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show user-specified samples in genomic evolution chart #5089

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@svihang8 svihang8 commented Jan 23, 2025

Fix cBioPortal/cbioportal#10763
Describe changes proposed in this pull request:

  • Enhanced VAFChartControls by adding a feature to select specific samples (Some, All, or None)

Checks

  • Has tests or has a separate issue that describes the types of test that should be created. If no test is included it should explicitly be mentioned in the PR why there is no test.
  • The commit log is comprehensible. It follows 7 rules of great commit messages. For most PRs a single commit should suffice, in some cases multiple topical commits can be useful. During review it is ok to see tiny commits (e.g. Fix reviewer comments), but right before the code gets merged to master or rc branch, any such commits should be squashed since they are useless to the other developers. Definitely avoid merge commits, use rebase instead.
  • Is this PR adding logic based on one or more clinical attributes? If yes, please make sure validation for this attribute is also present in the data validation / data loading layers (in backend repo) and documented in File-Formats Clinical data section!

Any screenshots or GIFs?

This is a visual feature so before/after screenshots have been added to highlight the impact of the feature.
Before Screenshot:-
Screenshot 2025-01-22 at 10 19 12 PM

Screenshot showing how 'All' works:-
Screenshot 2025-01-22 at 10 19 38 PM

Screenshot showing how 'None' works:-
Screenshot 2025-01-22 at 10 19 55 PM

Screenshot showing how selecting specific samples works:-
Screenshot 2025-01-22 at 10 20 35 PM

Screenshot showing compatibility with the groupBy functionality:-
Screenshot 2025-01-22 at 10 20 57 PM

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@svihang8 svihang8 marked this pull request as ready for review January 23, 2025 03:21
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@inodb
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inodb commented Jan 23, 2025

Thanks so much @svihang8 ! Looks great!

I think the "All" and "None" state are implied by the checkboxes, so maybe better to not have those separate?

image

Wondering also if there's another component on the cBioPortal website that could be used for this purpose. The selection box gets kinda big when you select a lot of samples (note that there are some patients with dozens of samples):

image

Maybe it's cleaner to use a component similar to the one on the mutations tab? See:

image

@inodb inodb changed the title Selection sample enhancement show only specific samples in genomic evolution chart Jan 24, 2025
@inodb inodb changed the title show only specific samples in genomic evolution chart show user-specified samples in genomic evolution chart Jan 24, 2025
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show only specific samples in genomic evolution chart
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