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Add cell level to differential expression #940

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cosa65
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@cosa65 cosa65 commented Nov 15, 2023

Description

Details

URL to issue

https://github.com/orgs/hms-dbmi-cellenics/projects/4/views/1?pane=issue&itemId=37286584

Link to staging deployment URL (or set N/A)

N/A
https://ui-martinfosco-ui52.scp-staging.biomage.net/

Links to any PRs or resources related to this PR

biomage-org#52

Integration test branch

master

Merge checklist

Your changes will be ready for merging after all of the steps below have been completed.

Code updates

Have best practices and ongoing refactors being observed in this PR

  • Migrated any selector / reducer used to the new format.
  • All new dependency licenses have been checked for compatibility.

Manual/unit testing

  • Tested changes using InfraMock locally or no tests required for change, e.g. Kubernetes chart updates.
  • Validated that current unit tests for code work as expected and are sufficient for code coverage or no unit tests required for change, e.g. documentation update.
  • Unit tests written or no unit tests required for change, e.g. documentation update.

Integration testing

You must check the box below to run integration tests on the latest commit on your PR branch.
Integration tests have to pass before the PR can be merged. Without checking the box, your PR
will not pass the required status checks for merging.

  • Started end-to-end tests on the latest commit.

Documentation updates

  • Relevant Github READMEs updated or no GitHub README updates required.
  • Relevant Wiki pages created/updated or no Wiki updates required.

Optional

  • Staging environment is unstaged before merging.
  • Photo of a cute animal attached to this PR.

…s instead of a single one and add CLM and CLMPerSample to them

Signed-off-by: cosa65 <[email protected]>
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📦 Next.js Bundle Analysis for ui

This analysis was generated by the Next.js Bundle Analysis action. 🤖

🎉 Global Bundle Size Decreased

Page Size (compressed)
global 579.8 KB (🟢 -553 B)
Details

The global bundle is the javascript bundle that loads alongside every page. It is in its own category because its impact is much higher - an increase to its size means that every page on your website loads slower, and a decrease means every page loads faster.

Any third party scripts you have added directly to your app using the <script> tag are not accounted for in this analysis

If you want further insight into what is behind the changes, give @next/bundle-analyzer a try!

Eight Pages Changed Size

The following pages changed size from the code in this PR compared to its base branch:

Page Size (compressed) First Load
/data-management 239.25 KB (-1 B) 819.05 KB
/experiments/[experimentId]/data-exploration 516 KB (🟢 -424 B) 1.07 MB
/experiments/[experimentId]/plots-and-tables/batch-differential-expression 74.53 KB (🟡 +65 B) 654.33 KB
/experiments/[experimentId]/plots-and-tables/dot-plot 489.18 KB (🟢 -359 B) 1.04 MB
/experiments/[experimentId]/plots-and-tables/embedding-continuous 481.58 KB (🟢 -325 B) 1.04 MB
/experiments/[experimentId]/plots-and-tables/marker-heatmap 581.41 KB (🟢 -106 B) 1.13 MB
/experiments/[experimentId]/plots-and-tables/violin 511.3 KB (🟢 -323 B) 1.07 MB
/experiments/[experimentId]/plots-and-tables/volcano 485.32 KB (🟡 +51 B) 1.04 MB
Details

Only the gzipped size is provided here based on an expert tip.

First Load is the size of the global bundle plus the bundle for the individual page. If a user were to show up to your website and land on a given page, the first load size represents the amount of javascript that user would need to download. If next/link is used, subsequent page loads would only need to download that page's bundle (the number in the "Size" column), since the global bundle has already been downloaded.

Any third party scripts you have added directly to your app using the <script> tag are not accounted for in this analysis

Next to the size is how much the size has increased or decreased compared with the base branch of this PR. If this percentage has increased by 20% or more, there will be a red status indicator applied, indicating that special attention should be given to this.

@cosa65 cosa65 added the safe to run Sensitive jobs are safe to be run label Nov 15, 2023
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codecov bot commented Nov 15, 2023

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (0926f29) 85.61% compared to head (621e690) 85.62%.
Report is 1 commits behind head on master.

Additional details and impacted files
@@           Coverage Diff           @@
##           master     #940   +/-   ##
=======================================
  Coverage   85.61%   85.62%           
=======================================
  Files         558      558           
  Lines       10284    10290    +6     
  Branches     2230     2230           
=======================================
+ Hits         8805     8811    +6     
  Misses       1423     1423           
  Partials       56       56           

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

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📦 Next.js Bundle Analysis for ui

This analysis was generated by the Next.js Bundle Analysis action. 🤖

⚠️ Global Bundle Size Increased

Page Size (compressed)
global 580.35 KB (🟡 +5 B)
Details

The global bundle is the javascript bundle that loads alongside every page. It is in its own category because its impact is much higher - an increase to its size means that every page on your website loads slower, and a decrease means every page loads faster.

