Visualizing Undirected Graph That's Too Large for GraphViz?

Question

I need advice for rendering an undirected graph with 178,000 nodes and 500,000 edges. I\'ve tried Neato, Tulip, and Cytoscape. Neato doesn\'t even come remotely close, and

Answer 1

First, I would like to second aliekens' suggestion to try sfdp. It is the large scale version of Neato.

As OJW suggests you could also just plot the nodes in R2. Your edges actually supply what he calls a "natural ordering." In particular you can plot the components of the second and third eigenvectors of the normalized graph Laplacian. This is the matrix L in this wikipedia page about spectral clustering. You should be able to write down this matrix without understanding the linear algebra behind it. Then, you have reduced your problem to approximately computing the first few eigenvectors of a large sparse matrix. This is traditionally done by iterative methods and is implemented in standard linear algebra packages. This method should scale up to very large graphs.