Hierarchical Diagram of Networks in sna or otherwise?
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).
G?bor Cs?rdi-2 wrote:
On Mon, May 4, 2009 at 8:31 PM, jebyrnes <byrnes at 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
G?bor Cs?rdi-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 <byrnes at 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 at 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.Csardi at unil.ch> ? ? UNIL DGM
______________________________________________ R-help at 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 at 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.Csardi at unil.ch> UNIL DGM
______________________________________________ R-help at 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.