[label projection] scVI+scArches+XGBoost

[scottgigante-immunai]

Submission type

• This submission adds a new method

Testing

• This submission was written in 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: )

Submission guidelines

• This submission follows the guidelines in our
  Contributing document
• I have checked to ensure there aren't other open Pull Requests for the
  same update/change (closes Scvi scarches xgb #494)

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

[github-actions]

[scottgigante-immunai]

Passing at https://tower.nf/orgs/openproblems-bio/workspaces/openproblems-bio/watch/ZlatnDwooPZPp

[LuckyMD]

This looks good to me. I don't recall all of the xgboost hyperparameters I initially selected, but this looks similar to what i would have gone for ^^. Thanks so much for doing this!

[codecov]

Codecov Report

Patch coverage: 97.29% and project coverage change: -0.12 ⚠️

Comparison is base (9d16650) 95.60% compared to head (d67bada) 95.48%.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #853      +/-   ##
==========================================
- Coverage   95.60%   95.48%   -0.12%     
==========================================
  Files         187      188       +1     
  Lines        4980     5055      +75     
  Branches      273      279       +6     
==========================================
+ Hits         4761     4827      +66     
- Misses        141      148       +7     
- Partials       78       80       +2     

Flag	Coverage Δ
unittests	95.48% <97.29%> (-0.12%)	⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
...ration/batch_integration_embed/metrics/cc_score.py	100.00% <ø> (ø)
...n/batch_integration_embed/metrics/iso_label_sil.py	100.00% <ø> (ø)
...ntegration/batch_integration_embed/metrics/kBET.py	100.00% <ø> (ø)
...integration/batch_integration_embed/metrics/pcr.py	100.00% <ø> (ø)
...ation/batch_integration_embed/metrics/sil_batch.py	100.00% <ø> (ø)
...tion/batch_integration_embed/metrics/silhouette.py	100.00% <ø> (ø)
...ch_integration_feature/metrics/hvg_conservation.py	100.00% <ø> (ø)
...tegration/batch_integration_graph/methods/bbknn.py	100.00% <ø> (ø)
...egration/batch_integration_graph/methods/combat.py	100.00% <ø> (ø)
...gration/batch_integration_graph/methods/fastmnn.py	100.00% <ø> (ø)
... and 82 more

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[mxposed]

Thank you, Scott!