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directly use adjusted pval for threshold #978

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merged 4 commits into from
Feb 13, 2024

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alexvpickering
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@alexvpickering alexvpickering commented Feb 2, 2024

Description

  • Instead of asking user for the desired -log10(adjusted p-value) threshold we just ask them for the adjusted p-value
  • default changed to adjusted p-value of 0.05 instead of 1e^-4 (why??)
  • legend defaults to top right ... because it is always covered in bottom right

staging:

https://ui-alex-ui978.staging.single-cell-platform.net/

Details

URL to issue

hms-dbmi-cellenics/issues#106

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N/A

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Integration test branch

master

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@alexvpickering alexvpickering added the safe to run Sensitive jobs are safe to be run label Feb 2, 2024
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github-actions bot commented Feb 2, 2024

📦 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 569.07 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.

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Ten 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-processing 537.31 KB (🟡 +40 B) 1.08 MB
/experiments/[experimentId]/plots-and-tables/dot-plot 495.22 KB (🟡 +38 B) 1.04 MB
/experiments/[experimentId]/plots-and-tables/embedding-categorical 485.63 KB (🟡 +40 B) 1.03 MB
/experiments/[experimentId]/plots-and-tables/embedding-continuous 515.83 KB (🟡 +39 B) 1.06 MB
/experiments/[experimentId]/plots-and-tables/frequency 487.68 KB (🟡 +39 B) 1.03 MB
/experiments/[experimentId]/plots-and-tables/marker-heatmap 584.88 KB (🟡 +38 B) 1.13 MB
/experiments/[experimentId]/plots-and-tables/normalized-matrix 170.37 KB (🟡 +37 B) 739.43 KB
/experiments/[experimentId]/plots-and-tables/trajectory-analysis 488.69 KB (🟡 +37 B) 1.03 MB
/experiments/[experimentId]/plots-and-tables/violin 517.97 KB (🟡 +38 B) 1.06 MB
/experiments/[experimentId]/plots-and-tables/volcano 490.81 KB (-8 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: Alex Pickering <[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 569.07 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!

Ten 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-processing 537.31 KB (🟡 +40 B) 1.08 MB
/experiments/[experimentId]/plots-and-tables/dot-plot 495.22 KB (🟡 +38 B) 1.04 MB
/experiments/[experimentId]/plots-and-tables/embedding-categorical 485.63 KB (🟡 +40 B) 1.03 MB
/experiments/[experimentId]/plots-and-tables/embedding-continuous 515.83 KB (🟡 +39 B) 1.06 MB
/experiments/[experimentId]/plots-and-tables/frequency 487.68 KB (🟡 +39 B) 1.03 MB
/experiments/[experimentId]/plots-and-tables/marker-heatmap 584.88 KB (🟡 +38 B) 1.13 MB
/experiments/[experimentId]/plots-and-tables/normalized-matrix 170.37 KB (🟡 +37 B) 739.43 KB
/experiments/[experimentId]/plots-and-tables/trajectory-analysis 488.69 KB (🟡 +37 B) 1.03 MB
/experiments/[experimentId]/plots-and-tables/violin 517.97 KB (🟡 +38 B) 1.06 MB
/experiments/[experimentId]/plots-and-tables/volcano 490.81 KB (-8 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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codecov bot commented Feb 2, 2024

Codecov Report

Attention: 1 lines in your changes are missing coverage. Please review.

Comparison is base (7e674c3) 85.18% compared to head (518ee28) 85.20%.

Files Patch % Lines
...s/plots/styling/volcano/ThresholdsGuidesEditor.jsx 0.00% 1 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##           master     #978      +/-   ##
==========================================
+ Coverage   85.18%   85.20%   +0.01%     
==========================================
  Files         548      548              
  Lines       10083    10083              
  Branches     2174     2174              
==========================================
+ Hits         8589     8591       +2     
+ Misses       1434     1432       -2     
  Partials       60       60              

☔ View full report in Codecov by Sentry.
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github-actions bot commented Feb 5, 2024

📦 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 569.07 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!

Ten 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-processing 537.3 KB (🟡 +38 B) 1.08 MB
/experiments/[experimentId]/plots-and-tables/dot-plot 495.22 KB (🟡 +38 B) 1.04 MB
/experiments/[experimentId]/plots-and-tables/embedding-categorical 485.63 KB (🟡 +40 B) 1.03 MB
/experiments/[experimentId]/plots-and-tables/embedding-continuous 515.83 KB (🟡 +39 B) 1.06 MB
/experiments/[experimentId]/plots-and-tables/frequency 487.68 KB (🟡 +39 B) 1.03 MB
/experiments/[experimentId]/plots-and-tables/marker-heatmap 584.88 KB (🟡 +38 B) 1.13 MB
/experiments/[experimentId]/plots-and-tables/normalized-matrix 170.37 KB (🟡 +37 B) 739.43 KB
/experiments/[experimentId]/plots-and-tables/trajectory-analysis 488.7 KB (🟡 +38 B) 1.03 MB
/experiments/[experimentId]/plots-and-tables/violin 517.97 KB (🟡 +38 B) 1.06 MB
/experiments/[experimentId]/plots-and-tables/volcano 490.81 KB (-8 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.

10
** (-1 * config.negLogpValueThreshold)
).toExponential(3);
const { adjPvalueThreshold } = config;
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@ogibson ogibson Feb 13, 2024

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Should this be config.adjPvalueThreshold?

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const { adjPvalueThreshold } = config; is a destructing assignment so it is just syntactic butter for const adjPvalueThreshold = config.adjPvalueThreshold

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Nice! Thanks.

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📦 Next.js Bundle Analysis for ui

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

Ten 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-processing 537.29 KB (🟡 +39 B) 1.08 MB
/experiments/[experimentId]/plots-and-tables/dot-plot 495.22 KB (🟡 +38 B) 1.04 MB
/experiments/[experimentId]/plots-and-tables/embedding-categorical 485.63 KB (🟡 +40 B) 1.03 MB
/experiments/[experimentId]/plots-and-tables/embedding-continuous 515.83 KB (🟡 +39 B) 1.06 MB
/experiments/[experimentId]/plots-and-tables/frequency 487.68 KB (🟡 +39 B) 1.03 MB
/experiments/[experimentId]/plots-and-tables/marker-heatmap 584.88 KB (🟡 +38 B) 1.13 MB
/experiments/[experimentId]/plots-and-tables/normalized-matrix 170.37 KB (🟡 +37 B) 739.51 KB
/experiments/[experimentId]/plots-and-tables/trajectory-analysis 488.7 KB (🟡 +38 B) 1.03 MB
/experiments/[experimentId]/plots-and-tables/violin 517.97 KB (🟡 +38 B) 1.06 MB
/experiments/[experimentId]/plots-and-tables/volcano 490.81 KB (-8 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.

@alexvpickering alexvpickering merged commit 58a2f3f into master Feb 13, 2024
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@alexvpickering alexvpickering deleted the change-volcano-threshold branch February 13, 2024 19:14
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2 participants