scanpy: Error in `sc.tl.umap`
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Minimal code sample (that we can copy&paste without having any data)
I am learning the example of Integrating data using ingest and BBKNN. When I run code
sc.tl.umap(adata_ref)
I get
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
<ipython-input-13-0e548e19df3a> in <module>
1 sc.pp.pca(adata_ref)
2 sc.pp.neighbors(adata_ref)
----> 3 sc.tl.umap(adata_ref)
~/miniconda3/envs/tf/lib/python3.6/site-packages/scanpy/tools/_umap.py in umap(adata, min_dist, spread, n_components, maxiter, alpha, gamma, negative_sample_rate, init_pos, random_state, a, b, copy, method, neighbors_key)
171 neigh_params.get('metric', 'euclidean'),
172 neigh_params.get('metric_kwds', {}),
--> 173 verbose=settings.verbosity > 3,
174 )
175 elif method == 'rapids':
TypeError: simplicial_set_embedding() missing 3 required positional arguments: 'densmap', 'densmap_kwds', and 'output_dens'
Versions
scanpy==1.6.0 anndata==0.7.5 umap==0.5.0 numpy==1.19.5 scipy==1.5.4 pandas==1.1.5 scikit-learn==0.24.0 statsmodels==0.12.1 python-igraph==0.8.3 leidenalg==0.8.3
About this issue
- Original URL
- State: closed
- Created 3 years ago
- Comments: 15 (4 by maintainers)
Commits related to this issue
- require umap<0.5, addresses https://github.com/theislab/scanpy/issues/1579 — committed to openproblems-bio/openproblems by scottgigante 3 years ago
- [ci skip] Merge PR 26180 Merge PR #26180, commits were: * Fix space in requirements * Update requirements from git Esspecially umap-learn hast to be restircted to version <0.5 see issue https://... — committed to bioconda/bioconda-recipes by LustigePerson 3 years ago
- Update setup.py changing scanpy version to avoid bug due to issue with umap-learn https://github.com/theislab/scanpy/issues/1579 — committed to odavalos/ACTINN-PyTorch by odavalos 3 years ago
- Fix umap-learn version Use umap-learn version priot to `0.5`. — committed to theislab/scvelo by WeilerP 3 years ago
Since
umap-learn
updated to version0.5.0
from0.4.6
, the interface may have changed.