Leo Lahti

The addTaxonomyTree creates rowTree based on taxonomic rank hierarchy. This is different from the actual phylogenetic tree and may cause confusion. I suggest to remove addTaxonomyTree from examples entirely, or...

This chapter should be carefully checked, there were various suboptimal choices.

Rearrange and improve the [outreach material](https://github.com/microbiome/outreach)

We should have some exercises about all major chapters / functionalities. List systematically what is missing and create issue/issues. At least: - dbRDA exercises will require an update - calculating...

Add new data resource

3

Add link and explanation of [Microbiome Compendium](https://github.com/seandavi/MicroBioMap#microbiome-compendium) in OMA.

Triplot examples for (db)RDA

2

RDA plots can indicate both features as well as covariates that influence ordination. Would be good to show examples in OMA, too. Here some examples: https://stackoverflow.com/questions/32194193/plotting-rda-vegan-in-ggplot Here some discussion on...

**Is your feature request related to a problem? Please describe.** The `agglomerateByRank` function only accepts ranks that are listed in `TAXONOMY_RANKS` of the _mia_ package. This prevents agglomeration to levels...

Compare to OSCA & OSTA books

2

Check and sync with the other similar books: - https://lmweber.org/OSTA-book/ - https://bioconductor.org/books/release/OSCA/

Heatmap tools in SEtools package

4

The SEtools package provides SE integration for pheatmap and ComplexHeatmap packages, see the [vignette](https://www.bioconductor.org/packages/release/bioc/vignettes/SEtools/inst/doc/SEtools.html). Consider whether this would be useful to update/improve the current heatmap plotting examples in OMA. They...

Probably good idea to ultimately release OMA via [bioconductor.org/books](https://bioconductor.org/books) [OSCA](https://bioconductor.org/books/release/OSCA/) is there, for instance.