyValuePairs)
> defaultNodeShape (graph, shape)
> defaultNodeSize (graph, size)
> nodeSize (graph, nodeAttributeName, keyValuePairs)
> nodeColor (graph, nodeAttributeName, keyValuePairs)
> nodeColorDiscrete (graph, nodeAttributeName, keyValuePairs)
> defaultNodeColor (graph, color)
> nodeBorderStyle (graph, nodeAttributeName, keyValuePairs)
> defaultNodeBorderStyle (graph, style)
> nodeBorderColor (graph, nodeAttributeName, keyValuePairs)
> defaultNodeBorderColor (graph, color)
> edgeColor (graph, edgeAttributeName, keyValuePairs)
> edgeColorDiscrete (graph, edgeAttributeName, keyValuePairs)
> defaultEdgeColor (graph, color)
> edgeStyle (graph, edgeAttributeName, keyValuePairs)
> defaultEdgeStyle (graph, style)
> targetArrow (graph, edgeAttributeName, keyValuePairs)
> defaultTargetArrow (graph, arrow)
> sourceArrow (graph, edgeAttributeName, keyValuePairs)
> defaultSourceArrow (graph, arrow)
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Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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