Thanks Tim,

Yes you are true if the adjacency matrix is a square matrix (NxN). But my adjacency is non square NxM matrix. 

Regards, 
Pankaj


________________________________
 From: "Tim Triche, Jr." <tim.triche@gmail.com>

Cc: "bioconductor@r-project.org" <bioconductor@r-project.org> 
Sent: Saturday, 24 March 2012 6:16 PM
Subject: Re: [BioC] Adjacency to network using R


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 ?





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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