doesn't RCytoscape take a graphNEL object as input for some routines?  In
Paul Shannon's workshop I seemed to remember this being the case (look at
the materials from Bioc2011, there should be a bunch of examples).
 Adjacency matrices are almost always much smaller when represented as
adjacency lists, and a graphAM can be coerced to a graphNEL for the purpose
you wish.

R> library(graph)
R> class?graphAM
R> class?graphNEL
# say your adj. matrix is in matrix 'mat'
R> graphmat <- new("graphAM", adjMat=mat, edgemode='directed')
R> graphlist <- as(graphmat, 'graphNEL')

# now from the vignette:
R> library(RCytoscape)
R> cw <- new.CytoscapeWindow ('vignette', graph=graphlist)
R> displayGraph(cw)

Is that the sort of thing you were thinking of ?



On Sat, Mar 24, 2012 at 8:46 AM, pankaj borah <pankajborah2k3@yahoo.co.in>wrote:

> Hi All,
>
>
> Can anyone help me with how to convert an adjacency matrix of (NxM)
> dimension  to cytoscape
> input file (edge list, SIF etc) using R ?
>
>
> Consider an adjacency of  5x10 dimension , where rows are genes
> and columns are metabolite(or vice versa). Now if I want to import it to
> any network visualization software how can I do that ?
>
>
> Thanks,
>
> Pankaj
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>
>
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-- 
*A model is a lie that helps you see the truth.*
*
*
Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>

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