add functions for spot_uniformity_within_cells - Githubissues

theislab / txsim

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add functions for spot_uniformity_within_cells #82

Closed RhineCloud closed 9 months ago

RhineCloud commented 9 months ago

Changes proposed in this pull request:

added spot_uniformity_within_cells to cell_and_spot_statistics wrapper function
- also checks that adata.uns["spots"] is present
added corresponding _get_<...>_grid function
added spot_uniformity_per_cell_score function to calculate statistic for uniformity
- the issue before with the unexpected scores when testing was a sampling issue rather than a maths issue

If new dependencies are needed:

new dependencies: convex_hull_image function from skimage.morphology

[x] adjusted dependencies in txsim/pyproject.toml
[ ] created PR in txsim-pipeline and updated txsim-pipeline/envs/txsim-env.yaml