bokulich-lab / RESCRIPt

REference Sequence annotation and CuRatIon Pipeline
BSD 3-Clause "New" or "Revised" License
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DOC: Add better description of rank propagation #117

Closed mikerobeson closed 2 years ago

mikerobeson commented 2 years ago

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 dEukaryota skHolozoa kAnimalia ks spLophotrochozoa pRotifera ps pi sc cMonogononta cs ci so oPloimida os sf f fs g__Brachionus
Propagated Ranks dEukaryota skHolozoa kAnimalia ksAnimalia spLophotrochozoa pRotifera psRotifera piRotifera scRotifera cMonogononta csMonogononta ciMonogononta soMonogononta oPloimida osPloimida sfPloimida fPloimida fsPloimida g__Brachionus

So if a user wanted infraclass w/o rank propagation they'd get: ci With Rank propagation they'd get: ciMonogononta`

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

mikerobeson commented 2 years ago

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