I am a new user to graph and Rgraphviz but until I updated to R 2.3.1 today and the latest version of graph, I had no problem displaying edge weight labels over my output using code lifted from the Rgraphviz vignette. Now, after updating, the edge weights all come out "1". Below is some test code that mimics what I have been doing, i.e. coercing an adjacency matrix to a graphNEL object. The individual points in the matrix are the edge weights I want to have labeled. As this suddenly appeared after updating, I suspect a problem with the package graph. Suggestions? Thanks, Mark test.matrix<-matrix(rep(c(1,2,3,4), 9), ncol=6, nrow=6) rownames(test.matrix)<-colnames(test.matrix)<-c("a", "b", "c", "d", "e", "f") result.gN<-as(test.matrix, Class="graphNEL") sessionInfo() Version 2.3.1 (2006-06-01) i386-pc-mingw32 attached base packages: [1] "splines" "tools" "stats" "graphics" "grDevices" "utils" "datasets" "methods" "base" other attached packages: XML Rgraphviz affycoretools GOstats Category hgu95av2 KEGG multtest genefilter survival xtable "0.99-7" "1.10.0" "1.4.0" "1.6.0" "1.4.1" "1.10.0" "1.8.1" "1.9.5" "1.10.1" "2.26" "1.3-2" RBGL annotate GO graph Ruuid limma affy affyio RWinEdt Biobase "1.8.1" "1.10.0" "1.6.5" "1.10.6" "1.10.0" "2.7.3" "1.10.0" "1.0.0" "1.7-4" "1.10.0" > Mark W. Kimpel MD ? Official Business Address: ? Department of Psychiatry Indiana University School of Medicine Biotechnology, Research, & Training Center 1345 W. 16th Street Indianapolis, IN ?46202 ? Preferred Mailing Address: ? 15032 Hunter Court Westfield, IN? 46074 ? (317) 490-5129 Home, Work, & Mobile 1-(317)-536-2730 FAX

Hi Mark, "Kimpel, Mark William" <mkimpel at="" iupui.edu=""> writes: > I am a new user to graph and Rgraphviz but until I updated to R 2.3.1 > today and the latest version of graph, I had no problem displaying > edge weight labels over my output using code lifted from the Rgraphviz > vignette. Now, after updating, the edge weights all come out > "1". Below is some test code that mimics what I have been doing, > i.e. coercing an adjacency matrix to a graphNEL object. The individual > points in the matrix are the edge weights I want to have labeled. > > As this suddenly appeared after updating, I suspect a problem with the > package graph. Yes and no. But first let me give you a different way to achieve your goal and then some discusson... > test.matrix<-matrix(rep(c(1,2,3,4), 9), ncol=6, nrow=6) > > rownames(test.matrix)<-colnames(test.matrix)<-c("a", "b", "c", "d", > "e", "f") > > result.gN<-as(test.matrix, Class="graphNEL") Instead of using the coerce method "as", you will have much more control over the end result if you call new explicitly to create a graph instance. Here's what I mean: ## Use the graphAM class, it is an adjacency matrix representation and ## is easy to initialize given an adjacency matrix g1 <- new("graphAM", test.matrix) Error in graph:::isValidAdjMat(adjMat, edgemode) : adjacency matrix must be symmetric for undirected graphs ## As you can see, the default is to create undirected graphs, but ## that isn't what you want if you have a nonsymmetric adj matrix. ## Let's try again: g1 <- new("graphAM", test.matrix, edgemode="directed") g1 A graphAM graph with directed edges Number of Nodes = 6 Number of Edges = 36 ## That looks good, but did we pick up the weights? edgeWeights(g1)[1] $a a b c d e f 1 1 1 1 1 1 ## Not yet. The graphAM class stores the adj mat as 0/1. Upon ## initialization, you can tell the system how to interpret the matrix ## values and store them in an edge attribute of your choosing. ## The 'values' arg should be a length 1 list providing the name of ## the edge attribute and the default value for the matrix element ## values. g1 <- new("graphAM", test.matrix, values=list(weight=1), edgemode="directed") edgeWeights(g1)[1] $a a b c d e f 1 3 1 3 1 3 ## But you wanted a graphNEL. That conversion is easy and does ## preserve node and edge attributes: g2 <- as(g1, "graphNEL") edgeWeights(g2)[1] Some discussion =============== 1. We need to take a look at the Rgraphviz vignette and update it where it makes sense to do so. 2. The past behavior of the matrix => graph as() methods is to create undirected graphs. For backwards compatibility, we should continue with this. But I think it makes more sense to create directed graphs since they are more general. I also think we should encourage use of new() because it gives the user more control. 3. As for picking up the weights from a call to as(), again for backwards compatibility we should probably just make this work. Edge weights are special in that they are the most commonly used edge attribute. The new fangled node/edge attribute system treats all attributes (almost) equally. They are all stored in the same way and can all be accessed using the same API (see the attributes vignette). An edge attribute named "weight" is, in the current release, slightly more equal :-) The edgeWeights method looks for this special name. In the devel version, we've added additional flexibility to edgeWeights to avoid lock-in to "weight" as a special name and to make it easier to verify that the actual edge weight values are of the expected type (some algorithms want integers, for example). ok, maybe I should stop there before this becomes a book. Comments and further questions welcome. Best, + seth

