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filter_obs is broken with latest AnnData #146

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grst opened this issue Aug 30, 2024 · 0 comments
Open

filter_obs is broken with latest AnnData #146

grst opened this issue Aug 30, 2024 · 0 comments
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bug Something isn't working

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@grst
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grst commented Aug 30, 2024

Describe the bug
Running mu.pp.filter_obs results in a ValueError with the latest AnnData

To Reproduce

import scanpy as sc
import muon as mu

adata = sc.datasets.pbmc3k_processed()
mdata = mu.MuData({
    "A": adata[:500, ].copy(),
    "B": adata[500:, ].copy()
})
mu.pp.filter_obs(mdata, "A:louvain", lambda x: x == "B cells")
---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Cell In[22], [line 1](vscode-notebook-cell:?execution_count=22&line=1)
----> [1](vscode-notebook-cell:?execution_count=22&line=1) mu.pp.filter_obs(mdata, "A:louvain", lambda x: x == "B cells")

File ~/apps/micromamba/envs/test_scirpy/lib/python3.11/site-packages/muon/_core/preproc.py:763, in filter_obs(data, var, func)
    [761](https://file .vscode-resource.vscode-cdn.net/home/sturm/projects/2020/scirpy/docs/tutorials/~/apps/micromamba/envs/test_scirpy/lib/python3.11/site-packages/muon/_core/preproc.py:761) obsmap = data.obsmap[m][obs_subset]
    [762](https://file .vscode-resource.vscode-cdn.net/home/sturm/projects/2020/scirpy/docs/tutorials/~/apps/micromamba/envs/test_scirpy/lib/python3.11/site-packages/muon/_core/preproc.py:762) obsidx = obsmap > 0
--> [763](https://file .vscode-resource.vscode-cdn.net/home/sturm/projects/2020/scirpy/docs/tutorials/~/apps/micromamba/envs/test_scirpy/lib/python3.11/site-packages/muon/_core/preproc.py:763) filter_obs(mod, mod.obs_names[obsmap[obsidx] - 1])
    [764](https://file .vscode-resource.vscode-cdn.net/home/sturm/projects/2020/scirpy/docs/tutorials/~/apps/micromamba/envs/test_scirpy/lib/python3.11/site-packages/muon/_core/preproc.py:764) maporder = np.argsort(obsmap[obsidx])
    [765](https://file .vscode-resource.vscode-cdn.net/home/sturm/projects/2020/scirpy/docs/tutorials/~/apps/micromamba/envs/test_scirpy/lib/python3.11/site-packages/muon/_core/preproc.py:765) nobsmap = np.empty(maporder.size)

File ~/apps/micromamba/envs/test_scirpy/lib/python3.11/site-packages/muon/_core/preproc.py:728, in filter_obs(data, var, func)
    [725](https://file .vscode-resource.vscode-cdn.net/home/sturm/projects/2020/scirpy/docs/tutorials/~/apps/micromamba/envs/test_scirpy/lib/python3.11/site-packages/muon/_core/preproc.py:725) data._n_obs = data.obs.shape[0]
    [727](https://file .vscode-resource.vscode-cdn.net/home/sturm/projects/2020/scirpy/docs/tutorials/~/apps/micromamba/envs/test_scirpy/lib/python3.11/site-packages/muon/_core/preproc.py:727) # Subset .obsm
--> [728](https://file .vscode-resource.vscode-cdn.net/home/sturm/projects/2020/scirpy/docs/tutorials/~/apps/micromamba/envs/test_scirpy/lib/python3.11/site-packages/muon/_core/preproc.py:728) for k, v in data.obsm.items():
    [729](https://file .vscode-resource.vscode-cdn.net/home/sturm/projects/2020/scirpy/docs/tutorials/~/apps/micromamba/envs/test_scirpy/lib/python3.11/site-packages/muon/_core/preproc.py:729)     data.obsm[k] = v[obs_subset]
    [731](https://file .vscode-resource.vscode-cdn.net/home/sturm/projects/2020/scirpy/docs/tutorials/~/apps/micromamba/envs/test_scirpy/lib/python3.11/site-packages/muon/_core/preproc.py:731) # Subset .obsp

File ~/apps/micromamba/envs/test_scirpy/lib/python3.11/site-packages/anndata/_core/aligned_mapping.py:422, in AlignedMappingProperty.__get__(self, obj, objtype)
    [420](https://file .vscode-resource.vscode-cdn.net/home/sturm/projects/2020/scirpy/docs/tutorials/~/apps/micromamba/envs/test_scirpy/lib/python3.11/site-packages/anndata/_core/aligned_mapping.py:420)     return self  # type: ignore
    [421](https://file .vscode-resource.vscode-cdn.net/home/sturm/projects/2020/scirpy/docs/tutorials/~/apps/micromamba/envs/test_scirpy/lib/python3.11/site-packages/anndata/_core/aligned_mapping.py:421) if not obj.is_view:
--> [422](https://file .vscode-resource.vscode-cdn.net/home/sturm/projects/2020/scirpy/docs/tutorials/~/apps/micromamba/envs/test_scirpy/lib/python3.11/site-packages/anndata/_core/aligned_mapping.py:422)     return self.construct(obj, store=getattr(obj, f"_{self.name}"))
    [423](https://file .vscode-resource.vscode-cdn.net/home/sturm/projects/2020/scirpy/docs/tutorials/~/apps/micromamba/envs/test_scirpy/lib/python3.11/site-packages/anndata/_core/aligned_mapping.py:423) parent_anndata = obj._adata_ref
    [424](https://file .vscode-resource.vscode-cdn.net/home/sturm/projects/2020/scirpy/docs/tutorials/~/apps/micromamba/envs/test_scirpy/lib/python3.11/site-packages/anndata/_core/aligned_mapping.py:424) idxs = (obj._oidx, obj._vidx)
...
---> [97](https://file .vscode-resource.vscode-cdn.net/home/sturm/projects/2020/scirpy/docs/tutorials/~/apps/micromamba/envs/test_scirpy/lib/python3.11/site-packages/anndata/_core/aligned_mapping.py:97)     raise ValueError(msg)
     [99](https://file .vscode-resource.vscode-cdn.net/home/sturm/projects/2020/scirpy/docs/tutorials/~/apps/micromamba/envs/test_scirpy/lib/python3.11/site-packages/anndata/_core/aligned_mapping.py:99) name = f"{self.attrname.title().rstrip('s')} {key!r}"
    [100](https://file .vscode-resource.vscode-cdn.net/home/sturm/projects/2020/scirpy/docs/tutorials/~/apps/micromamba/envs/test_scirpy/lib/python3.11/site-packages/anndata/_core/aligned_mapping.py:100) return coerce_array(val, name=name, allow_df=self._allow_df)

ValueError: Value passed for key 'X_pca' is of incorrect shape. Values of obsm must match dimensions ('obs',) of parent. Value had shape (500,) while it should have had (69,).

Expected behaviour
Filter the mudata object as this has worked previously

System

anndata==0.10.9
mudata==0.3.1
muon==0.1.6
scanpy==1.10.2
@grst grst added the bug Something isn't working label Aug 30, 2024
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