🎨 rename enrichment group to upregulated in x - #82
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Pull request overview
This PR updates enrichment analysis output labeling to avoid the potentially confusing “upregulated vs downregulated” terminology by switching to “upregulated in ” for both directions (group1 vs group2).
Changes:
- Updated
run_up_down_regulation_enrichmentto emitdirectionasupregulated in {g1}/upregulated in {g2}. - Updated the expected
directionvalues in the enrichment integration test to match the new labeling.
Reviewed changes
Copilot reviewed 2 out of 2 changed files in this pull request and generated 2 comments.
| File | Description |
|---|---|
src/acore/enrichment_analysis/__init__.py |
Changes direction strings to “upregulated in {group}” for both branches. |
tests/enrichment_analysis/test_enrichment.py |
Updates expected direction values to the new “upregulated in timepointX” labels. |
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- downregulation w.r.t to what needs to be stated always
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Summary
Upregulated vs Downregulated can be confusing. Therefore we switch to upregulated in group 1 vs upregulated in group 2.
Related to Multiomics-Analytics-Group/vuecore#45
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List of changes proposed in this PR (pull-request)
directioncolumn entries are changed to reflectupregulated in xChecks
In case you add a new module or update one, please check the following tasks:
__init__.pyin the new folder, so thatthey are available when the subpackage is imported.
src/acore/typesfolder.Optimal is to have only one output schema of results per subpackage or module.
datafolder, or reuse an existing one for testingdocs/api_examples_modulefolder with that dataindex.mdfile in thedocsfolder with the new example/testsfolder with the name of the subpackage or moduleusing pytest or unittests to test your new functionality.