hits=-2.5 tests=BAYES_00,FORGED_RCVD_HELO,SPF_HELO_PASS,SPF_PASS,UNPAR SEABLE_RELAY X-USF-Spam-Flag: NO > Deepayan, > > We are making progress. I just updated Rgraphviz-devel. Simply adjusting > the way adjusting my parameters to "layoutGraph" as you suggested fixed > the font size problem! I did not have to add it at the nodeRenderInfo > stage. Attached is a postscript file documenting the results, which > would look prettier if I had bothered to adjust the size of the output. > > Unfortunately, now nAttrs$fillcolor is being ignored, even if it is > added as an argument to noRenderInfo. This should be honored if you render the graph via graphviz, instead of R. > Also, I would very much like to use many of the other shapes available > via graphviz. If I was willing to do some of the coding (I know some C), Again, if you render the graph via graphviz, you can use any of the shapes for nodes that graphviz supports (more than 30 of them). At this time, you can specify your own node shapes if you render it via R, but not via graphviz. just the opposite to the above. > would you point me in the right direction so that I might provide a > patch with more shapes? Li

Hi Mark, to get you all the way, take a look at this: require(Rgraphviz) # Generate random graph set.seed(123) nodeNames <- letters[1:10] M <- 1:4 g1 <- randomGraph(nodeNames, M, .2) nAttrs <- list() #node width nAttrs$width <- rep(3, length(nodeNames)) names(nAttrs$width)<-nodeNames #node height nAttrs$height <- rep(3, length(nodeNames)) names(nAttrs$height)<-nodeNames #font size fontsize <- rep(c(1, 2), (length(nodeNames)/2)) names(fontsize)<-nodeNames #layout and render x <- layoutGraph(g1, nodeAttr=nAttrs) nodeRenderInfo(x) <- list(cex=fontsize) renderGraph(x, graph.pars=list(nodes=list(fill="black", textCol="white"))) I didn't set the node shape at all, because the default for dot is to use "ellipse", and since you fix your node widths and node heights to the same size, this boils down to a circle. I also set the fill and text color as attributes in the graph.pars argument to renderGraph, but Deepayan's suggestion works, too. The only difference is, that the latter permanently assigns the colors to the graph object x, while the former takes effect only for the current rendering operation. nodeRenderInfo(x) <- list(cex=fontsize, fill="black", textCol="white") renderGraph(x) fillcolor is ignored in your example because in the new rendering API this parameter is called fill (we tried to stay closer to R's base graphic parameter names, and thinking of that now, maybe we should rename textCol to font.col or something similar). I just uploaded a much more detailed vignette and some bug fixes, and these changes should be available soon in Rgraphviz version 1.17.12. If you know how to access the svn repository you can get this update immediately. In the Vignette there are also tables of the available parameters for nodes, edges and the whole graph and I will update the documentation accordingly ASAP. Everything that affects the graph layout can still be passed on to Graphviz as nodeAttrs, edgeAttrs or attrs arguments. For instance, the following would change the node shapes: nAttrs$shape <- c("circle", "rect", rep(c("ellipse", "box"), 4)) names(nAttrs$shape )<- nodeNames x <- layoutGraph(g1, nodeAttr=nAttrs) renderGraph(x) Again, since widths and heights of the nodes are constant, there's no difference between ellipse and circle (box and rect are synonyms, anyways). You can see the difference here: nAttrs$width <- rep(6, length(nodeNames)) names(nAttrs$width)<-nodeNames x <- layoutGraph(g1, nodeAttr=nAttrs) renderGraph(x) Another Graphviz parameter that I find quite useful is fixedsize. If this is set to TRUE (the default) all nodes will be forced to have the same size unless manually changed. For FALSE, the node sizes will be computed from the labels, so longer labels will create larger nodes. As far as I remeber, this has to be given to the attrs argument, something like this: attrs <- list(node=list(fixedsize=FALSE)) x <- layoutGraph(g1, nodeAttr=nAttrs, attrs=attrs) I'm affaid I can't really point you to the C code for the Graphviz interaction (we tried to stay clear of that, it's so easy to break things there...), but agopen is the workhorse in Rgraphviz to talk to the Graphviz library. Starting there and working your way though the code should quickly get you to the interesting C calls. Once you've figured out a way to access the different shapes in Graphviz and how to get the coordinates back into R, it is straightforward to render them. Everything that is stored in the Ragraph object (the return value of agopen) can be accessed by our rendering API. Cheers, Florian Mark W Kimpel schrieb: > Deepayan, > > We are making progress. I just updated Rgraphviz-devel. Simply > adjusting the way adjusting my parameters to "layoutGraph" as you > suggested fixed the font size problem! I did not have to add it at the > nodeRenderInfo stage. Attached is a postscript file