[BioC] problem with latest version of graph

Kimpel, Mark William mkimpel at iupui.edu
Wed Jun 7 03:16:58 CEST 2006

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.




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")

Version 2.3.1 (2006-06-01) 

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 

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