[BioC] tool for drawing interaction network

[Gilbert Feng]

Hi, Guido

I don't know other packages, but igraph (R package) can do similar stuff. It
has tcl/tk interactive mode, but you can move the nodes to generate a
goodlook netowrk. In other words, length of edge can be manually adjusted,
however, you can use the width of edge for your index scores. The details
can be found in the manual.

Best

Gilbert


On 5/20/10 5:06 PM, "Hooiveld, Guido" <Guido.Hooiveld at 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.
> 
> 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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