Re: [igraph] best method of preserving network interactions in a 2D map?

[Tamás Nepusz]

>         Suppose I would like to preserve the input similarities (or 
> distances) as much as possible so that 
> if I computed the Euclidean distances from the resulting network 2D 
> coordinates, I would get an excellent 
> agreement with the original input distances (similar to multidimensional 
> scaling). 
> 
>         Is this possible using the igraph package?  If so, what functions and 
> options should be used. 
Hmm... you mentioned multidimensional scaling above. The good news is that 
igraph 0.6 will actually include multidimensional scaling as a graph layout 
algorithm, so if you are not afraid of compiling the development version from 
source, you can make use of igraph_layout_mds from the C core directly, or the 
corresponding interfaces from R or Python. (Of course the latter would also 
require you to compile the R or Python interface for 0.6 as well).

If you use igraph from R and you do not wish to upgrade to 0.6 yet, you can try 
the cmdscale function in R which can calculate the node positions given the 
distance matrix, and then you can simply give the result matrix in the 
layout=... parameter when you plot the graph. More info about the cmdscale 
function is here:

http://stat.ethz.ch/R-manual/R-devel/library/stats/html/cmdscale.html

Hope this helps.

Cheers,
Tamas