cell2location with max normalisation flexibility

[vitkl]

I think this is necessary to properly analyse the data where total UMI is completely decoupled from biological RNA count https://github.com/openproblems-bio/openproblems/issues/589#issuecomment-1325831148

Submission type

• [x] This submission adds a new method
• [x] This submission fixes a bug (link to related issue: https://github.com/openproblems-bio/openproblems/issues/589#issuecomment-1325831148) I guess you can say it's a bug.

Testing

• [x] This submission was written on a forked copy of openproblems
• [ ] Nextflow test pipeline is passing on this base branch of this pull request (include link to passed test on NF Tower found in GitHub Actions summary: )
• [ ] If this pull request is not ready for review (including passing the Nextflow test pipeline), I will open this PR as a draft (click on the down arrow next to the "Create Pull Request" button)

Submission guidelines

• [x] This submission follows the guidelines in our Contributing document
• [x] I have checked to ensure there aren't other open Pull Requests for the same update/change

PR review checklist

This PR will be evaluated on the basis of the following checks:

• [ ] The task addresses a valid open problem in single-cell analysis
• [ ] The latest version of master is merged and tested
• [ ] The methods/metrics are imported to __init__.py and were tested in the pipeline
• [ ] Method and metric decorators are annotated with paper title, year, author, code version, and date
• [ ] The README gives an outline of the methods, metrics and datasets in the folder
• [ ] The sample test data is appropriate to test implementation of all methods and metrics (for new tasks)

[codecov[bot]]

Codecov Report

Base: 95.06% // Head: 95.06% // Increases project coverage by +0.00% :tada:

Coverage data is based on head (be78846) compared to base (a796e02). Patch coverage: 100.00% of modified lines in pull request are covered.

Additional details and impacted files

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[vitkl]

Would be great if you add this @scottgigante-immunai

[vitkl]

We normally don't recommend using fully flexible normalisation (detection_alpha=1) because it completely removes the relationship between estimated cell abundance and the number of cells you see in the image. I analysed a number of datasets, such as https://www.biorxiv.org/content/10.1101/2021.11.26.470108v1, where over-normalisation leads to the spurious mapping of a subset of cell types to low UMI count regions.

However, the simulation in this project are designed to require fully flexible normalisation.

[scottgigante-immunai]

@vitkl looks like you haven't added it to methods/__init__.py, so this new method is not run in tests.

[scottgigante-immunai]

Also please open PRs as drafts until tests pass.

Nextflow test pipeline is passing on this base branch of this pull request (include link to passed test on NF Tower found in GitHub Actions summary: ) If this pull request is not ready for review (including passing the Nextflow test pipeline), I will open this PR as a draft (click on the down arrow next to the "Create Pull Request" button)

[vitkl]

@scottgigante-immunai I don't understand why the test fail (https://github.com/vitkl/openproblems/actions/runs/3556951870/jobs/5974765854) hence I don't create these as a draft PR

[scottgigante-immunai]

That one was my fault. Should be fixed now

[scottgigante-immunai]

Tests passing at https://tower.nf/orgs/openproblems-bio/workspaces/openproblems-bio/watch/3reAegSoEpYtFz !

[vitkl]

The tests seem to pass on my branch https://github.com/vitkl/openproblems/actions/runs/3560607225

[scottgigante-immunai]

Thanks @vitkl !