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

Most upvoted comments

Since umap-learn updated to version 0.5.0 from 0.4.6, the interface may have changed.