Hierarchical Diagram of Networks in sna or otherwise?

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.


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
 >>

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.

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
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--
Gabor Csardi <Gabor.Csardi at unil.ch> ? ? UNIL DGM

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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.

--
Gabor Csardi <Gabor.Csardi at unil.ch> ? ? UNIL DGM

--
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.

-- 
Gabor Csardi <Gabor.Csardi at unil.ch>     UNIL DGM