Comments (3)
falexwolf
commented on July 18, 2024
Ah, yes... thanks for pointing this out... It should work but there is something non-trivial, as the data matrix is cast to a vector when it has a single column or row (just like numpy arrays) so that flattening is unnecessary. I never looked into this on the level of the file, though... We're giving the whole file backing an overhaul anyways and will fix it during that.
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flying-sheep
commented on July 18, 2024
iām very sure i got rid of that behavior at one point and enforced that the data matrix was always 2D.
we should go back to that behavior, mohammad is struggling with problems regarding this as well.
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falexwolf
commented on July 18, 2024
Finally fixed via #55.
Btw @mckinsel, looking at your call above: You can also init an AnnData directly from a DataFrame (adata = AnnData(df)) since a few weeks.
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Related Issues (20)
- `to_df` docstrings
- dask.array.store but with anndata schema HOT 1
- Indexing With a Dask Array HOT 5
- adata.raw = adata HOT 1
- GPU CI tests failing HOT 2
- Add working `GroupStorageType` type annotation
- 0.10.6 - Cannot write files due to implicit conversion to str dtype. HOT 2
- Saving .h5ad with pd.Series in .uns results in IORegistryError HOT 3
- `read_elem_as_dask` HOT 8
- `FileNotFoundError: [Errno 2] No such file or directory: 'llvm-config'` on CI HOT 2
- Upcoming Scipy 1.13 incompatible with file-backed sparse matrices
- CZI files' `var` count changd
- `/` in column names makes AnnData Zarr object unreadable on windows HOT 12
- String indexes in var lead to UserWarning HOT 1
- Move tests out of the package
- Refactor `BaseCompressedSparseDataset` and subclasses to remove `backed_{csr,csc}_matrix`
- concat_on_disk should use int64 indptrs by default so that it can concatenate large files HOT 4
- TypeError: Can't implicitly convert non-string objects to strings HOT 4
- Error concatenating scRNA with visium dataset
- Error: Expected a python object, received a character HOT 1
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