Introduce plotForest

[RiboRings]

Hi!

The plotForest viz is ready to be shared! (check vignettes for usage)

It features methods for both (Tree)SE and dataframes containing statistical results. All relevant variables (effects, CI upper and lower boundaries, pvals, id cols) are encoded by arguments for convenience and flexibility.

plotForest can be applied to both rowData and colData, with the option to add tree hierarchy and labels on the side, and also comparing between two groups (paired forest plot).

While minor aesthetic add-ons could be considered for future PRs, I think the main functionality is already there and is quite broad.

Happy to hear your comments,
Giulio

[antagomir]

Awesome! Just some suggestions.

[RiboRings]

Now the vignettes use DAA results from Maaslin3.

While testing, I also added plotForest visualisation to the differential abundance chapter of OMA, for all the different methods. I could open a PR there.

[TuomasBorman]

Some comments. Looks good!

[codecov]

Codecov Report

❌ Patch coverage is 79.68750% with 39 lines in your changes missing coverage. Please review.
✅ Project coverage is 61.39%. Comparing base (5a7c3ae) to head (3cc9f90).
⚠️ Report is 12 commits behind head on devel.

Files with missing lines	Patch %	Lines
R/plotForest.R	79.47%	39 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##            devel     #220      +/-   ##
==========================================
+ Coverage   57.71%   61.39%   +3.68%     
==========================================
  Files          21       22       +1     
  Lines        3493     3865     +372     
==========================================
+ Hits         2016     2373     +357     
- Misses       1477     1492      +15     

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[TuomasBorman]

Sorry for the delay. Here are couple final comments; most of them are thoughts and can be ignored if justified

[TuomasBorman]

Awesome, thank you!