Seth, Thank you for the "mini-vignette"! It will be most helpful :) I will let more experiences users of the package comment on your specific ideas. Mark Mark W. Kimpel MD (317) 490-5129 Home, Work, & Mobile 1-(317)-536-2730 FAX -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Seth Falcon Sent: Wednesday, June 07, 2006 10:10 AM To: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] problem with latest version of graph Hi Mark, "Kimpel, Mark William" <mkimpel at="" iupui.edu=""> writes: > I am a new user to graph and Rgraphviz but until I updated to R 2.3.1 > today and the latest version of graph, I had no problem displaying > edge weight labels over my output using code lifted from the Rgraphviz > vignette. Now, after updating, the edge weights all come out > "1". Below is some test code that mimics what I have been doing, > i.e. coercing an adjacency matrix to a graphNEL object. The individual > points in the matrix are the edge weights I want to have labeled. > > As this suddenly appeared after updating, I suspect a problem with the > package graph. Yes and no. But first let me give you a different way to achieve your goal and then some discusson... > test.matrix<-matrix(rep(c(1,2,3,4), 9), ncol=6, nrow=6) > > rownames(test.matrix)<-colnames(test.matrix)<-c("a", "b", "c", "d", > "e", "f") > > result.gN<-as(test.matrix, Class="graphNEL") Instead of using the coerce method "as", you will have much more control over the end result if you call new explicitly to create a graph instance. Here's what I mean: ## Use the graphAM class, it is an adjacency matrix representation and ## is easy to initialize given an adjacency matrix g1 <- new("graphAM", test.matrix) Error in graph:::isValidAdjMat(adjMat, edgemode) : adjacency matrix must be symmetric for undirected graphs ## As you can see, the default is to create undirected graphs, but ## that isn't what you want if you have a nonsymmetric adj matrix. ## Let's try again: g1 <- new("graphAM", test.matrix, edgemode="directed") g1 A graphAM graph with directed edges Number of Nodes = 6 Number of Edges = 36 ## That looks good, but did we pick up the weights? edgeWeights(g1)[1] $a a b c d e f 1 1 1 1 1 1 ## Not yet. The graphAM class stores the adj mat as 0/1. Upon ## initialization, you can tell the system how to interpret the matrix ## values and store them in an edge attribute of your choosing. ## The 'values' arg should be a length 1 list providing the name of ## the edge attribute and the default value for the matrix element ## values. g1 <- new("graphAM", test.matrix, values=list(weight=1), edgemode="directed") edgeWeights(g1)[1] $a a b c d e f 1 3 1 3 1 3 ## But you wanted a graphNEL. That conversion is easy and does ## preserve node and edge attributes: g2 <- as(g1, "graphNEL") edgeWeights(g2)[1] Some discussion =============== 1. We need to take a look at the Rgraphviz vignette and update it where it makes sense to do so. 2. The past behavior of the matrix => graph as() methods is to create undirected graphs. For backwards compatibility, we should continue with this. But I think it makes more sense to create directed graphs since they are more general. I also think we should encourage use of new() because it gives the user more control. 3. As for picking up the weights from a call to as(), again for backwards compatibility we should probably just make this work. Edge weights are special in that they are the most commonly used edge attribute. The new fangled node/edge attribute system treats all attributes (almost) equally. They are all stored in the same way and can all be accessed using the same API (see the attributes vignette). An edge attribute named "weight" is, in the current release, slightly more equal :-) The edgeWeights method looks for this special name. In the devel version, we've added additional flexibility to edgeWeights to avoid lock-in to "weight" as a special name and to make it easier to verify that the actual edge weight values are of the expected type (some algorithms want integers, for example). ok, maybe I should stop there before this becomes a book. Comments and further questions welcome. Best, + seth _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor