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

ENH: group BUSCO stats into collapsible sections for better display #148

Merged
merged 34 commits into from
May 1, 2024

Conversation

misialq
Copy link
Contributor

@misialq misialq commented Mar 14, 2024

This PR addresses the problem of displaying BUSCO results for hundreds and thousands of MAGs. The problem with the previous solution was its reliance on vegafusion transformer which caused some installation issues in our distro. This PR tries to approach the problem differently:

  • split the entire DataFrame with all the results into smaller partitions, each containing max. 100 MAGs
  • display plots per partition
  • place the plots in collapsible Bootstrap accordion to not overwhelm the user with all the plots
  • allow to pick a specific sample from a dropdown and identify the section of the accordion where it sits so that the user doesn't need to uncollapse everything

Closes #140.

Copy link

codecov bot commented Apr 19, 2024

Codecov Report

Attention: Patch coverage is 97.86822% with 11 lines in your changes are missing coverage. Please review.

Project coverage is 97.72%. Comparing base (3b48539) to head (37a7241).
Report is 1 commits behind head on main.

Files Patch % Lines
q2_moshpit/partition/busco.py 36.36% 7 Missing ⚠️
q2_moshpit/busco/tests/test_busco.py 96.55% 2 Missing ⚠️
q2_moshpit/busco/busco.py 98.71% 1 Missing ⚠️
q2_moshpit/busco/types/_format.py 95.00% 1 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main     #148      +/-   ##
==========================================
- Coverage   97.76%   97.72%   -0.04%     
==========================================
  Files          53       64      +11     
  Lines        3126     3390     +264     
==========================================
+ Hits         3056     3313     +257     
- Misses         70       77       +7     

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

@misialq misialq requested a review from Sann5 April 19, 2024 11:15
@misialq misialq marked this pull request as ready for review April 19, 2024 11:15
Co-authored-by: Santiago Castro Dau <[email protected]>
q2_moshpit/busco/utils.py Outdated Show resolved Hide resolved
q2_moshpit/partition/mags.py Outdated Show resolved Hide resolved
q2_moshpit/partition/mags.py Outdated Show resolved Hide resolved
Copy link
Contributor

@Sann5 Sann5 left a comment

Choose a reason for hiding this comment

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

Hey Michal! Crazy amount of work that you put into this one 👨🏼‍💻! I really like how it looks now ✨ . Also I imagine the added information with in the index page (the histograms) can be very valuable to users 📈 .

Most of my review I did in single comments already. This is just the conclusion message.

  • ✅ All test pass in my local machine.
  • ✅ I tried the action on two different inputs and I could not find any issues with the visualizations.

@misialq misialq merged commit 897d7e0 into bokulich-lab:main May 1, 2024
9 checks passed
@misialq misialq deleted the fix-busco branch May 1, 2024 18:43
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.

BUG: evaluate-busco brakes when input mags > ~1,300
2 participants