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LouisFaure / scFates

a scalable python suite for tree inference and advanced pseudotime analysis from scRNAseq data.
https://scfates.readthedocs.io/
BSD 3-Clause "New" or "Revised" License
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issue with scf.tl.cluster and scf.pl.trends functions in notebook #19

Closed 16nikita closed 1 year ago

16nikita commented 1 year ago

Hi, I am following the tutorial for 'basic curved trajectory analysis' and running into problems with the steps for clustering significant features. This line: scf.tl.cluster(adata,knn=100,metric="correlation") outputs the error "TypeError: cluster() got an unexpected keyword argument 'knn'", and the parameter knn is not present in the documentation, so I changed knn to n_neighbors, which worked. However, down the line, when I run scf.pl.trends, it outputs the error "IndexError: arrays used as indices must be of integer (or boolean) type".

Do you have any suggestions for why this might be happening or how to fix it?

LouisFaure commented 1 year ago

Hi, some changes in the main packages were unfortunately not tested on that notebook. I have updated it (removed some irrelevant parts as well) and I have now tested with the latest version of scFates (v1.0.4): it works on my side. Let me know if that is the case for you as well.

LouisFaure commented 1 year ago

Now version v1.0.5 fixes the IndexError issue with scf.pl.trends