scverse / pertpy

Perturbation Analysis in the scverse ecosystem.
https://pertpy.readthedocs.io/en/latest/
MIT License
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Add dgidb and pharmgkb for drug annotation #575

Closed wxicu closed 2 months ago

wxicu commented 3 months ago

PR Checklist

Description of changes

Do you probably have any suggestions how to interact with enrichment funtion better?

Technical details

Additional context

codecov[bot] commented 3 months ago

Codecov Report

Attention: Patch coverage is 45.61404% with 93 lines in your changes are missing coverage. Please review.

Project coverage is 62.27%. Comparing base (0f888e8) to head (36beb40).

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #575 +/- ## ========================================== - Coverage 62.66% 62.27% -0.40% ========================================== Files 43 43 Lines 5164 5296 +132 ========================================== + Hits 3236 3298 +62 - Misses 1928 1998 +70 ``` | [Files](https://app.codecov.io/gh/theislab/pertpy/pull/575?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/metadata/\_drug.py](https://app.codecov.io/gh/theislab/pertpy/pull/575?src=pr&el=tree&filepath=pertpy%2Fmetadata%2F_drug.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=theislab#diff-cGVydHB5L21ldGFkYXRhL19kcnVnLnB5) | `84.21% <83.51%> (-3.29%)` | :arrow_down: | | [pertpy/tools/\_enrichment.py](https://app.codecov.io/gh/theislab/pertpy/pull/575?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) | `47.27% <0.00%> (-5.08%)` | :arrow_down: | | [pertpy/metadata/\_look\_up.py](https://app.codecov.io/gh/theislab/pertpy/pull/575?src=pr&el=tree&filepath=pertpy%2Fmetadata%2F_look_up.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=theislab#diff-cGVydHB5L21ldGFkYXRhL19sb29rX3VwLnB5) | `8.71% <3.22%> (-1.74%)` | :arrow_down: |
wxicu commented 3 months ago

@Zethson

  1. df() and dict() function is added. If this structure is ok then i will adapt to other metadata classes
  2. add two new parameters in plotting function. I am not good at naming, but hope the structure is what we expect
  3. if all above is fine, i will add pharmgkb database soon