[BioC] Rgraphviz in windows 7 - problem with GUI?

[Martin Morgan]

If your problem really is the same as the thread you replied to, I do not think there is a solution yet. Martin

----- Original Message -----
> Hi, I got the similar problem when I run the KEGGgraph package. Below
> is the
> detailed information. please note that I use 64-bit windows 7
> 
> I run the following codes:
> 
> mapkKGML <- system.file("extdata/hsa04010.xml",
> package="KEGGgraph")
> 
> 
> 
> 
> 
> ###################################################
> 
> ### chunk number 4: parsemapk
> 
> ###################################################
> 
> mapkG <- parseKGML2Graph(mapkKGML,expandGenes=TRUE)
> 
> mapkG
> 
> 
> 
> 
> 
> ###################################################
> 
> ### chunk number 5: parsemapk2
> 
> ###################################################
> 
> mapkpathway <- parseKGML(mapkKGML)
> 
> mapkpathway
> 
> mapkG2 <- KEGGpathway2Graph(mapkpathway, expandGenes=TRUE)
> 
> mapkG2
> 
> 
> 
> 
> 
> ###################################################
> 
> ### chunk number 6: nodeandedge
> 
> ###################################################
> 
> mapkNodes <- nodes(mapkG)
> 
> nodes(mapkG)[1:3]
> 
> mapkEdges <- edges(mapkG)
> 
> edges(mapkG)[1]
> 
> 
> 
> 
> 
> ###################################################
> 
> ### chunk number 7: keggnodedata
> 
> ###################################################
> 
> mapkGnodedata <- getKEGGnodeData(mapkG)
> 
> mapkGnodedata[[2]]
> 
> 
> 
> 
> 
> ###################################################
> 
> ### chunk number 8: keggnodedataalt eval=FALSE
> 
> ###################################################
> 
> ## getKEGGnodeData(mapkG, 'hsa:5924')
> 
> 
> 
> 
> 
> ###################################################
> 
> ### chunk number 9: keggedgedata
> 
> ###################################################
> 
> mapkGedgedata <- getKEGGedgeData(mapkG)
> 
> mapkGedgedata[[4]]
> 
> 
> 
> 
> 
> ###################################################
> 
> ### chunk number 10: keggedgedataalt eval=FALSE
> 
> ###################################################
> 
> ## getKEGGedgeData(mapkG,'hsa:627~hsa:4915')
> 
> 
> 
> 
> 
> ###################################################
> 
> ### chunk number 11: inout
> 
> ###################################################
> 
> mapkGoutdegrees <- sapply(edges(mapkG), length)
> 
> mapkGindegrees <- sapply(inEdges(mapkG), length)
> 
> topouts <- sort(mapkGoutdegrees, decreasing=T)
> 
> topins <- sort(mapkGindegrees, decreasing=T)
> 
> topouts[1:3]
> 
> topins[1:3]
> 
> 
> 
> 
> 
> ###################################################
> 
> ### chunk number 12: subsetprepare
> 
> ###################################################
> 
> library(Rgraphviz)
> 
> set.seed(123)
> 
> randomNodes <- sample(nodes(mapkG), 25)
> 
> mapkGsub <- subGraph(randomNodes, mapkG)
> 
> mapkGsub
> 
> 
> 
> 
> 
> ###################################################
> 
> ### chunk number 13: makeattr
> 
> ###################################################
> 
> makeAttr <- function(graph, default, valNodeList) {
> 
> tmp <- nodes(graph)
> 
> x <- rep(default, length(tmp)); names(x) <- tmp
> 
> 
> 
> if(!missing(valNodeList)) {
> 
> stopifnot(is.list(valNodeList))
> 
> allnodes <- unlist(valNodeList)
> 
> stopifnot(all(allnodes %in% tmp))
> 
> for(i in seq(valNodeList)) {
> 
> x[valNodeList[[i]]] <- names(valNodeList)[i]
> 
> }
> 
> }
> 
> return(x)
> 
> }
> 
> 
> 
> 
> 
> ###################################################
> 
> ### chunk number 14: subsetplot
> 
> ###################################################
> 
> outs <- sapply(edges(mapkGsub), length) > 0
> 
> ins <- sapply(inEdges(mapkGsub), length) > 0
> 
> ios <- outs | ins
> 
> 
> 
> ## translate the KEGG IDs into Gene Symbol
> 
> if(require(org.Hs.eg.db)) {
> 
> ioGeneID <- translateKEGGID2GeneID(names(ios))
> 
> nodesNames <- sapply(mget(ioGeneID, org.Hs.egSYMBOL, ifnotfound=NA),
> "[[",1)
> 
> } else {
> 
> nodesNames <- names(ios)
> 
> }
> 
> names(nodesNames) <- names(ios)
> 
> 
> 
> nAttrs <- list();
> 
> nAttrs$fillcolor <- makeAttr(mapkGsub, "lightgrey",
> list(orange=names(ios)[ios]))
> 
> nAttrs$label <- nodesNames
> 
> 
> Everything is fine so far, and the sessionInfo() is following:
> 
> 
> 
> R version 2.10.1 (2009-12-14)
> 
> i386-pc-mingw32
> 
> 
> 
> locale:
> 
> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United
> States.1252
> 
> [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
> 
> 
> [5] LC_TIME=English_United States.1252
> 
> 
> 
> attached base packages:
> 
> [1] grid stats graphics grDevices utils datasets methods
> base
> 
> 
> 
> other attached packages:
> 
> [1] org.Hs.eg.db_2.3.6 RSQLite_0.8-4 DBI_0.2-5
> AnnotationDbi_1.8.2
> Biobase_2.6.1
> 
> [6] KEGGgraph_1.2.2 Rgraphviz_1.24.0 graph_1.26.0
> XML_2.6-0
> 
> 
> 
> 
> loaded via a namespace (and not attached):
> 
> [1] tools_2.10.1
> 
> 
> 
> However when I run
> 
> plot(mapkGsub, "neato", nodeAttrs=nAttrs,
> 
> attrs=list(node=list(fillcolor="lightgreen",
> 
> width="0.75", shape="ellipse"),
> 
> edge=list(arrowsize="0.7")))
> 
> 
> 
> 
> The R GUI stopped, and shows that:
> 
> R for windows GUI front-end has stopped working
> 
> A problem caused the program to stop working correctly. Windows will
> close
> the program and notify you if a solution is available
> 
> 
> 
> Anybody can tell me why this happens and how to solve it?
> 
> Thanks,
> 
> Grace
> 
> On Sat, Dec 25, 2010 at 12:03 AM, Alessandro Magrini <
> alessandro.magrini at hotmail.it> wrote:
> 
> > mmh no...I have 32-bit Windows 7.
> >
> > graphviz works correctly, I have installed the version suggested
> > (2.20.3.1)...
> >
> > _______________________________________________
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> >
> 
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> 
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