Add COZI to nhood_enrichment() #1023
Open
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Merge main into cozi_nhood_enrichment to sync with upstream
for more information, see https://pre-commit.ci
|
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 +/- ##
===========================================
- Coverage 66.63% 23.95% -42.68%
===========================================
Files 40 41 +1
Lines 6060 6186 +126
Branches 1015 1036 +21
===========================================
- Hits 4038 1482 -2556
- Misses 1662 4687 +3025
+ Partials 360 17 -343
🚀 New features to boost your workflow:
|
|
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? |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
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