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theislab / scvelo

RNA Velocity generalized through dynamical modeling
https://scvelo.org
BSD 3-Clause "New" or "Revised" License
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TypeError: unsupported operand type(s) for -: 'str' and 'str' #1209

Closed suhuanhou closed 6 months ago

suhuanhou commented 7 months ago

>>> scv.pp.filter_and_normalize(adata) /share/home/shh/miniconda3/envs/scVelo/lib/python3.9/site-packages/scvelo/preprocessing/utils.py:705: DeprecationWarning: log1p is deprecated since scVelo v0.3.0 and will be removed in a future version. Please use log1p from scanpy.pp instead. log1p(adata) Normalized count data: X, spliced, unspliced. Logarithmized X. >>> scv.pp.moments(adata) computing neighbors finished (0:00:37) --> added 'distances' and 'connectivities', weighted adjacency matrices (adata.obsp) computing moments based on connectivities finished (0:00:34) --> added 'Ms' and 'Mu', moments of un/spliced abundances (adata.layers) >>> scv.tl.velocity(adata, mode = "stochastic") computing velocities finished (0:04:46) --> added 'velocity', velocity vectors for each individual cell (adata.layers) >>> scv.tl.velocity_graph(adata) computing velocity graph (using 1/144 cores) 0%| | 0/54272 [00:00<?, ?cells/s] finished (0:01:21) --> added 'velocity_graph', sparse matrix with cosine correlations (adata.uns) *>>> scv.pl.velocity_embedding_stream(adata, basis="umap") TypeError: unsupported operand type(s) for -: 'str' and 'str' computing velocity embedding

*>>>

WeilerP commented 6 months ago

I cannot reproduce the error. Please use the provided issue templates for bugs and all relevant information.