On Thu, May 20, 2010 at 3:06 PM, Hooiveld, Guido <Guido.Hooiveld@wur.nl>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.
>
>
Drawing networks is easy using the Rgraphviz package. See the 'graph' and
'Rgraphviz' vignettes. There's also a chapter on it in the Bioc case studies
book.

Michael

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@wur.nl
>
>
>
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