Skip to content

Conversation

@julienmortier
Copy link
Collaborator

This PR contains 2 functions to do neighborhood clustering (using K-means clustering) based on the cell type composition of neighboring cells. It is similar to what is possible in Scimap (https://scimap.xyz/tutorials/md/spatial_lda_scimap/) and ark-analysis. The current implementation is still somewhat slow so improvements are definitely still possible. A similar approach using LDA would also be interesting in the future.

@codecov-commenter
Copy link

codecov-commenter commented Oct 17, 2025

Codecov Report

❌ Patch coverage is 0% with 35 lines in your changes missing coverage. Please review.
✅ Project coverage is 61.26%. Comparing base (3ce0b49) to head (ac8686d).

Files with missing lines Patch % Lines
src/harpy/table/_nhood_clustering.py 0.00% 35 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main     #160      +/-   ##
==========================================
- Coverage   61.58%   61.26%   -0.33%     
==========================================
  Files          91       92       +1     
  Lines        6677     6712      +35     
  Branches     1060     1061       +1     
==========================================
  Hits         4112     4112              
- Misses       2131     2166      +35     
  Partials      434      434              
Files with missing lines Coverage Δ
src/harpy/table/_nhood_clustering.py 0.00% <0.00%> (ø)
🚀 New features to boost your workflow:
  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

3 participants