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theislab / cellrank_notebooks

Tutorials and examples for CellRank.
https://cellrank.org
BSD 3-Clause "New" or "Revised" License
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Plotting smooth gene expression trends along lineages #27

Closed sidrahmaryam closed 4 years ago

sidrahmaryam commented 4 years ago

Hello, Thank you for the wonderful pipeline.

I am facing an issue while running the section of 'basics', plot smooth gene expression trends along lineages.

As before that we need to run scv.tl.diffmap(adata) When i run it, it shows an error : TypeError: '>=' not supported between instances of 'tuple' and 'int'

Please help as what could be the possible reason for that. I have already run dynamical mode of scVelo.

Thank you for the help in advance.

michalk8 commented 4 years ago

Hi @sidrahmaryam , it's more of a scanpy issue, since scvelo just imports diffmap from there: https://github.com/theislab/scvelo/blob/master/scvelo/tools/__init__.py#L12 I remember encountering this error myself using scanpy==1.5.* and updating to scanpy==1.6.0 seems to have fixed it. Let me know if this helps - if not, please try opening an here: https://github.com/theislab/scanpy/issues

sidrahmaryam commented 4 years ago

Thank you so much for the suggestion.

Yes it did solve. 💯

michalk8 commented 4 years ago

Glad that it worked.