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Split spatial analysis module #938

Merged
merged 9 commits into from
Feb 28, 2023
Merged

Split spatial analysis module #938

merged 9 commits into from
Feb 28, 2023

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camisowers
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@camisowers camisowers commented Feb 28, 2023

If you haven't already, please read through our contributing guidelines before opening your PR

What is the purpose of this PR?

Addresses part of #901. Splits the relatively large spatial_analysis.py between the kmeans neighborhood analysis and spatial enrichment code. Will make finding and checking the spatial enrichment easier in the future as well.

How did you implement your changes

New files:

  • neighborhood_analysis.py and neighborhood_analysis_test.py
  • spatial_enrichment.py and spatial_enrichment_test.py

Also adds in missing `cell_type_col' for mixing score functions in the notebook.

Remaining issues

If we decide to unquarantine the spatial enrichment notebook, we'll need to update the imports.

@camisowers camisowers added the enhancement New feature or request label Feb 28, 2023
@camisowers camisowers self-assigned this Feb 28, 2023
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@alex-l-kong alex-l-kong left a comment

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LGTM

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@srivarra srivarra left a comment

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Looks good!

@ngreenwald ngreenwald merged commit 97e6baa into main Feb 28, 2023
@ngreenwald ngreenwald deleted the refactor_modules branch February 28, 2023 23:17
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4 participants