Fixed visium() to support file counts without dataset_id #91
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giovp
approved these changes
Nov 2, 2023
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| # Yhe second element of the returned tuple is the full library as contained in the metadata of | ||
| # VisiumKeys.COUNTS_FILE. For instance for the spatialdata-sandbox/visium dataset it is: | ||
| # spaceranger100_count_30458_ST8059048_mm10-3_0_0_premrna | ||
| # We discard this value and use the one inferred from the filename of VisiumKeys.COUNTS_FILE, or the one provided by | ||
| # the user in dataset_id | ||
| adata, _ = _read_counts(path, counts_file=counts_file, library_id=library_id, **kwargs) |
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is this needed? maybe we can prvent the function to return the dataset_id if it has been already set before anyway>?
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Yes we could modify _read_counts() to drop it. I think we don't need the dataset_id from the metadata.
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wait actually there is an error |
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Ah! Working now? |
Co-authored-by: Giovanni Palla <[email protected]>
Codecov Report
Additional details and impacted files@@ Coverage Diff @@
## main #91 +/- ##
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- Coverage 41.54% 41.25% -0.29%
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Files 16 16
Lines 869 875 +6
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Hits 361 361
- Misses 508 514 +6
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yes, LGTM! |
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I cleaned up a bit
visium(), which now supports raw data that doesn't contain thelibrary_idin the filename of the count file.I tested it on:
spatialdata-ioto construct theSpatialDataobject, thanks to using spatialdata-io for the visium dataset giovp/spatialdata-sandbox#31.@giovp can you please give a quick look?