documenting the > results, which would look prettier if I had bothered to adjust the > size of the output. > > Unfortunately, now nAttrs$fillcolor is being ignored, even if it is > added as an argument to noRenderInfo. > > Also, I would very much like to use many of the other shapes available > via graphviz. If I was willing to do some of the coding (I know some > C), would you point me in the right direction so that I might provide > a patch with more shapes? > > Thanks, > Mark > > > Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry > Indiana University School of Medicine > > 15032 Hunter Court, Westfield, IN 46074 > > (317) 490-5129 Work, & Mobile & VoiceMail > (317) 204-4202 Home (no voice mail please) > > mwkimpel<at>gmail<dot>com > > ****************************************************************** > > > Deepayan Sarkar wrote: >> On 1/30/08, Mark W Kimpel <mwkimpel at="" gmail.com=""> wrote: >>> Sorry for the complex prior example, I shouldn't write emails late at >>> night. Below is a self-contained, reproducible example. >>> >>> I've made some progress and can get the following script to flow >>> without >>> error messages. The fontsize, however, is not varying as I believe it >>> should and when I substitute "ellipse" for circle the width and height >>> parameters do not appropriately effect the shape. >> >> There are certain attributes which need to be supplied at the layout >> step, especially shape, width, and height, as without these the edges >> (which need to start from node boundaries) will not be placed >> properly. So, you need to supply nAttrs to layoutGraph as >> >> x <- layoutGraph(g1, nodeAttrs = nAttrs) >> >> Of course, it's not clear from the documentation that you can do this! >> >>> I also do not understand where I can specify "neato" vs. "dot" for the >>> rendering layout. >> >> Same goes for this; you can do >> >> x <- layoutGraph(g1, nodeAttrs = nAttrs, layoutType = "neato") >> >> The trick is to notice that the default layout function in >> 'layoutGraph' is 'layoutGraphviz', which is unexported, but you can >> get it's argument list by >> >>> args(Rgraphviz:::layoutGraphviz) >> function (x, layoutType = "dot", name = "graph", recipEdges = >> "combined", >> nodeAttrs = list(), edgeAttrs = list(), ...) >> >> >> Unfortunately, the fontsize doesn't seem to be retained in the result >> of layoutGraph, and I'm not sure yet if that's a bug in our wrapper or >> a limitation of the graphviz interface. We will look into it. >> >>> Also, where to specify a title. >> >> Generally speaking, our new model is that once the layout is done, you >> should be able to modify other attributes before rendering. These >> attributes are divided into three types: those for nodes, those for >> edges, and those for the whole graph, and these can be accessed and >> modified using nodeRenderInfo(), edgeRenderInfo(), and >> graphRenderInfo(), respectively. >> >> So, to come back to your problem, once you have the layout done, you >> can modify the fontsize and title as follows: >> >> nodeRenderInfo(x) <- list(fontsize = nAttrs$fontsize * 5) >> graphRenderInfo(x) <- list(main = "Main title") >> >> and then finally render it with >> >> renderGraph(x) >> >> Obviously there are many warts still to be worked out. >> >> -Deepayan >> >>> Thanks, mark >>> >>> >>> #################### >>> require(Rgraphviz) >>> # Generate random graph >>> set.seed(123) >>> nodeNames <- letters[1:10] >>> M <- 1:4 >>> g1 <- randomGraph(nodeNames, M, .2) >>> >>> nAttrs <- list() >>> >>> #node shapes >>> nAttrs$shape <- rep("circle", length(nodeNames)) >>> names(nAttrs$shape )<- nodeNames >>> >>> #node width >>> nAttrs$width <- rep(3, length(nodeNames)) >>> names(nAttrs$width)<-nodeNames >>> >>> #node height >>> nAttrs$height <- rep(3, length(nodeNames)) >>> names(nAttrs$height)<-nodeNames >>> >>> #node colors >>> nAttrs$fillcolor <-rep("black", length(nodeNames)) >>> names(nAttrs$fillcolor) <- nodeNames >>> >>> #font color >>> nAttrs$fontcolor <- rep("white", length(nodeNames)) >>> names(nAttrs$fontcolor)<-nodeNames >>> >>> #font size >>> nAttrs$fontsize <- rep(c(1, 2), (length(nodeNames)/2)) >>> names(nAttrs$fontsize)<-nodeNames >>> >>> postscript(file="my.test.graph.ps", paper="special",width=4, height=5) >>> #set up graphics device >>> x <- layoutGraph(g1) >>> nodeRenderInfo(x) = nAttrs >>> renderGraph(x) >>> dev.off()## close the graphics device >>> >>> >>> >>> Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry >>> Indiana University School of Medicine >>> >>> 15032 Hunter Court, Westfield, IN 46074 >>> >>> (317) 490-5129 Work, & Mobile & VoiceMail >>> (317) 204-4202 Home (no voice mail please) >>> >>> mwkimpel<at>gmail<dot>com >> > -------------------------------------------------------------------- ---- > > _______________________________________________ > 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 -- Florian Hahne, PhD Computational Biology Program Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-3148 fhahne at fhcrc.org