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

BioFabric (www.BioFabric.org) is another tool for visualizing large graphs. It should be able to handle the network described (178,000 nodes and 500,000 edges) OK, though the initial layout may take awhile. The network show here (from the Stanford Large Network Dataset Collection) is the Stanford Web Network, which has 281,903 nodes and 2,312,497 edges:

BioFabric's scalability is due to the fact that it represents nodes not as points, but as horizontal lines. The edges are then shown as vertical lines. For some intuition about how this works, there is the Super-Quick BioFabric Demo, which is a small network that is animated using D3.

The primary application is written in Java. At the moment, it can only export PNG images, not PDFs. There is a PDF export option from RBioFabric, though that is a very simple implementation that cannot handle really large networks yet.

Full disclosure: BioFabric is a tool that I wrote.