trouble with pbmc notebook
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- Dominant language
- Python
- Stars
- 323
- Forks
- 43
- PR merge metrics
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Description
this is being run within the recommended container
for snap.pl.umap(data, color='leiden', interactive=False, height=500)
---------------------------------------------------------------------------
KeyError Traceback (most recent call last)
Cell In[17], line 1
----> 1 snap.pl.umap(data, color='leiden', interactive=False, height=500)
File [/usr/local/lib/python3.11/site-packages/snapatac2/plotting/__init__.py:265](http://127.0.0.1:8888/usr/local/lib/python3.11/site-packages/snapatac2/plotting/__init__.py#line=264), in umap(adata, color, use_rep, marker_size, marker_opacity, sample_size, **kwargs)
234 """Plot the UMAP embedding.
235
236 Parameters
(...)
261 returned, which can then be further customized using the plotly API.
262 """
263 from natsort import index_natsorted
--> 265 embedding = adata.obsm[use_rep]
267 if isinstance(color, str):
268 groups = adata.obs[color].to_numpy()
File [/usr/local/lib/python3.11/site-packages/anndata/_core/aligned_mapping.py:196](http://127.0.0.1:8888/usr/local/lib/python3.11/site-packages/anndata/_core/aligned_mapping.py#line=195), in AlignedActualMixin.__getitem__(self, key)
195 def __getitem__(self, key: str) -> V:
--> 196 return self._data[key]
KeyError: 'X_umap'```
Contributor guide
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with the PBMC notebook step calling snap.pl.umap and inspect snapatac2/plotting/init.py around the umap entry point at line 265. Reproduce the KeyError in the recommended container, then trace why the input lacks X_umap; the issue is done when the notebook call runs successfully with the expected embedding.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter-notebook, python
- Domain
- bioinformatics, data
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100