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IMP: replace volatility with lineplot for evaluate_* visualizers #204

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merged 5 commits into from
Oct 10, 2024

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lizgehret
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@lizgehret lizgehret commented Oct 1, 2024

Closes qiime2/q2-vizard#32

This PR will replace the use of longitudinal volatility with the new lineplot that's now available within q2-vizard. The following visualizers will receive this replacement:

  • evaluate-classifications
  • evaluate-taxonomy

@lizgehret lizgehret self-assigned this Oct 1, 2024
@lizgehret lizgehret marked this pull request as draft October 1, 2024 23:44
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lizgehret commented Oct 2, 2024

This is now currently hooked up and working for evaluate-taxonomy (preview can be seen here), but lineplot requires an update before this will be working as it currently does with the volatility viz. I'm going to update that viz with a new spec that will allow for y dropdowns (still with a fixed x).

Note regarding CI failures: RESCRIPt can't currently be built because it doesn't know what vizard is. I'll address this once the functionality is working (as vizard just needs to be added to the amplicon distro in order to resolve this).

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Changes in lineplot have been implemented (merged PR here), and this is all working as expected!

I tested this using the data provided in the RESCRIPt tutorial, and the results look essentially identical (just with slightly different visual scaling).

@lizgehret lizgehret marked this pull request as ready for review October 2, 2024 22:15
@lizgehret lizgehret requested a review from nbokulich October 2, 2024 22:15
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@nbokulich would you mind reviewing this when you get the chance? 🙂

Actual code changes are very minimal, so mainly just user testing to make sure the updated visualizations look as you'd expect.

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Test failure has been addressed - now that the output of evaluate-classifications no longer includes the table that's used as input for lineplot, I've separated the functionality that generates that table into a helper method so that can still be utilized in the unit test that checks the actual stats.

@lizgehret lizgehret assigned ebolyen and unassigned lizgehret Oct 3, 2024
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LGTM, nice way to refactor this so that we are still testing the validation.

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ebolyen commented Oct 3, 2024

@nbokulich do you want to take a glance at this before I merge?

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Hey @nbokulich sorry to keep bugging you! Most of us will be at a conference all of next week, so I'm hoping to get all PRs merged by EOW in preparation for the release. Could you let me know if you have any thoughts/feedback before then?

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thanks for the reminder @lizgehret , got tied up with teaching stuff last week.

I tested with a few different databases to do a side-by-side comparison with the new viz. Looks great!

@lizgehret lizgehret merged commit 16d8226 into master Oct 10, 2024
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@lizgehret lizgehret deleted the add-lineplot branch October 10, 2024 15:36
@lizgehret lizgehret self-assigned this Oct 22, 2024
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IMP: add lineplot into rescript
3 participants