Adjacency to network using R
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pankaj borah ▴ 120
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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 [[alternative HTML version deleted]]
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Tim Triche ★ 4.2k
@tim-triche-3561
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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 > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- *A model is a lie that helps you see the truth.* * * Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> [[alternative HTML version deleted]]
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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 >       [[alternative HTML version deleted]] > > >_______________________________________________ >Bioconductor mailing list >Bioconductor@r-project.org >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- A model is a lie that helps you see the truth. Howard Skipper [[alternative HTML version deleted]]
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How have you ended up with a non-square adjacency matrix? (can it be made square by adding additional columns/rows set to 0?) Alternatively, why not enumerate and add the edges between nodes for all [N,M] such that mat[n,m] != 0. (see the RCytoscape vignette for more on this and export functions) On Sat, Mar 24, 2012 at 12:33 PM, pankaj borah <pankajborah2k3@yahoo.co.in>wrote: > 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> > *To:* pankaj borah <pankajborah2k3@yahoo.co.in> > *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 ? > > > > 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 > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > -- > *A model is a lie that helps you see the truth.* > * > * > Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> > > > > -- *A model is a lie that helps you see the truth.* * * Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> [[alternative HTML version deleted]]
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How have I ended up with a non-square adjacency matrix: It is something like this - > m<-matrix(rnorm(1000),nrow=100,ncol=10,dimnames=list(paste("met",c(1 :100)))) > g<-matrix(rnorm(10000),nrow=1000,ncol=10,dimnames=list(paste("gen",c (1:1000)))) > cm<-cm <- cor(t(m),t(g)) > cm<-cor(t(m),t(g)) > ADJ<-ifelse(c(cm)>0.75,1,0) > dim(ADJ)<-dim(cm) > str(ADJ)  num [1:100, 1:1000] 0 0 0 0 0 0 0 0 0 0 ... Now need to convert the ADJ to a edge list or sif. I have tried igraph package. But, it can convert square Adjacency matrix to edge list or a graphNEL object. Is there a way that I can convert my non square AM to a graph object or edge list ? Pankaj ________________________________ From: "Tim Triche, Jr." <tim.triche@gmail.com> Cc: "bioconductor@r-project.org" <bioconductor@r-project.org> Sent: Saturday, 24 March 2012 9:08 PM Subject: Re: [BioC] Adjacency to network using R How have you ended up with a non-square adjacency matrix?  (can it be made square by adding additional columns/rows set to 0?) Alternatively, why not enumerate and add the edges between nodes for all [N,M] such that mat[n,m] != 0. (see the RCytoscape vignette for more on this and export functions) wrote: 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 >>       [[alternative HTML version deleted]] >> >> >>_______________________________________________ >>Bioconductor mailing list >>Bioconductor@r-project.org >>https://stat.ethz.ch/mailman/listinfo/bioconductor >>Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> > > > >-- >A model is a lie that helps you see the truth. > > >Howard Skipper > > > -- A model is a lie that helps you see the truth. Howard Skipper [[alternative HTML version deleted]]
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so here's a cheesy way to do it (as if I ever do things any other way), picking up where you left off: R> rownames(ADJ) = paste('met', 1:NROW(ADJ), sep='') R> colnames(ADJ) = paste('gen', 1:NCOL(ADJ), sep='') R> edges = which(ADJ==1, arr.ind=TRUE) R> mets = unique(rownames(ADJ)[edges[,1]]) R> gens = unique(colnames(ADJ)[edges[,2]]) R> nodes = c(mets, gens) R> gNEL = new('graphNEL', nodes=nodes) R> for(i in seq_along(rownames(edges))) { x = edges[i,] gNEL <- graph::addEdge(rownames(ADJ)[x[1]], colnames(ADJ)[x[2]], gNEL) } R> gNEL A graphNEL graph with undirected edges Number of Nodes = 566 Number of Edges = 646 Now the thing that bothers me about this is, what about tight correlations between metabolites or between genes? Might not you want to have a within-type graph for each, and a map from cliques in the metabolite graph to cliques in the gene graph? I do not know the answer to this, mind you, but it would concern me a little -- it almost seems like what you really might prefer would be to treat it as 100 variable selection problems (gene -> metabolite) and/or 10000 variable selection problems (metabolite -> gene) using something like SparseNet or glmnet, but that's just my take on the problem. Moving right along, then... # make sure Cytoscape is running with the CytoscapeRPC plugin v1.7 or higher, listening on port 9000 R> library(RCytoscape) R> cw <- new.CytoscapeWindow('ADJ', graph=gNEL) R> displayGraph(cw) So now the graph is in Cytoscape. More stuff is in the RCytoscape vignette. Don't forget to press the "apply force-directed layout" button to expand it. --t On Sat, Mar 24, 2012 at 4:00 PM, pankaj borah <pankajborah2k3@yahoo.co.in>wrote: > How have I ended up with a non-square adjacency matrix: > It is something like this - > > > > m<-matrix(rnorm(1000),nrow=100,ncol=10,dimnames=list(paste("met",c(1 :100)))) > > > g<-matrix(rnorm(10000),nrow=1000,ncol=10,dimnames=list(paste("gen",c (1:1000)))) > > cm<-cm <- cor(t(m),t(g)) > > cm<-cor(t(m),t(g)) > > ADJ<-ifelse(c(cm)>0.75,1,0) > > dim(ADJ)<-dim(cm) > > str(ADJ) > num [1:100, 1:1000] 0 0 0 0 0 0 0 0 0 0 ... > > Now need to convert the ADJ to a edge list or sif. I have tried igraph > package. But, it can convert square Adjacency matrix to edge list or a > graphNEL object. Is there a way that I can convert my non square AM to a > graph object or edge list ? > > Pankaj > ------------------------------ > *From:* "Tim Triche, Jr." <tim.triche@gmail.com> > *To:* pankaj borah <pankajborah2k3@yahoo.co.in> > *Cc:* "bioconductor@r-project.org" <bioconductor@r-project.org> > *Sent:* Saturday, 24 March 2012 9:08 PM > > *Subject:* Re: [BioC] Adjacency to network using R > > How have you ended up with a non-square adjacency matrix? (can it be made > square by adding additional columns/rows set to 0?) > > Alternatively, why not enumerate and add the edges between nodes for all > [N,M] such that mat[n,m] != 0. > (see the RCytoscape vignette for more on this and export functions) > > > On Sat, Mar 24, 2012 at 12:33 PM, pankaj borah <pankajborah2k3@yahoo.co.in> > wrote: > > 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> > *To:* pankaj borah <pankajborah2k3@yahoo.co.in> > *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 ? > > > > 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 > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > -- > *A model is a lie that helps you see the truth.* > * > * > Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> > > > > > > > -- > *A model is a lie that helps you see the truth.* > * > * > Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> > > > > -- *A model is a lie that helps you see the truth.* * * Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> [[alternative HTML version deleted]]
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