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feat: add geneset initialization #803

Merged
merged 15 commits into from
Mar 7, 2024
Merged

feat: add geneset initialization #803

merged 15 commits into from
Mar 7, 2024

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atarashansky
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@atarashansky atarashansky commented Mar 3, 2024

Genesets are stored as a JSON blob in the obs tiledb metadata under key "genesets". The new endpoint added to the server simply forwards this blob to the client.

The client added back geneset initialization from CELLxGENE Annotate.

Each cell type present in a CellGuide CXG has its own marker gene set from CellGuide.

Also added some QOL improvements to the categorical data:

  • Ordering of labels in decreasing order by mean expression when coloring by continuous metadata
  • Removal of cells with 0 labels when subsetting/unsubsetting
  • Unsubset and subset hotkeys

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codecov bot commented Mar 3, 2024

Codecov Report

Attention: Patch coverage is 44.44444% with 15 lines in your changes are missing coverage. Please review.

Project coverage is 77.47%. Comparing base (bd4f07a) to head (0943d1b).

❗ Current head 0943d1b differs from pull request most recent head bf18b89. Consider uploading reports for the commit bf18b89 to get more accurate results

Files Patch % Lines
server/dataset/cxg_dataset.py 27.27% 8 Missing ⚠️
server/common/rest.py 28.57% 5 Missing ⚠️
server/app/api/v3.py 83.33% 1 Missing ⚠️
server/dataset/dataset.py 66.66% 1 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main     #803      +/-   ##
==========================================
- Coverage   77.74%   77.47%   -0.27%     
==========================================
  Files          88       88              
  Lines        6802     6856      +54     
==========================================
+ Hits         5288     5312      +24     
- Misses       1514     1544      +30     
Flag Coverage Δ
frontend 77.47% <44.44%> (-0.27%) ⬇️
javascript 77.47% <44.44%> (-0.27%) ⬇️
smokeTest ∅ <ø> (∅)
unitTest 77.47% <44.44%> (-0.27%) ⬇️

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@atarashansky atarashansky requested review from tihuan and seve March 5, 2024 23:55
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@seve seve left a comment

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Just a couple items for discussion

client/src/components/geneExpression/index.tsx Outdated Show resolved Hide resolved
client/src/components/geneExpression/index.tsx Outdated Show resolved Hide resolved
client/src/components/geneExpression/index.tsx Outdated Show resolved Hide resolved
@atarashansky atarashansky requested review from tihuan and seve March 6, 2024 20:14
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PR looks great! Thanks for all the code comments to provide the context, Alec 🥇 ! Just some nits otherwise LGTM!

client/server/development.js Show resolved Hide resolved
client/src/actions/index.ts Outdated Show resolved Hide resolved
client/src/components/geneExpression/index.tsx Outdated Show resolved Hide resolved
client/src/components/geneExpression/index.tsx Outdated Show resolved Hide resolved
@atarashansky atarashansky merged commit 0d204de into main Mar 7, 2024
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@atarashansky atarashansky deleted the atar-gene-sets branch March 7, 2024 00:09
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3 participants