Any third party scripts you have added directly to your app using the <script> tag are not accounted for in this analysis

If you want further insight into what is behind the changes, give @next/bundle-analyzer a try!

Four Pages Changed Size

The following pages changed size from the code in this PR compared to its base branch:

Page Size (compressed) First Load
/data-management 239.25 KB (-1 B) 819.6 KB
/experiments/[experimentId]/data-exploration 516.46 KB (🟡 +51 B) 1.07 MB
/experiments/[experimentId]/plots-and-tables/batch-differential-expression 74.53 KB (🟡 +65 B) 654.88 KB
/experiments/[experimentId]/plots-and-tables/volcano 485.32 KB (🟡 +51 B) 1.04 MB
Details

Only the gzipped size is provided here based on an expert tip.

First Load is the size of the global bundle plus the bundle for the individual page. If a user were to show up to your website and land on a given page, the first load size represents the amount of javascript that user would need to download. If next/link is used, subsequent page loads would only need to download that page's bundle (the number in the "Size" column), since the global bundle has already been downloaded.

Any third party scripts you have added directly to your app using the <script> tag are not accounted for in this analysis

Next to the size is how much the size has increased or decreased compared with the base branch of this PR. If this percentage has increased by 20% or more, there will be a red status indicator applied, indicating that special attention should be given to this.

Signed-off-by: cosa65 <[email protected]>
@cosa65 cosa65 force-pushed the add-cell-level-to-differential-expression branch from 72e84be to 45c3617 Compare November 15, 2023 13:06
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📦 Next.js Bundle Analysis for ui

This analysis was generated by the Next.js Bundle Analysis action. 🤖

⚠️ Global Bundle Size Increased

Page Size (compressed)
global 580.35 KB (🟡 +5 B)
Details

The global bundle is the javascript bundle that loads alongside every page. It is in its own category because its impact is much higher - an increase to its size means that every page on your website loads slower, and a decrease means every page loads faster.

Any third party scripts you have added directly to your app using the <script> tag are not accounted for in this analysis

If you want further insight into what is behind the changes, give @next/bundle-analyzer a try!

Four Pages Changed Size

The following pages changed size from the code in this PR compared to its base branch:

Page Size (compressed) First Load
/data-management 239.25 KB (-1 B) 819.6 KB
/experiments/[experimentId]/data-exploration 516.44 KB (🟡 +26 B) 1.07 MB
/experiments/[experimentId]/plots-and-tables/batch-differential-expression 74.51 KB (🟡 +40 B) 654.86 KB
/experiments/[experimentId]/plots-and-tables/volcano 485.29 KB (🟡 +26 B) 1.04 MB
Details

Only the gzipped size is provided here based on an expert tip.

First Load is the size of the global bundle plus the bundle for the individual page. If a user were to show up to your website and land on a given page, the first load size represents the amount of javascript that user would need to download. If next/link is used, subsequent page loads would only need to download that page's bundle (the number in the "Size" column), since the global bundle has already been downloaded.

Any third party scripts you have added directly to your app using the <script> tag are not accounted for in this analysis

Next to the size is how much the size has increased or decreased compared with the base branch of this PR. If this percentage has increased by 20% or more, there will be a red status indicator applied, indicating that special attention should be given to this.

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📦 Next.js Bundle Analysis for ui

This analysis was generated by the Next.js Bundle Analysis action. 🤖

⚠️ Global Bundle Size Increased

Page Size (compressed)
global 580.35 KB (🟡 +5 B)
Details

The global bundle is the javascript bundle that loads alongside every page. It is in its own category because its impact is much higher - an increase to its size means that every page on your website loads slower, and a decrease means every page loads faster.

Any third party scripts you have added directly to your app using the <script> tag are not accounted for in this analysis

If you want further insight into what is behind the changes, give @next/bundle-analyzer a try!

Four Pages Changed Size

The following pages changed size from the code in this PR compared to its base branch:

Page Size (compressed) First Load
/data-management 239.25 KB (-1 B) 819.6 KB
/experiments/[experimentId]/data-exploration 516.47 KB (🟡 +23 B) 1.07 MB
/experiments/[experimentId]/plots-and-tables/batch-differential-expression 74.61 KB (🟡 +99 B) 654.96 KB
/experiments/[experimentId]/plots-and-tables/volcano 485.33 KB (🟡 +23 B) 1.04 MB
Details

Only the gzipped size is provided here based on an expert tip.

First Load is the size of the global bundle plus the bundle for the individual page. If a user were to show up to your website and land on a given page, the first load size represents the amount of javascript that user would need to download. If next/link is used, subsequent page loads would only need to download that page's bundle (the number in the "Size" column), since the global bundle has already been downloaded.

