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pinellolab / STREAM

STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data
http://stream.pinellolab.org
GNU Affero General Public License v3.0
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AttributeError: 'Graph' object has no attribute 'node' #134

Closed Pawan291 closed 2 years ago

Pawan291 commented 2 years ago

Hello,

I am quite new to the STREAM as I recently started to use this for my scRNA seq analysis using one of the notebooks as a reference from tutorials. I am facing the above error at the Trajectory inference step at this command:

st.seed_elastic_principal_graph(adata,n_clusters=10)

I have already downgraded networkx to 2.1 as it was suggested in one of the issues but am still, getting this same error. Could you please help me with this?

Thank you

huidongchen commented 2 years ago

Hi, thanks for the feedback. Given such information, unfortunately it's difficult for me to tell the problem.

Can you share with me a notebook along with a dummy dataset to reproduce the error? i am happy to take a closer look.

Also, are you using the latest version v1.1? if not, can you also try to upgrade it tov1.1 since several package-incompatible issues are fixed in the latest version.

Pawan291 commented 2 years ago

Hi,

Thanks for responding to my query. I just uninstalled stream and other packages and then reinstalled it again. Now, I am not facing this error again and everything is working smoothly at the moment.

I have not upgraded to version 1.1 but I will upgrade it.

Thanks for the suggestion and for the help :)