Reorder genes plots

[jszpila314]

Description

Added a separate tab under gene selection in the marker heatmap plot to allow reordering of genes.

Details

URL to issue

https://biomage.atlassian.net/browse/BIOMAGE-1918
https://ui-jakub-ui742.scp-staging.biomage.net/

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

N/A

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.

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

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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.

[github-actions]

📦 Next.js Bundle Analysis

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⚠️ Global Bundle Size Increased

Page	Size (compressed)
global	521.31 KB (🟡 +28 B)

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Thirteen 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	301.08 KB (🟡 +45 B)	822.38 KB
/experiments/[experimentId]/data-exploration	535.3 KB (🟡 +6 B)	1.03 MB
/experiments/[experimentId]/data-processing	499.88 KB (-3 B)	1021.19 KB
/experiments/[experimentId]/plots-and-tables	14.89 KB (🟡 +1 B)	536.2 KB
/experiments/[experimentId]/plots-and-tables/dot-plot	476.66 KB (🟡 +2 B)	997.96 KB
/experiments/[experimentId]/plots-and-tables/embedding-categorical	473.28 KB (🟡 +2 B)	994.58 KB
/experiments/[experimentId]/plots-and-tables/embedding-continuous	473.97 KB (🟡 +2 B)	995.28 KB
/experiments/[experimentId]/plots-and-tables/frequency	475.07 KB (🟡 +2 B)	996.38 KB
/experiments/[experimentId]/plots-and-tables/heatmap	547.24 KB (🟡 +4 B)	1.04 MB
/experiments/[experimentId]/plots-and-tables/marker-heatmap	572.04 KB (🟡 +22.43 KB)	1.07 MB
/experiments/[experimentId]/plots-and-tables/violin	474.11 KB (🟡 +2 B)	995.42 KB
/experiments/[experimentId]/plots-and-tables/volcano	477.46 KB (🟡 +2 B)	998.76 KB
/settings/profile	25.37 KB (-1 B)	546.68 KB

Details

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[cosa65]

I took a look overall since you mentioned it is a work in progress. It looks good!

One suggestion I would make to get rid of the lag between dropping a gene and the list updating would be having onGeneReorder call

setGeneTreeData(composeGeneTree(newOrder));
debouncedUpdatePlotConfig(newOrder)

with debouncedUpdatePlotConfig being something like this:

const debouncedUpdatePlotConfig = useCallback(
    _.debounce((newOrder) => dispatch(updatePlotConfig(plotUuid, { selectedGenes: newOrder })), time), [],
  );

(time here can be pretty small probably, it's just about it updating a little bit later).

With these 2 changes it should no longer need to wait for redux to finish updating before setting the gene in its new place in the list, so it might look faster (with the plot updating a little bit later).

If you search for _.debounce you should find some places where similar things were done in case you want to check other examples. I think it was done a lot in "Data Processing".

[codecov]

Codecov Report

Merging #742 (d8558a8) into master (d9d93d4) will increase coverage by 0.13%.
The diff coverage is 96.29%.

@@            Coverage Diff             @@
##           master     #742      +/-   ##
==========================================
+ Coverage   82.79%   82.93%   +0.13%     
==========================================
  Files         481      483       +2     
  Lines        8249     8302      +53     
  Branches     1628     1633       +5     
==========================================
+ Hits         6830     6885      +55     
+ Misses       1357     1356       -1     
+ Partials       62       61       -1     

Impacted Files	Coverage Δ
[...imentId]/plots-and-tables/marker-heatmap/index.jsx](https://codecov.io/gh/hms-dbmi-cellenics/ui/pull/742/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=hms-dbmi-cellenics#diff-c3JjL3BhZ2VzL2V4cGVyaW1lbnRzL1tleHBlcmltZW50SWRdL3Bsb3RzLWFuZC10YWJsZXMvbWFya2VyLWhlYXRtYXAvaW5kZXguanN4)	88.32% <50.00%> (+0.08%)	⬆️
src/components/plots/GeneReorderTool.jsx	97.43% <97.43%> (ø)
.../hierarchical-tree-genes/HierarchicalTreeGenes.jsx	100.00% <100.00%> (ø)
src/utils/array-move.js	100.00% <0.00%> (+30.00%)	⬆️

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[cosa65]

If you want to test it one option could be to get the onDrop prop your HierarchicalTreeGenes component passed to Tree and then trigger it yourself.

   const tree = component.find('HierarchicalTreeGenes Tree');
    tree.getElement().props.onDrop(dropInfo);
    component.update();

It would involve using enzyme (which kind of breaks a little bit the idea/philosophy of using rtl, but since rtl doesn't support drag and drop I think it makes sense in this case).

This is just and idea because I read this comment, but it's not necessarily something you need to do.

[ivababukova]

@jszpila314, before implementing a new interface for the genes reorder functionality, did you try to make the existing Select component do the reorder?

I was looking at the Select component examples in Antd: https://ant.design/components/select/, this specific type:

I also saw this Stackoverflow post that shows how to make each of the boxes draggable: https://stackoverflow.com/questions/49498684/cannot-get-antd-select-tags-to-be-draggable Have you tried this? Before implementing a new design, it is better to check if we can adjust the existing one to do what we want.

[ivababukova]

My suggestion in my previous comment should work. I did a couple of small trials here: https://codesandbox.io/s/eager-archimedes-6uj4fk?file=/index.js What you need to do is to make each entry in config.selectedGenes in the MarkerGeneSelection component have a label with draggable: true in it. Basically, this thing for each gene entry in selectedGenes:

label: (
            <div
              onMouseDown={e => {
                e.stopPropagation();
              }}
            >
              <div
                draggable="true"
                onDragStart={() => {
                  message.info("Drag should work");
                }}
              >
                  <p>MY_GENE</p>
              </div>
            </div>
          )

You can create a new state variable transformedSelectedGenes that has this structure:

  const [transformedSelectedGenes, setTransformedSelectedGenes] = useState([]);

and have a function that populates the entries in this new variable and call it:

const populateEntries = () => {
  const newGenes = []
  
  config.selectedGenes.forEach((geneName) => {
    newGenes.append(
      {
              key: geneName,
              label: (
                <div
                  onMouseDown={e => {
                    e.stopPropagation();
                  }}
                >
                  <div
                    draggable="true"
                    onDragStart={() => {
                      message.info("Drag should work");
                    }}
                  >
                      <p>geneName</p>
                  </div>
                </div>
              )
     })
  })
}

setTransformedSelectedGenes(newGenes);
}

Then you pass transformedSelectedGenes to be the value of Space in MarkerGeneSelection:

value={transformedSelectedGenes}

And you should get the same UI, but draggable and reorderable. Afterwards, you will need to take a look and see if the backend takes this order into an account and if not, fix it.

This is just a pseudo-code, it won't compile if you paste it, but I hope that it helps with getting the idea of what I mean. I think that it is worth a try, it should work. There is no point implementing a brand new separate interface just for ordering genes if we can make the existing interface reorder them.