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adjusted CellComposite and CellLabels loading in read_nanostring #766

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merged 7 commits into from Nov 21, 2023

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FrancescaDr
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Description

  • instead of automatic loading of all fov it checks if the fov variables exists in CellCompositon and CellLabels, like has been done for metadata loading
  • optional loading of .uns variables from CellComposition and CellLabels (not all CosmX nano string data has the information available, e.i. bowel disease data does not have CellLabels information )

How has this been tested?

Tested with two different patients from CosmX Lung (test/test_nanostring.py) and loading with data from CosmX bowel disease data

Closes

closes #585

@giovp
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giovp commented Oct 26, 2023

hi @FrancescaDr could you please rebase from main ? it should fix tests. Also could you remove the tests for the reader? after that we can merge it!

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codecov-commenter commented Nov 7, 2023

Codecov Report

Merging #766 (6f48274) into main (c528ce7) will decrease coverage by 0.07%.
The diff coverage is 0.00%.

Additional details and impacted files
@@            Coverage Diff             @@
##             main     #766      +/-   ##
==========================================
- Coverage   69.94%   69.87%   -0.07%     
==========================================
  Files          39       39              
  Lines        5476     5481       +5     
  Branches     1024     1025       +1     
==========================================
  Hits         3830     3830              
- Misses       1358     1363       +5     
  Partials      288      288              
Files Coverage Δ
src/squidpy/read/_read.py 35.86% <0.00%> (-2.07%) ⬇️

@giovp giovp merged commit aa60e26 into scverse:main Nov 21, 2023
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Nanostring reader error
3 participants