On Jun 13, 2007, at 2:12 AM, Mark W Kimpel wrote: > Kasper, > > Thanks for your suggestions. Based on your experience with > Graphviz, do > you think my idea of rendering the edges and nodes in separate > layers is > doable and the right way to go? I have no experience with layers in Graphviz, but I would assume they have some way of handling this problem, which might be pretty common - and layers sound like it could be it. You have a quite large graph, so in any way you might want to look for Graphviz based tools in order to explore it (see the graphviz homepage under tools I think) - or is the R plotting looking reasonable? For other reasons I am myself looking at displaying a 20.000 node bipartite graph (or rather will be soon), so if anyone has any good software suggestions, I am open as well. Having said all of that, what you are asking is a reasonable request, which should be incorporated into Rgraphviz. However, I certainly do not have time to work on that right now :( Kasper > 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) 663-0513 Home (no voice mail please) > > ****************************************************************** > > Kasper Daniel Hansen wrote: >> On Jun 12, 2007, at 11:20 AM, Mark W Kimpel wrote: >> >>> I am using Rgraphviz in "neato" mode to layout a graph with about >>> 500 >>> nodes and 1500 edges. Rgraphviz first renders the nodes and then the >>> edges, meaning that I have a lot of edges overlapping with nodes. I >>> would like to put the edges behind the nodes to avoid this. >>> >>> In reviewing documentation of both Graphviz and Rgraphviz, I do not >>> think using the "no overlap" option would work with a graph of this >>> size. Being able to see each and every edge is also not important >>> for my >>> application, so I am wondering if I can use layers to render the >>> edges >>> in a layer behind the nodes. >>> >>> Will this work? If not, any other suggestions? If it will, could an >>> expert supply me with some sample code to render edges and nodes in >>> separate layers? I could not find any in the documentation I >>> reviewed. >> >> In the code for Rgraphviz we just use Graphviz to layout the >> graph, ie. >> we get the (x,y) positions of the nodes and the function forms of the >> lines. Having those (and some other parameters we also need) we >> render >> (draw) the graph using standard R functions. So I doubt that Graphviz >> has any option that will affect this from the point of view of >> Rgraphviz. You could export the graph in dot format and then use the >> command line version of Graphviz to actually render (draw) the graph. >> \ >> Or you could try and hack the R code as you please. That should >> not be >> terrible hard in fact. You can get the relevant code by >> R> getMethod("plot", "Ragraph") >> >> (Ragraph is the name of the object after we retrieve it from Graphviz >> layout routine). >> >> Kasper >> >> >>> 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) 663-0513 Home (no voice mail please) >>> >>> _______________________________________________ >>> 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 >> >> > > _______________________________________________ > 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