theislab / scib

Benchmarking analysis of data integration tools
MIT License
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Update isolated_labels.py #368

Closed danielStrobl closed 1 year ago

danielStrobl commented 1 year ago

As mentioned in https://github.com/theislab/scib/issues/367, the isolated label metrics do not compute what they should. By calculating the individual silhouette scores and then taking the mean over only the cells of the cluster, this should be fixed.

LuckyMD commented 1 year ago

I guess you'll need to adapt the tests as well for this.

codecov[bot] commented 1 year ago

Codecov Report

Merging #368 (3aa8303) into main (1be0daa) will not change coverage. The diff coverage is 100.00%.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #368 +/- ## ======================================= Coverage 53.13% 53.13% ======================================= Files 22 22 Lines 1848 1848 ======================================= Hits 982 982 Misses 866 866 ``` | Flag | Coverage Δ | | |---|---|---| | unittests | `53.13% <100.00%> (ø)` | | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=theislab#carryforward-flags-in-the-pull-request-comment) to find out more. | [Impacted Files](https://codecov.io/gh/theislab/scib/pull/368?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=theislab) | Coverage Δ | | |---|---|---| | [scib/metrics/isolated\_labels.py](https://codecov.io/gh/theislab/scib/pull/368?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=theislab#diff-c2NpYi9tZXRyaWNzL2lzb2xhdGVkX2xhYmVscy5weQ==) | `94.33% <100.00%> (ø)` | |
LuckyMD commented 1 year ago

Please also adapt the perfect score test

danielStrobl commented 1 year ago

ah bit too fast

LuckyMD commented 1 year ago

@mumichae could you still review this please?