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Use Maaslin only and report method in plot #543

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merged 5 commits into from
Oct 10, 2023

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@asizemore asizemore commented Oct 9, 2023

Resolves #541

Discussed in the mbio meeting, @dpbisme raised concerns about the method selection becoming too complicated for users. Instead he suggested choosing the method based on the data, so that the user doesn't have to choose.
UPDATE: New decision is to only use the 'Maaslin' method for this first roll out. Code has been updated so as to only use Maaslin as the differential abundance method.

This PR

  1. Removes the Method input selector
  2. Sets the differentialAbundanceMethod to always be Maaslin
  3. Reports the method used in the volcano plot subtitle.

@asizemore asizemore changed the title Auto-select diff abund method based on data Use Maaslin only and report method in plot Oct 10, 2023
@asizemore asizemore marked this pull request as ready for review October 10, 2023 11:03
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LGTM!

@asizemore asizemore merged commit f5d1c47 into main Oct 10, 2023
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@asizemore asizemore deleted the fix-541-remove-diff-abund-method branch October 10, 2023 17:12
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volcano: remove Method and instead report method used in plot
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