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

From: James T Metz
Subject: [igraph] best method of preserving network interactions in a 2D map?
Date: Sun, 14 Aug 2011 14:35:30 -0500

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.

        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

Office (847) 936 - 0441
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