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SystemsGenetics / KINC

Knowledge Independent Network Construction
MIT License
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Visualization Tool Transivity #156

Closed JohnHadish closed 4 years ago

JohnHadish commented 4 years ago

The kinc-3D-viewer.py fails if the graph given to it is not "simple". This means that it will fail for most graphs produced by GMMs that have more than one condition, as there is the possibility for there to be two edges between the same node pair.

Error message:

Reading network file...
Reading GEM file...
Reading experioment annotation file...
Traceback (most recent call last):
  File "../kinc-3d-viewer.py", line 1266, in <module>
    main()
  File "../kinc-3d-viewer.py", line 1242, in main
    glayout = calculate_2d_layout(net, net_prefix, args.redo_layout, args.iterations)
  File "../kinc-3d-viewer.py", line 202, in calculate_2d_layout
    t = pd.Series(g.transitivity_local_undirected(), index=g.vs['name'])
igraph._igraph.InternalError: Error at /project/vendor/source/igraph/src/triangles.c:492: Transitivity works on simple graphs only, Invalid value
spficklin commented 4 years ago

Oddly, I can't reproduce this. See screenshot below. I suspect the problem is a different version of the python igraph library.. I tested with version 0.7.1.post6-5. What version are you using?

image

JohnHadish commented 4 years ago

Fixed by pull request 167