On 12/20/2012 03:07 PM, Kasper Daniel Hansen wrote: > The issue is that agread() returns an object of class Ragraph and not > a standard graph. Ragraph is really an internal class. > Unfortunately, you cannot convert from Ragraph to a standard graph > (which is quite unfortunately). > > What you are doing, is using the > edgeRenderInfo() > paradigm as described in the vignette "newRgraphvizInterface". This > works on graph objects, but not Ragraph. > > Instead, you need to use the old style layout functions, like > plot( , nodeAttrs = list(), edgeAttrs = list()) I played around with this just a little this morning and found toFile() to be useful, e.g., toFile(g, filename="/tmp/foo.svg", fileType="svg") to recreate the output from graphviz (fileType from graphvizCapabilities()$deviceType), and things like > edgeData(g, "R", "R", "arrowhead") R~R "dot" > edgeData(g, "R", "R", "arrowhead") <- "normal" (as documented on ?Ragraph) to manipulate. Martin > > Let me end by saying that your request is completely reasonable and it > is unfortunate that it is not easy to do. Recently, I spent a lot of > time fixing up the C code for Rgraphviz and the next step is cleaning > up the R code. However, due to other commitments, this may take a > while to materialize. > > Best, > Kasper > > On Wed, Dec 19, 2012 at 4:32 PM, Alexis Dinno <alexis.dinno at="" pdx.edu=""> wrote: >> Hi, >> >> I would love to integrate interoperability with Rgraphviz in my LoopAnalyst >> package on CRAN. Unfortunately, Rgraphiz does not seem to behave well with >> graphs read from dot files. The dot file >> (http://doyenne.com/personal/files/Levins.dot) can be read an rendered by >> agread(), but does not turn out so nicely, presumably because of how node, edge >> and arrowhead attributes are handled. >> >> Here's how dot from graphviz renders my graph: >> http://doyenne.com/personal/files/Levins.png >> >> >> But if in R I type: >> g <- agread("/Users/Alexis/Desktop/Levins.dot") >> plot(g) >> >> I get: http://doyenne.com/personal/files/Levins2.png >> >> So I would like to edit the various parameters according to Rgraphviz, BUT, I >> get the following errors with the following commands: >> >> edgemode(g) <- "directed" >> Error in function (classes, fdef, mtable) : >> unable to find an inherited method for function ?edgemode<-? for >> signature ?"Ragraph", "character"? >> >> >> edgeRenderInfo(g) <- list(arrowhead=c("R~R"="dot", "R~H"="normal", >> "H~R"="dot", "H~x"="normal", "H~y"="normal", "x~H"="dot", "y~H"="dot", >> "y~y"="dot"), arrowtail="open") >> Error in function (classes, fdef, mtable) : >> unable to find an inherited method for function ?isDirected? for >> signature ?"Ragraph"? >> >> >> Can you help? >> >> Thank you! >> >> Alexis >> >> >> Here's the content of Levins.dot: >> >> >> digraph G { >> graph [bgcolor = "transparent", size = "18!,18!", nodesep="1", ranksep="1", >> rankdir="LR"]; >> node [fixedsize=true, fontname="Sans", fontsize="70.85", shape=circle, >> height="2", width="2", style="setlinewidth(5)"]; >> edge [style="setlinewidth(4)", arrowsize=3]; >> "R" [color="#8000BF"]; >> "R" -> "R" [color="#8000BF", arrowhead=dot]; >> "R" -> "H" [color="#8000BF"]; >> "H" [color="#0000BF"]; >> "H" -> "R" [color="#0000BF", arrowhead=dot]; >> "H" -> "x" [color="#0000BF"]; >> "H" -> "y" [color="#0000BF"]; >> "x" [color="#00BF00"]; >> "x" -> "H" [color="#00BF00", arrowhead=dot]; >> "y" [color="#BF0000"]; >> "y" -> "H" [color="#BF0000", arrowhead=dot]; >> "y" -> "y" [color="#BF0000", arrowhead=dot]; >> } >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793

Hi Paul, > There's a 'gridGraphviz' package on R-Forge that is in very early stages; it > has lots of holes, but I have plugged a couple so that you get a reasonable > result for your example below. > > With the latest version on ... > > https://r-forge.r-project.org/projects/gridgraph/ It is not remotely clear how to install packages from this link. However, I found version 0.1 on CRAN. > ... try the following code ... > > library(gridGraphviz) > g <- agread("Levins.dot") > grid.graph(g) > > ... which gets the edges better and the following ... But which does not draw the nodes or their labels at all. > grid.newpage() > pushViewport(viewport(width=.9, height=.9, gp=gpar(lex=4))) > grid.graph(g, newpage=FALSE, nodesOnTop=FALSE) > > ... makes the "arrows" look better. Not on my system (v. 2.15.2 x86_64-apple-darwin9.8.0/x86_64 (64-bit)): > grid.graph(g, newpage=FALSE, nodesOnTop=FALSE) Error in grid.graph(g, newpage = FALSE, nodesOnTop = FALSE) : unused argument(s) (nodesOnTop = FALSE) But thank you for bringing your incipient package to my attention! :)