Can't read in protein antibody capture data

[flying-sheep]

Description

See scverse/scanpy#3113

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 reproducible example

adata = sq.read.visium(path, count_file='filtered_feature_bc_matrix.h5', load_images=True)

Traceback

---------------------------------------------------------------------------
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'

Version

cc @alexanderchang1

[alexanderchang1]

Hi,

Does this depreciation mean squidpy will be a drop in replacement for scanpy functions like sc.pl.spatial(prop_adata, color = "Cancer Cells")? We have vignettes for an ongoing project that will need modification. Is there a post to read about the depreciation changes?

Secondly, are you able to pull the same changes I put on the PR for Scanpy, or should I fork Squidpy and try editing it here? I'm not familiar with pull requests and have read the contributing documentation, but I am still struggling to get it to pass the checks. It's a relatively straightforward change of 6 lines to add existing gex_only read_10x_h5 functionality to the read_visium function.

See here: scverse/scanpy@0b89362

[flying-sheep]

Hi! Again, sorry for not replying to you, only to then close your PR and move your issue.

I’m pretty sure sc.pl.spatial was the base for the initial version of sq.pl.spatial_scatter, but since then, the squidpy version has seen a lot of development, so I wouldn’t be surprised if there were some slight differences (apart from the added functionality). You can see an example notebook for this function here: https://squidpy.readthedocs.io/en/stable/notebooks/examples/plotting/plot_scatter.html

are you able to pull the same changes I put on the PR for Scanpy, or should I fork Squidpy and try editing it here?

Maybe no change is necessary:

• try specifying counts_file (note the “s”) and try again!
• if you also specify gex_only=False, it should be passed through!