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

[Gábor Csárdi]

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

>
> 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
>>> --
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>>
>>
>>
>> --
>> Gabor Csardi <Gabor.Csardi at unil.ch>     UNIL DGM
>>
>> ______________________________________________
>> R-help at r-project.org mailing list
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>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
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>>
>>
>
> --
> 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