Convert cell_metadata index from integer to string for latest MERFISH public data #679
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In the latest MERFISH public data, the cell_metadata index is recognized as an integer, which requires conversion to a string format. This commit adds a function to convert the index to a string, ensuring compatibility with downstream applications.
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Codecov Report
Additional details and impacted files@@ Coverage Diff @@
## main #679 +/- ##
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- Coverage 78.51% 78.49% -0.03%
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Files 33 33
Lines 4706 4706
Branches 922 916 -6
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- Hits 3695 3694 -1
Misses 735 735
- Partials 276 277 +1
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This was referenced May 9, 2023
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I've used the change in my local copy of squidpy successfully for the past weeks. When I downloaded the new version things stopped working today. I then realized that the change occurred in the wrong function. This change was in "def visium()" but it was meant for "def vizgen()" |
dfhannum
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May 24, 2023
Reverted to previous code (prior scverse#679) for read_visium
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Description
In the latest MERFISH public data, the cell_metadata index is recognized as an integer, which requires conversion to a string format. This commit adds a function to convert the index to a string, ensuring compatibility with downstream applications.
How has this been tested?
When attempting to load the latest public data from https://vizgen.com/data-release-program/, specifically the FFPE_Human_Immuno_oncology dataset, I have encountered an issue where the 'obs' of the Anndata object is filled with NaN values. This issue is caused by the presence of different index types between 'adata.obs' and 'coords', which leads to errors when merging them.
I have found that this issue can be resolved by setting the data type of 'coords' as 'str'. After making this adjustment, the 'obs' of the Anndata object is populated with the expected data.