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I have a finite but huge metric graph with say 1000 vertices. It comes say as 10000x10000 symmetric matrix filled by $0,1,\dots$ and $\infty$; 0's on the diagonal and $\infty$ is for pairs of vertices which are not connected. (Most of the vertices have degree 3.)

I need to find a way to visualize this graph. I hope it will help me to see some patterns.

Is there any software which could help? Say, I want to draw this graph in the space in a form which reflects its metric geometry.

flag	asked Feb 26 at 20:59 ε-δ 1,038●5●16

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Have you tried with Graphviz ? Or with Sage and with the plot3d() method ? Maybe your graph is too big to be drawn correctly with these tools anyway. – Samuele Giraudo Feb 26 at 21:04

@Samuelle, no I did not, can it take the metric into account? – ε-δ Feb 26 at 21:22

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Where does this graph come from? – Per Alexandersson Feb 26 at 21:28

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Btw, how about reading the answer on stackexchange to the same question? stackoverflow.com/questions/243616/… – Per Alexandersson Feb 26 at 21:29

@Per: the data comes from DNA – ε-δ Feb 28 at 5:06

meij · Answer 1 · 2013-02-26 22:26:55Z UTC

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Take reciprocals of the off-diagonal entries and treat this as a weighted adjacency matrix. Then use a spectral layout.

answered Feb 26 at 22:26

meij
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Markus Redeker · Answer 2 · 2013-03-13 12:24:29Z UTC

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You could try yEd. It can import data in various formats, and there is an image on their web site of a graph with 13,500 nodes and 26,000 edges, which is much larger than your graph.

answered Mar 13 at 12:24

Markus Redeker
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Visualizing a graph

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