How do you load a GraphML file into Cytoscape 3?

Question

[hannahcatabia]

I cannot find anything in the tutorial that explains how to do this step-by-step.

Answer 1

[Jean-Karim Heriche]

GraphML is supported by Cytoscape 3. Just go to File > Import > Network > from file and select your file. With Cytoscape 2, you need the GraphMLReader plugin.

[hannahcatabia]

Hi. When I do this, I receive an error saying Cytoscape Task: null entry. What does this mean? Is this a problem with my file, or with my Cytoscape download? Is there a graphml sample file somewhere I can download to see if it works in Cytoscape? I created my .graphml file in NetworkX in Python, and I'm not sure why Cytoscape isn't reading it.

[Jean-Karim Heriche]

This is most likely due to a malformed file. Check the GraphML primer for a description of the format and some examples. Also check NetworkX and Cytoscape docs. It's possible that NetworkX and Cytoscape have diverging views on what constitute a proper GraphML format. For example, they may not support all the features that the format allows.