Problems importing GML file to Cytoscape

[Ana Av]

Hello. I'm working with networkx library and after I export my graph to a GML file and import it to Cytoscape I only visualize a straight line with no nodes. The nodes data are in the table panel but I can´t see them. In the GML file I use the attribute 'graphics' to define x and y positions, I don't know if that is what is causing the problem.

[Brett Settle]

Hi Ana,

Could you supply me with the GML file you are using to load the network, so I can figure out what is happening?

Thanks,

Brett

[Ana Av]

Sure.

Thank you.

[Brett Settle]

Good news, it looks like the network is being loaded correctly! Zooming in on the bottom of the line shows:

The GML file contains 339 nodes, but only 184 of them have xy coordinates.  Nodes that do have coordinates are located around (475922.6845, 2089130.49), while nodes without a location are automatically placed at (0, 0). This leads to a line-like view because the two clusters are so far away from each other. If you apply a layout (Grid), you can see that all the nodes and edges were loaded correctly.

I would suggest adding a false location to the nodes that are missing a location, or normalizing the existing node locations around (0, 0). 

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Brett Settle

Programmer Analyst II, Cytoscape Consortium

Ideker Lab, UCSD