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

[jebyrnes]

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 <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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>>>> 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.
> 
> 

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