[BioC] tool for drawing interaction network

[Michael Imbeault]

Have a look at Gephi (http://gephi.org/) as an alternative to Cytoscape.

They have a library to import graphs - python, php, c++ or java.

Michael

On 20/05/2010 6:06 PM, Hooiveld, Guido wrote:
> Dear list,
>
> Does anyone know of a method (tool), preferably available in BioC, that allows the drawing of an interaction network of which the topology is based on user-defined input?
>
> I have a set of (KEGG) pathways, of which i calculated an 'overlap index'. That is, the more genes are common in two sets the higher the overlap index score is.
> Now i would like to create a interaction network consisting of nodes (pathways) and edges such way that the overlap index determines the distance between the nodes (length of the edge). Thus, ideally, the higher the overlap index is between two pathways (nodes), the closer the nodes are grouped together in the network.
>
> I am new to this type of data representation and would appreciate any suggestion! Cytoscape? Currently i am visualizing this data using a heatmap but i think representation in an interaction network would be much more informative.
>
> Thanks,
> Guido
>
>
> ------------------------------------------------
> Guido Hooiveld, PhD
> Nutrition, Metabolism&  Genomics Group
> Division of Human Nutrition
> Wageningen University
> Biotechnion, Bomenweg 2
> NL-6703 HD Wageningen
> the Netherlands
> tel: (+)31 317 485788
> fax: (+)31 317 483342
> internet:   http://nutrigene.4t.com<http://nutrigene.4t.com/>
> email:      guido.hooiveld at wur.nl
>
>
>
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