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Display metadata key on x axis instead of hardcoded string in frequency plot #892

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ivababukova
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@ivababukova ivababukova commented Sep 14, 2023

Description

See issue: hms-dbmi-cellenics/issues#51

Staging: https://ui-ivababukova-ui53.scp-staging.biomage.net/

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…cy plot

Signed-off-by: ivababukova <iva@biomage.net>
@ivababukova ivababukova added the safe to run Sensitive jobs are safe to be run label Sep 14, 2023
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Codecov Report

Attention: 2 lines in your changes are missing coverage. Please review.

Comparison is base (169b2e1) 85.58% compared to head (31c5a0e) 85.59%.

Files Patch % Lines
...ponents/plots/styling/frequency/SelectCellSets.jsx 77.77% 2 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##           master     #892      +/-   ##
==========================================
+ Coverage   85.58%   85.59%   +0.01%     
==========================================
  Files         558      558              
  Lines       10288    10284       -4     
  Branches     2231     2230       -1     
==========================================
- Hits         8805     8803       -2     
+ Misses       1427     1425       -2     
  Partials       56       56              

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@@ -156,7 +156,7 @@ const generateSpec = (config, plotData, xNamesToDisplay, yNamesToDisplay) => {
orient: 'bottom',
scale: 'x',
zindex: 1,
title: config.axes.xAxisText,
title: config.xAxisGrouping,
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Why this rename? how was xAxisGrouping different from xAxisText before or were they the same?

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@ivababukova ivababukova Sep 15, 2023

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this rename causes us to use the value of xAxisGrouping, which points to the name of the hierarchy (which is the goal of this issue). axes.xAxisText was a hardcoded value in the initial state.

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I think xAxisGrouping is using the key (not the name) of the hierarchy we want, which can be not legible by a user. (in some cases it could even a uuid), so I think we should go back to using xAxisText and fix it so that it updates when the xAxisGrouping changes too

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Good point @cosa65 I brought xAxisText back and I am setting it to the label of the selected option. What do you think?

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/experiments/[experimentId]/plots-and-tables/frequency 516.82 KB (🟡 +1 B) 1.09 MB
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/experiments/[experimentId]/plots-and-tables/frequency 482.06 KB (🟡 +1 B) 1.04 MB
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/experiments/[experimentId]/plots-and-tables/frequency 482.06 KB (🟡 +1 B) 1.04 MB
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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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/experiments/[experimentId]/plots-and-tables/frequency 482.06 KB (🟡 +1 B) 1.04 MB
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/experiments/[experimentId]/plots-and-tables/frequency 482.06 KB (🟡 +1 B) 1.04 MB
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Signed-off-by: ivababukova <iva@biomage.net>
Comment on lines +48 to +52
let metadataToGroupByDisabled = false;
let tooltipText;
if (!metadataGroupByOptions || metadataGroupByOptions.length === 1) {
metadataToGroupByDisabled = true;
tooltipText = 'The x-axis cannot be changed as this dataset has only a single sample.';
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I found out that this code has a bug -- the tooltip with the message was never displayed, even in cases when we have only 1 sample. So I fixed it.

ivababukova added 2 commits November 15, 2023 16:30
Signed-off-by: ivababukova <iva@biomage.net>
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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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/experiments/[experimentId]/data-exploration 515.95 KB (🟢 -475 B) 1.07 MB
/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/frequency 482.1 KB (🟡 +41 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
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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

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/experiments/[experimentId]/plots-and-tables/frequency 482.1 KB (🟡 +41 B) 1.04 MB
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@ivababukova ivababukova reopened this Nov 16, 2023
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/experiments/[experimentId]/plots-and-tables/frequency 482.1 KB (🟡 +41 B) 1.04 MB
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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.

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Can you add a test which checks if the axis titles change?

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/experiments/[experimentId]/plots-and-tables/frequency 482.1 KB (🟡 +41 B) 1.04 MB
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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.

