Converting cell_metadata from integer to string for latest MERFISH public data #692
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Changing coordinate index to string
Reverted to previous code (prior scverse#679) for read_visium
Codecov Report
Additional details and impacted files@@ Coverage Diff @@
## main #692 +/- ##
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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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Oh, I accidentally edited another part and requested it. Appreciate for fixing it :) |
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thank you @dfhannum , this was bad overlook from our side, I'll go on and merge it! |
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Description
A previous pull request #679 by @djlee1 addressed this issue but implemented the code in the read_visium() function rather than in read_vizgen().
Here I made the changes to read_vizgen(). Looking through current issues on squidpy I didn't see any with the read_visium() function that would be addressed by the change, so I reverted to the previous version of the read_visium() code.
How has this been tested?
I've tested this locally on the public MERSCOPE data mentioned in #686, and the AnnData observations data frame was correctly populated with values rather than NaNs.
I also confirmed that the changes didn't effect previous squidpy tutorials using Vizgen data (mouse brain, mouse liver).