Hi Paul
I would really appreciate a plugin to connect/control/share data with
Cytoscape and R. Great idea!
At present I am working on ontologies and I would like to use Cytoscape to
get and show some results obtained with R.
How can I participate on this idea?

Cristóbal Fresno
PhD Student, National University of Córdoba, Argentina

2010/6/21 Paul Shannon <pshannon@systemsbiology.org>

> 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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