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

[James T Metz]

Igraph List,

        Suppose
I have a set of interactions e.g., similarities or distances where distance
= 1 - similarity
for a set of nodes.  I can read
in those interactions, generate a network and output the 2D coordinates.

        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.

        I
already know how to generate a network and output coordinates, but I am
currently not obtaining
very good agreement between the input
distances and the network 2D distances between nodes.  I have
tried various weight functions where
weight = f(similarity), but I can not seem to get this to work very
well either.

        Am
I trying to do something that is not currently possible with Igraph, or
am I just ignorant of
the appropriate function and options?

        I
greatly welcome comments and suggestions.

        Thank
you.

        Regards,
        Jim
Metz
        

James T. Metz, Ph.D.
Senior Scientist III Chemistry

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