Any third party scripts you have added directly to your app using the <script> tag are not accounted for in this analysis

Next to the size is how much the size has increased or decreased compared with the base branch of this PR. If this percentage has increased by 20% or more, there will be a red status indicator applied, indicating that special attention should be given to this.

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📦 Next.js Bundle Analysis for ui

This analysis was generated by the Next.js Bundle Analysis action. 🤖

⚠️ Global Bundle Size Increased

Page Size (compressed)
global 580.35 KB (🟡 +5 B)
Details

The global bundle is the javascript bundle that loads alongside every page. It is in its own category because its impact is much higher - an increase to its size means that every page on your website loads slower, and a decrease means every page loads faster.

Any third party scripts you have added directly to your app using the <script> tag are not accounted for in this analysis

If you want further insight into what is behind the changes, give @next/bundle-analyzer a try!

Four Pages Changed Size

The following pages changed size from the code in this PR compared to its base branch:

Page Size (compressed) First Load
/data-management 239.25 KB (-1 B) 819.6 KB
/experiments/[experimentId]/data-exploration 516.47 KB (🟡 +23 B) 1.07 MB
/experiments/[experimentId]/plots-and-tables/batch-differential-expression 74.61 KB (🟡 +99 B) 654.96 KB
/experiments/[experimentId]/plots-and-tables/volcano 485.33 KB (🟡 +23 B) 1.04 MB
Details

Only the gzipped size is provided here based on an expert tip.

First Load is the size of the global bundle plus the bundle for the individual page. If a user were to show up to your website and land on a given page, the first load size represents the amount of javascript that user would need to download. If next/link is used, subsequent page loads would only need to download that page's bundle (the number in the "Size" column), since the global bundle has already been downloaded.

Any third party scripts you have added directly to your app using the <script> tag are not accounted for in this analysis

Next to the size is how much the size has increased or decreased compared with the base branch of this PR. If this percentage has increased by 20% or more, there will be a red status indicator applied, indicating that special attention should be given to this.

Signed-off-by: cosa65 <[email protected]>
Signed-off-by: cosa65 <[email protected]>
@cosa65 cosa65 marked this pull request as ready for review November 16, 2023 14:32
@cosa65 cosa65 changed the title [DRAFT] Add cell level to differential expression Add cell level to differential expression Nov 16, 2023
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📦 Next.js Bundle Analysis for ui

This analysis was generated by the Next.js Bundle Analysis action. 🤖

⚠️ Global Bundle Size Increased

Page Size (compressed)
global 580.35 KB (🟡 +5 B)
Details

The global bundle is the javascript bundle that loads alongside every page. It is in its own category because its impact is much higher - an increase to its size means that every page on your website loads slower, and a decrease means every page loads faster.

Any third party scripts you have added directly to your app using the <script> tag are not accounted for in this analysis

If you want further insight into what is behind the changes, give @next/bundle-analyzer a try!

Three Pages Changed Size

The following pages changed size from the code in this PR compared to its base branch:

Page Size (compressed) First Load
/experiments/[experimentId]/data-exploration 516.47 KB (🟡 +23 B) 1.07 MB
/experiments/[experimentId]/plots-and-tables/batch-differential-expression 74.61 KB (🟡 +99 B) 654.96 KB
/experiments/[experimentId]/plots-and-tables/volcano 485.33 KB (🟡 +23 B) 1.04 MB
Details

Only the gzipped size is provided here based on an expert tip.

First Load is the size of the global bundle plus the bundle for the individual page. If a user were to show up to your website and land on a given page, the first load size represents the amount of javascript that user would need to download. If next/link is used, subsequent page loads would only need to download that page's bundle (the number in the "Size" column), since the global bundle has already been downloaded.

Any third party scripts you have added directly to your app using the <script> tag are not accounted for in this analysis

Next to the size is how much the size has increased or decreased compared with the base branch of this PR. If this percentage has increased by 20% or more, there will be a red status indicator applied, indicating that special attention should be given to this.

Signed-off-by: cosa65 <[email protected]>
Copy link
Contributor

📦 Next.js Bundle Analysis for ui

This analysis was generated by the Next.js Bundle Analysis action. 🤖

⚠️ Global Bundle Size Increased

Page Size (compressed)
global 580.35 KB (🟡 +5 B)
Details

The global bundle is the javascript bundle that loads alongside every page. It is in its own category because its impact is much higher - an increase to its size means that every page on your website loads slower, and a decrease means every page loads faster.

Any third party scripts you have added directly to your app using the <script> tag are not accounted for in this analysis

If you want further insight into what is behind the changes, give @next/bundle-analyzer a try!

