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scverse / pertpy

Perturbation Analysis in the scverse ecosystem.
https://pertpy.readthedocs.io/en/latest/
MIT License
92 stars 19 forks source link

Harmonize plots #574

Closed namsaraeva closed 3 months ago

namsaraeva commented 3 months ago

Most changes include enabling of showing/saving the plots and unifying (some) parameter names across different modules. Some functions got a palette/colorbar arguments.

Some imports and typos were fixed as well.

codecov[bot] commented 3 months ago

Codecov Report

Attention: Patch coverage is 9.30233% with 39 lines in your changes are missing coverage. Please review.

Project coverage is 63.06%. Comparing base (03bd173) to head (4ae6377).

:exclamation: Current head 4ae6377 differs from pull request most recent head d9795d0. Consider uploading reports for the commit d9795d0 to get more accurate results

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #574 +/- ## ========================================== - Coverage 63.48% 63.06% -0.42% ========================================== Files 43 43 Lines 5094 5131 +37 ========================================== + Hits 3234 3236 +2 - Misses 1860 1895 +35 ``` | [Files](https://app.codecov.io/gh/theislab/pertpy/pull/574?dropdown=coverage&src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=theislab) | Coverage Δ | | |---|---|---| | [pertpy/plot/\_coda.py](https://app.codecov.io/gh/theislab/pertpy/pull/574?src=pr&el=tree&filepath=pertpy%2Fplot%2F_coda.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=theislab#diff-cGVydHB5L3Bsb3QvX2NvZGEucHk=) | `100.00% <ø> (ø)` | | | [pertpy/tools/\_scgen/\_scgen.py](https://app.codecov.io/gh/theislab/pertpy/pull/574?src=pr&el=tree&filepath=pertpy%2Ftools%2F_scgen%2F_scgen.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=theislab#diff-cGVydHB5L3Rvb2xzL19zY2dlbi9fc2NnZW4ucHk=) | `63.83% <100.00%> (ø)` | | | [pertpy/tools/\_mixscape.py](https://app.codecov.io/gh/theislab/pertpy/pull/574?src=pr&el=tree&filepath=pertpy%2Ftools%2F_mixscape.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=theislab#diff-cGVydHB5L3Rvb2xzL19taXhzY2FwZS5weQ==) | `79.41% <50.00%> (-0.40%)` | :arrow_down: | | [pertpy/tools/\_coda/\_base\_coda.py](https://app.codecov.io/gh/theislab/pertpy/pull/574?src=pr&el=tree&filepath=pertpy%2Ftools%2F_coda%2F_base_coda.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=theislab#diff-cGVydHB5L3Rvb2xzL19jb2RhL19iYXNlX2NvZGEucHk=) | `56.08% <0.00%> (-0.19%)` | :arrow_down: | | [pertpy/tools/\_enrichment.py](https://app.codecov.io/gh/theislab/pertpy/pull/574?src=pr&el=tree&filepath=pertpy%2Ftools%2F_enrichment.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=theislab#diff-cGVydHB5L3Rvb2xzL19lbnJpY2htZW50LnB5) | `52.34% <33.33%> (+0.32%)` | :arrow_up: | | [pertpy/tools/\_dialogue.py](https://app.codecov.io/gh/theislab/pertpy/pull/574?src=pr&el=tree&filepath=pertpy%2Ftools%2F_dialogue.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=theislab#diff-cGVydHB5L3Rvb2xzL19kaWFsb2d1ZS5weQ==) | `13.21% <5.88%> (-0.27%)` | :arrow_down: | | [pertpy/tools/\_milo.py](https://app.codecov.io/gh/theislab/pertpy/pull/574?src=pr&el=tree&filepath=pertpy%2Ftools%2F_milo.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=theislab#diff-cGVydHB5L3Rvb2xzL19taWxvLnB5) | `46.61% <0.00%> (-2.40%)` | :arrow_down: |
namsaraeva commented 3 months ago

todo: add scgen examples 2 and 3

namsaraeva commented 3 months ago

scgen examples need to be added, but in a separate pr, i'll open an issue

Zethson commented 3 months ago

@namsaraeva could you please write a proper PR description and explain how you handled colors the way you did? On a quick glance I don't see tooo many changes to the color handling in the plots