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Can't read in protein antibody capture data #3113

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alexanderchang1 opened this issue Jun 18, 2024 · 7 comments · Fixed by alexanderchang1/scanpy#1
Closed
3 tasks done

Can't read in protein antibody capture data #3113

alexanderchang1 opened this issue Jun 18, 2024 · 7 comments · Fixed by alexanderchang1/scanpy#1
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Area - IO Reading and writing Area – Spatial 🗺

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@alexanderchang1
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alexanderchang1 commented Jun 18, 2024 •
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Please make sure these conditions are met

  • I have checked that this issue has not already been reported.
  • I have confirmed this bug exists on the latest version of scanpy.
  • (optional) I have confirmed this bug exists on the main branch of scanpy.

What happened?

I'm trying to read in visium data with antibody capture data but for some reason the antibody capture data is not registering. Is there something I'm doing wrong? I couldn't find documentation on how to do this. Although I do see the antibody capture data in the web_summary.html

However read_10x_mtx method works directly on the folder, is there a way to add gex_only functionality to the read_visium function?

Minimal code sample

print(key)
        adata = sc.read_visium(path, count_file='filtered_feature_bc_matrix.h5', load_images=True, )
        print(adata)
        
        # Separate RNA and protein data
        rna_data = adata[:, adata.var['feature_types'] == 'Gene Expression']
        protein_data = adata[:, adata.var['feature_types'] == 'Antibody Capture']
        
        # Verify the separated data
        print("RNA data shape:", rna_data.shape)
        print("Protein data shape:", protein_data.shape)

Error output

MWS22-14789

AnnData object with n_obs × n_vars = 2256 × 18085
    obs: 'in_tissue', 'array_row', 'array_col'
    var: 'gene_ids', 'feature_types', 'genome', 'isotype_control', 'normalized', 'pattern', 'read', 'secondary_name', 'sequence'
    uns: 'spatial'
    obsm: 'spatial'
RNA data shape: (2256, 18085)
Protein data shape: (2256, 0)

Versions

1.10.1
@alexanderchang1 alexanderchang1 added Bug 🐛 Triage 🩺 This issue needs to be triaged by a maintainer labels Jun 18, 2024
@alexanderchang1
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Hi, I just wanted to follow up on this.

@flying-sheep
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Hi, I don’t have much experience with that data. Does squidpy work better? https://squidpy.readthedocs.io/en/stable/api/squidpy.read.visium.html

scanpy doesn’t have much support for spatial analysis, squidpy is built for it.

@flying-sheep flying-sheep added Needs info❔ More information needed and removed Triage 🩺 This issue needs to be triaged by a maintainer labels Aug 5, 2024
@alexanderchang1
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Hi, let me give that a shot.

@alexanderchang1
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alexanderchang1 commented Oct 10, 2024 •
edited by flying-sheep
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Hi, I tried that and got this error. I think it's because it's recognizing both antibody data and gene data and throwing an error.

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
Cell In[7], line 13
     11 key = get_second_to_last_split(path)
     12 print(key)
---> 13 adata = sq.read.visium(path, count_file='filtered_feature_bc_matrix.h5', load_images=True)
     15 # Create unique cell identifiers
     16 adata.obs_names = f'sample_{key}_' + adata.obs_names

File /bgfs/alee/LO_LAB/Personal/Alexander_Chang/alc376/envs/popari_env/lib/python3.12/site-packages/squidpy/read/_read.py:67, in visium(path, counts_file, library_id, load_images, source_image_path, **kwargs)
     34 """
     35 Read *10x Genomics* Visium formatted dataset.
     36 
   (...)
     64     - :attr:`anndata.AnnData.uns` ``['spatial']['{library_id}']['metadata']`` - various metadata.
     65 """  # noqa: E501
     66 path = Path(path)
---> 67 adata, library_id = _read_counts(path, count_file=counts_file, library_id=library_id, **kwargs)
     69 if not load_images:
     70     return adata

TypeError: squidpy.read._utils._read_counts() got multiple values for keyword argument 'count_file'

This was referenced Oct 11, 2024
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@alexanderchang1
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Hi,

@flying-sheep I've tagged you in the merge request. The reason why this function is necessary in Scanpy is because Visium allows for antibody capture data as well. This fix neatly resolves it. Please let me know if there's anything I need to do to get the merge approved. We have a project using protein and gex data being submitted soon and we would ideally like the pip install be able to pull directly from a version of scanpy that has this functionality.

@flying-sheep
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Hi, sorry that I didn’t answer earlier: we decided to deprecate scanpy’s spatial functions in favor of squidpy:

scanpy/src/scanpy/readwrite.py

Lines 394 to 395 in de75ed9

.. deprecated:: 1.11.0
Use :func:`squidpy.read.visium` instead.

I’m happy to help fix the error you encounter there!

@flying-sheep flying-sheep closed this as not planned Won't fix, can't repro, duplicate, stale Jan 23, 2025
@flying-sheep flying-sheep mentioned this issue Jan 23, 2025
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@flying-sheep
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OK, moved it to scverse/squidpy#940

@flying-sheep flying-sheep added Area – Spatial 🗺 Area - IO Reading and writing and removed Needs info❔ More information needed labels Jan 23, 2025
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