fraenkel-lab/OmicsIntegrator2

Louvain clustering output

Closed this issue · 4 comments

iamjli commented

OmicsIntegrator2/src/graph.py

Line 366 in 11a24e1

louvain_clustering(augmented_forest)

Getting the following error:
image

iamjli commented

If I comment this line out, the next line gives this error:

image

alexlenail commented

@iamjli unfortunately I can't support all branches of OI2.

  • The first error suggests the python-louvain package is having trouble with networkx 2.0's new API. We were seeing this error a couple months ago and resolved it (I forget how)
  • The second error is because the subcellular localization data needs to be a pd.DataFrame, not a pd.Series now -- that's my bad, a miscommunication between myself and @brycehwang. It's fixed in master.

I ran the example notebook in master and it works for me. Does it work for you?

iamjli commented

Thanks @zfrenchee. I have been working off master but am still getting the python-louvain error.

Your most recent commit fixed the subcellular localization problem though, thanks!

alexlenail commented

Closing (see #71)