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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.

ivababukova added 2 commits November 16, 2023 13:39
Signed-off-by: ivababukova <iva@biomage.net>
Signed-off-by: ivababukova <iva@biomage.net>
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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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Page Size (compressed) First Load
/data-management 238.98 KB (🟢 -281 B) 818.84 KB
/experiments/[experimentId]/data-exploration 519.92 KB (🟡 +3.47 KB) 1.07 MB
/experiments/[experimentId]/data-processing 538.77 KB (🟡 +5.61 KB) 1.09 MB
/experiments/[experimentId]/plots-and-tables 15.63 KB (🟢 -74 B) 595.49 KB
/experiments/[experimentId]/plots-and-tables/batch-differential-expression 74.5 KB (🟢 -12 B) 654.36 KB
/experiments/[experimentId]/plots-and-tables/dot-plot 495.29 KB (🟡 +5.75 KB) 1.05 MB
/experiments/[experimentId]/plots-and-tables/embedding-categorical 486.02 KB (🟡 +5.83 KB) 1.04 MB
/experiments/[experimentId]/plots-and-tables/embedding-continuous 487.71 KB (🟡 +5.82 KB) 1.04 MB
/experiments/[experimentId]/plots-and-tables/frequency 487.93 KB (🟡 +5.87 KB) 1.04 MB
/experiments/[experimentId]/plots-and-tables/marker-heatmap 584.9 KB (🟡 +3.39 KB) 1.14 MB
/experiments/[experimentId]/plots-and-tables/normalized-matrix 170.65 KB (🟢 -92 B) 750.51 KB
/experiments/[experimentId]/plots-and-tables/trajectory-analysis 489.49 KB (🟡 +5.82 KB) 1.04 MB
/experiments/[experimentId]/plots-and-tables/violin 517.37 KB (🟡 +5.75 KB) 1.07 MB
/experiments/[experimentId]/plots-and-tables/volcano 491.14 KB (🟡 +5.83 KB) 1.05 MB
/repository 108.63 KB (🟢 -159 B) 688.5 KB
/settings/profile 25.5 KB (🟢 -138 B) 605.37 KB
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.

ivababukova and others added 2 commits November 16, 2023 16:15
Signed-off-by: ivababukova <iva@biomage.net>
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🎉 Global Bundle Size Decreased

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global 579.86 KB (🟢 -490 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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Sixteen 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 238.95 KB (🟢 -283 B) 818.81 KB
/experiments/[experimentId]/data-exploration 519.92 KB (🟡 +3.47 KB) 1.07 MB
/experiments/[experimentId]/data-processing 538.77 KB (🟡 +5.61 KB) 1.09 MB
/experiments/[experimentId]/plots-and-tables 15.63 KB (🟢 -74 B) 595.49 KB
/experiments/[experimentId]/plots-and-tables/batch-differential-expression 74.5 KB (🟢 -12 B) 654.36 KB
/experiments/[experimentId]/plots-and-tables/dot-plot 495.29 KB (🟡 +5.75 KB) 1.05 MB
/experiments/[experimentId]/plots-and-tables/embedding-categorical 486.02 KB (🟡 +5.83 KB) 1.04 MB
/experiments/[experimentId]/plots-and-tables/embedding-continuous 487.71 KB (🟡 +5.82 KB) 1.04 MB
/experiments/[experimentId]/plots-and-tables/frequency 487.93 KB (🟡 +5.87 KB) 1.04 MB
/experiments/[experimentId]/plots-and-tables/marker-heatmap 584.9 KB (🟡 +3.39 KB) 1.14 MB
/experiments/[experimentId]/plots-and-tables/normalized-matrix 170.65 KB (🟢 -92 B) 750.51 KB
/experiments/[experimentId]/plots-and-tables/trajectory-analysis 489.49 KB (🟡 +5.82 KB) 1.04 MB
/experiments/[experimentId]/plots-and-tables/violin 517.37 KB (🟡 +5.75 KB) 1.07 MB
/experiments/[experimentId]/plots-and-tables/volcano 491.14 KB (🟡 +5.83 KB) 1.05 MB
/repository 108.63 KB (🟢 -159 B) 688.5 KB
/settings/profile 25.5 KB (🟢 -138 B) 605.37 KB
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.

@ivababukova ivababukova merged commit 649bd8a into hms-dbmi-cellenics:master Nov 16, 2023
14 checks passed
@cosa65 cosa65 deleted the ivababukova/issues-51 branch November 17, 2023 12:13
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