Add COZI to nhood_enrichment() #1023
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Merge main into cozi_nhood_enrichment to sync with upstream
for more information, see https://pre-commit.ci
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I get a resolution-too-deep error for dependencies for ubuntu related to tox and the error for macos also seems to be connected to tox. I only added an import warnings in the code, so I did not change any dependencies. Can someone help? |
Merge CLI changes from upstream
Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #1023 +/- ##
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- Coverage 66.63% 23.95% -42.68%
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Files 40 41 +1
Lines 6060 6186 +126
Branches 1015 1036 +21
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- Hits 4038 1482 -2556
- Misses 1662 4687 +3025
+ Partials 360 17 -343
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Hi, sorry I just saw this. I'd like to understand what happens here before I give it an OK. Could we maybe set a meeting in the scverse zulip? |
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Description
normalizationparameter for conditional and total normalization of neighbor counts tonhood_enrichment()as described in Schiller et al bioRxiv.normalization=conditional. CCR is the proportion of cells of an index type that neighbors cells of the neighbor type.nhood_enrichment_dotplot()to plot zscore and CCR at once.min_cell_countparameter tonhood_enrichment()to filter out clusters of cells with counts below the set threshold. Filtered out interaction z-scores are replaced with NA.How has this been tested?
Added additional test functions for nhood_enrichment with conditional normalization and CCR. Test images for dotplot are missing, all other tests run successfully.
TODO