Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

feat: clarify why marker genes are unavailable #6225

Merged
merged 16 commits into from
Nov 21, 2023

Conversation

joyceyan
Copy link
Contributor

@joyceyan joyceyan commented Nov 14, 2023

Reason for Change

https://app.zenhub.com/workspaces/single-cell-5e2a191dad828d52cc78b028/issues/gh/chanzuckerberg/single-cell-data-portal/5608

Changes

shows the info icon for all cell types, and implements the copy changes as described in the figma. there are now 3 "empty states" that we show users:

  1. if the tissue type is blood, then we explain that we don't show marker genes for blood since the cell types are closely related
  2. if there are < 25 cells for the cell type, then we explain that we don't show marker genes with such a low cell count
  3. if there are no marker genes, we retain the existing copy we have

Testing steps

blood cells
image

cell types with < 25 cells
image

no marker genes at all
image

i also updated the geneUtils.ts test to verify that the info icon always shows up

Checklist 🛎️

  • Add product, design, and eng as reviewers for rdev review

  • For UI changes, add screenshots/videos, so the reviewers know what you expect them to see

  • For UI changes, add e2e tests to prevent regressions

Notes for Reviewer

Copy link
Contributor

Deployment Summary

@joyceyan joyceyan force-pushed the joyce/marker-genes-unavail branch from 9990f13 to 6f2937d Compare November 15, 2023 17:30
Copy link

codecov bot commented Nov 15, 2023

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (3a1c359) 91.79% compared to head (f74c06c) 91.79%.

Additional details and impacted files
@@           Coverage Diff           @@
##             main    #6225   +/-   ##
=======================================
  Coverage   91.79%   91.79%           
=======================================
  Files         175      175           
  Lines       14207    14207           
=======================================
  Hits        13042    13042           
  Misses       1165     1165           
Flag Coverage Δ
unittests 91.79% <ø> (ø)

Flags with carried forward coverage won't be shown. Click here to find out more.

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

@joyceyan joyceyan force-pushed the joyce/marker-genes-unavail branch 3 times, most recently from 11e1f08 to 78b3b6f Compare November 17, 2023 16:18
@signechambers1
Copy link

LGTM!

@joyceyan joyceyan force-pushed the joyce/marker-genes-unavail branch from 6ef546c to 19ae852 Compare November 17, 2023 18:38
/>
</InfoButtonWrapper>
)}
{cellType && cellType.optionId === COMPARE_OPTION_ID_FOR_AGGREGATED && (
Copy link
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

here, the logic is just updated to always display the info icon button. most of the line changes are just whitespace

@joyceyan joyceyan force-pushed the joyce/marker-genes-unavail branch from 3fda70a to a5292bc Compare November 17, 2023 19:38
@@ -21,7 +21,10 @@ describe("CSV download tests", () => {
}) => {
// set app state
await goToWMG(page, SHARED_LINK_NO_GROUP);
await expect(page.locator("canvas")).not.toHaveCount(0);

// Loading WMG with several genes + filters set takes a bit longer to load. We need the filters
Copy link
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

previously, these tests were taking faster to load because the blood cell types didn't have the info icon on them. since this PR adds them in, these tests appear to timeout more frequently. i tried updating the URL's to only have one gene or only one tissue type, but the tests would still timeout with the 10000ms default.

we do want WMG to load faster, but that's out of scope for this PR, so i think increasing the timeout is fine.

@joyceyan joyceyan requested review from tihuan and kaloster November 21, 2023 15:49
Copy link
Contributor

@kaloster kaloster left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

LGTM!

@joyceyan joyceyan merged commit 7851ae1 into main Nov 21, 2023
@joyceyan joyceyan deleted the joyce/marker-genes-unavail branch November 21, 2023 16:32
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

3 participants