[R] Hierarchical Diagram of Networks in sna or otherwise?

William Revelle lists at revelle.net
Mon May 4 20:51:08 CEST 2009


At 11:31 AM -0700 5/4/09, jebyrnes wrote:
>Nearly.  The algorithm turns up slightly different graphs each time (and
>set.seed doesn't seem to make it consistent) and periodically chokes.  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?  If it's simple,
>I'd be willing to take a whack at it.
>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 <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
>  >>

If you like the dot output from graphviz you can 
get that using Rgraphviz from bioconductor. 
Although somewhat difficult to install, once 
installed it works beautifully.


William Revelle		http://personality-project.org/revelle.html
Professor			http://personality-project.org/personality.html
Department of Psychology             http://www.wcas.northwestern.edu/psych/
Northwestern University	http://www.northwestern.edu/
Attend  ISSID/ARP:2009               http://issid.org/issid.2009/

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