Three Pages Changed Size

The following pages changed size from the code in this PR compared to its base branch:

Page Size (compressed) First Load
/experiments/[experimentId]/data-exploration 516.47 KB (🟡 +23 B) 1.07 MB
/experiments/[experimentId]/plots-and-tables/batch-differential-expression 74.61 KB (🟡 +99 B) 654.96 KB
/experiments/[experimentId]/plots-and-tables/volcano 485.33 KB (🟡 +23 B) 1.04 MB
Details

Only the gzipped size is provided here based on an expert tip.

First Load is the size of the global bundle plus the bundle for the individual page. If a user were to show up to your website and land on a given page, the first load size represents the amount of javascript that user would need to download. If next/link is used, subsequent page loads would only need to download that page's bundle (the number in the "Size" column), since the global bundle has already been downloaded.

Any third party scripts you have added directly to your app using the <script> tag are not accounted for in this analysis

Next to the size is how much the size has increased or decreased compared with the base branch of this PR. If this percentage has increased by 20% or more, there will be a red status indicator applied, indicating that special attention should be given to this.

if (!data) {
return;
}
return data.filter(
(root) => (!type || properties[root.key].type === type),
(root) => (!types || types.includes(properties[root.key].type)),
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@StefanBabukov StefanBabukov Nov 17, 2023

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will this be false or '[]'? maybe you should check for !types.length?

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I didn't understnad, which part are you asking about?

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📦 Next.js Bundle Analysis for ui

This analysis was generated by the Next.js Bundle Analysis action. 🤖

⚠️ Global Bundle Size Increased

Page Size (compressed)
global 579.87 KB (🟡 +4 B)
Details

The global bundle is the javascript bundle that loads alongside every page. It is in its own category because its impact is much higher - an increase to its size means that every page on your website loads slower, and a decrease means every page loads faster.

Any third party scripts you have added directly to your app using the <script> tag are not accounted for in this analysis

If you want further insight into what is behind the changes, give @next/bundle-analyzer a try!

Three Pages Changed Size

The following pages changed size from the code in this PR compared to its base branch:

Page Size (compressed) First Load
/experiments/[experimentId]/data-exploration 519.94 KB (🟡 +23 B) 1.07 MB
/experiments/[experimentId]/plots-and-tables/batch-differential-expression 74.6 KB (🟡 +99 B) 654.46 KB
/experiments/[experimentId]/plots-and-tables/volcano 491.16 KB (🟡 +23 B) 1.05 MB
Details

Only the gzipped size is provided here based on an expert tip.

First Load is the size of the global bundle plus the bundle for the individual page. If a user were to show up to your website and land on a given page, the first load size represents the amount of javascript that user would need to download. If next/link is used, subsequent page loads would only need to download that page's bundle (the number in the "Size" column), since the global bundle has already been downloaded.

Any third party scripts you have added directly to your app using the <script> tag are not accounted for in this analysis

Next to the size is how much the size has increased or decreased compared with the base branch of this PR. If this percentage has increased by 20% or more, there will be a red status indicator applied, indicating that special attention should be given to this.

Copy link
Contributor

📦 Next.js Bundle Analysis for ui

This analysis was generated by the Next.js Bundle Analysis action. 🤖

⚠️ Global Bundle Size Increased

Page Size (compressed)
global 579.87 KB (🟡 +4 B)
Details

The global bundle is the javascript bundle that loads alongside every page. It is in its own category because its impact is much higher - an increase to its size means that every page on your website loads slower, and a decrease means every page loads faster.

Any third party scripts you have added directly to your app using the <script> tag are not accounted for in this analysis

If you want further insight into what is behind the changes, give @next/bundle-analyzer a try!

Three Pages Changed Size

The following pages changed size from the code in this PR compared to its base branch:

Page Size (compressed) First Load
/experiments/[experimentId]/data-exploration 519.94 KB (🟡 +23 B) 1.07 MB
/experiments/[experimentId]/plots-and-tables/batch-differential-expression 74.6 KB (🟡 +99 B) 654.46 KB
/experiments/[experimentId]/plots-and-tables/volcano 491.16 KB (🟡 +23 B) 1.05 MB
Details

Only the gzipped size is provided here based on an expert tip.

First Load is the size of the global bundle plus the bundle for the individual page. If a user were to show up to your website and land on a given page, the first load size represents the amount of javascript that user would need to download. If next/link is used, subsequent page loads would only need to download that page's bundle (the number in the "Size" column), since the global bundle has already been downloaded.

Any third party scripts you have added directly to your app using the <script> tag are not accounted for in this analysis

Next to the size is how much the size has increased or decreased compared with the base branch of this PR. If this percentage has increased by 20% or more, there will be a red status indicator applied, indicating that special attention should be given to this.

@cosa65 cosa65 merged commit f317670 into hms-dbmi-cellenics:master Nov 21, 2023
14 checks passed
@cosa65 cosa65 deleted the add-cell-level-to-differential-expression branch November 21, 2023 11:54
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