No worries. I've actually switched to using Rgraphviz from bioconductor, and the results are pretty great (after the initial head-pounding to get it setup).
Gábor Csárdi-2 wrote: > > On Mon, May 4, 2009 at 8:31 PM, jebyrnes <byr...@msi.ucsb.edu> wrote: >> >> Nearly. The algorithm turns up slightly different graphs each time (and >> set.seed doesn't seem to make it consistent) > > Hmmm, that should not happen, I'll check it out. > >> and periodically chokes. > > Can you send me the graph for which this happens? > >> But >> better than what I had. Hrm. I don't know much about the algorithm >> graphviz uses for dot. Do you have a reference on hand? > > No, I don't. Have you checked the graphviz homepage? > >> If it's simple, >> I'd be willing to take a whack at it. > > I doubt that it is simple, but I think it would be very useful to have > a free implementation. (I would have already ported the graphviz > layout algorithms to igraph, but their licenses are not compatible.) > > Best, > Gabor > >> >> Gábor Csárdi-2 wrote: >>> >>> Jarrett, >>> >>> the 'igraph' package has a layout called layout.reingold.tilford that >>> is designed for trees, there is a slight chance that it is good enough >>> for you. >>> >>> Best, >>> Gabor >>> >>> On Wed, Apr 29, 2009 at 10:11 PM, jebyrnes <byr...@msi.ucsb.edu> wrote: >>>> >>>> I've been using sna to work with some networks, and am trying to >>>> visualize >>>> them easily. My networks are hierarchical (food webs). All of the >>>> layout >>>> engines I've tried with gplot don't seem to plot hierarchical networks, >>>> as >>>> one would using dot from graphviz. While I could do all of this by >>>> outputting to dotfiles and running it through graphviz, the graphics I >>>> get >>>> from R are much cleaner, and more easily integrated into my analyses. >>>> >>>> Is there any good way to diagram a hierarchical network in R, either >>>> with >>>> the sna library or otherwise? It strikes me that at least the >>>> Netindices >>>> package can calculate trophic levels. Could this be used for node >>>> placement? >>>> >>>> >>>> -Jarrett >>>> -- >>>> View this message in context: >>>> http://www.nabble.com/Hierarchical-Diagram-of-Networks-in-sna-or-otherwise--tp23301819p23301819.html >>>> Sent from the R help mailing list archive at Nabble.com. >>>> >>>> ______________________________________________ >>>> R-help@r-project.org mailing list >>>> https://stat.ethz.ch/mailman/listinfo/r-help >>>> PLEASE do read the posting guide >>>> http://www.R-project.org/posting-guide.html >>>> and provide commented, minimal, self-contained, reproducible code. >>>> >>> >>> >>> >>> -- >>> Gabor Csardi <gabor.csa...@unil.ch> UNIL DGM >>> >>> ______________________________________________ >>> R-help@r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/r-help >>> PLEASE do read the posting guide >>> http://www.R-project.org/posting-guide.html >>> and provide commented, minimal, self-contained, reproducible code. >>> >>> >> >> -- >> View this message in context: >> http://www.nabble.com/Hierarchical-Diagram-of-Networks-in-sna-or-otherwise--tp23301819p23374024.html >> Sent from the R help mailing list archive at Nabble.com. >> >> ______________________________________________ >> R-help@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide >> http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. >> > > > > -- > Gabor Csardi <gabor.csa...@unil.ch> UNIL DGM > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > > -- View this message in context: http://www.nabble.com/Hierarchical-Diagram-of-Networks-in-sna-or-otherwise--tp23301819p23391709.html Sent from the R help mailing list archive at Nabble.com. ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.