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microbiome / mia

Microbiome analysis
https://microbiome.github.io/mia/
Artistic License 2.0
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Use agglomerateByVariable when onRankOnly = FALSE #570

Closed Daenarys8 closed 3 weeks ago

Daenarys8 commented 4 weeks ago

562 change behavior of agglomerateByRank when onRankOnly is FALSE

TuomasBorman commented 4 weeks ago

You should add to parameter description that this parameter is deprecated. Moreover, what happens when we remove this parameter in the future --> it does not work anymore since the functionality is left in the code. This just blocks that it is not used anymore. The same variable is still there in the code.

I think you should

  1. Remove onRankOnly completely from this file without deprecation.
  2. In .get_tax_groups function, allow hidden parameter flow by adding ...
  3. Add input check to .get_tax_groups
  4. Pass parameters from agglomerateByRank to .get_tax_groups with ...

With that we can hide the functionality and prevent users to use it. Those that know that the option is available can still use it if necessary.

TuomasBorman commented 4 weeks ago

This means also that no deprecation messages