theislab/scvelo

TypeError: unsupported operand type(s) for -: 'str' and 'str'

suhuanhou opened this issue · 1 comments

*>>> 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

*>>>

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