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Re: [igraph] igraph network coordinates with constraints?

From: Gábor Csárdi
Subject: Re: [igraph] igraph network coordinates with constraints?
Date: Tue, 29 Nov 2011 16:27:15 -0500

OK, I have added support for this in the 0.6-main tree, for the
classic Fruchterman-Reingold and Kamada-Kawai layouts. It is actually
even more general. For each vertex and each coordinate (x, y & z in
3d) you can define lower and upper bounds. If for a given vertex the
lower bound matches the upper bound, then that vertex is not moved at
all (along that coordinate). For the vertices that can be moved freely
you can specify -Inf as a lower bound and Inf as an upper bound.

You can download a snapshot of the 0.6 R package from here:
Well, from tomorrow, the packages are build during the night.
This is an R source package. If you need a windows binary R package,
please let me know.

Be aware that the 0.6 R package in not backward compatible, since
vertices and edges are numbered from one instead of zero!


On Fri, Nov 18, 2011 at 9:51 AM, Gábor Csárdi <address@hidden> wrote:
> James,
> this is not currently possible. It is a good idea, we actually even
> have an issue for it:
> https://bugs.launchpad.net/igraph/+bug/734630
> However, as we are busy with other things now, it is unlikely that
> we'll implement it soon.
> If you are fluent in C, then you can try taking the code from igraph
> and modify it to fix some vertices, we can help you with that.
> Best,
> Gabor
> On Wed, Nov 16, 2011 at 12:07 PM, James T Metz <address@hidden> wrote:
>> Igraph Users,
>>         Is it possible to use the R igraph code and generate a network where
>> some of the coordinates
>> of nodes are constrained and other nodes are unconstrained?
>>         For example, I have a set of 10 objects with distance (or
>> similarity) information for those
>> objects.  I generate a network and coordinates for those 10 objects.  I now
>> have a new object.  I can
>> re-calculate a new distance (similarity) matrix for all 11 objects.
>>         However, if possible, I would like to preserve the original network
>> and coordinates of the
>> previous 10 objects, and I want to add the 11th object onto the previous
>> network in the most optimal
>> position for that 11th object only.
>>         Is this possible? If so, can someone provide some R code as a simple
>> example.
>>         Also, since the network generation is stochastic, again it is
>> important the the original
>> network be generated with the same coordinates each time (if possible).
>>         Thank you.
>>         Regards,
>>         Jim Metz
>> James T. Metz, Ph.D.
>> Senior Scientist III Chemistry
>> GPRD R4DG AP52 - 01D10P
>> Abbott Laboratories
>> 100 Abbott Park Road
>> Abbott Park, IL  60064 - 6100
>> U.S.A.
>> Office (847) 936 - 0441
>> FAX    (847) 938 - 2756
>> address@hidden
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> --
> Gabor Csardi <address@hidden>     MTA KFKI RMKI

Gabor Csardi <address@hidden>     MTA KFKI RMKI

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