bokulich-lab/RESCRIPt

DOC: Add better description of rank propagation

Closed this issue · 1 comments

Need to make it clear that rank propagation will propagate taxonomy ranks for all available taxonomy, using forward fill prior to subsetting the ranks requested by the user. That is :

Accession Taxonomy-Ranks
All Available Ranks d__Eukaryota sk__Holozoa k__Animalia ks__ sp__Lophotrochozoa p__Rotifera ps__ pi__ sc__ c__Monogononta cs__ ci__ so__ o__Ploimida os__ sf__ f__ fs__ g__Brachionus
Propagated Ranks d__Eukaryota sk__Holozoa k__Animalia ks__Animalia sp__Lophotrochozoa p__Rotifera ps__Rotifera pi__Rotifera sc__Rotifera c__Monogononta cs__Monogononta ci__Monogononta so__Monogononta o__Ploimida os__Ploimida sf__Ploimida f__Ploimida fs__Ploimida g__Brachionus

So if a user wanted infraclass w/o rank propagation they'd get: ci__With Rank propagation they'd get:ci__Monogononta`

There is probably a better example we can use...

I've added a description of rank propagation under the drop menu "Rank-Propagation", just before the "Species-labels: caveat emptor!" drop menu.