Question: How do you load a GraphML file into Cytoscape 3?
0
gravatar for hannahcatabia
4.1 years ago by
United States
hannahcatabia0 wrote:

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

cytoscape graphml • 3.4k views
ADD COMMENTlink modified 4.1 years ago by Jean-Karim Heriche21k • written 4.1 years ago by hannahcatabia0
3
gravatar for Jean-Karim Heriche
4.1 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche21k wrote:

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.

 

ADD COMMENTlink written 4.1 years ago by Jean-Karim Heriche21k

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.

ADD REPLYlink written 4.1 years ago by hannahcatabia0

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.

ADD REPLYlink written 4.1 years ago by Jean-Karim Heriche21k
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