david-barnett / microViz

R package for microbiome data visualization and statistics. Uses phyloseq, vegan and the tidyverse. Docker image available.
https://david-barnett.github.io/microViz/
GNU General Public License v3.0
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Subsetting aitchison distance #105

Closed jorondo1 closed 1 year ago

jorondo1 commented 1 year ago

Hi, Following the recommendations in the doc for PERMANOVA using aitchison distances (option 2):

pass an object with untransformed (or 'identity' transformed) taxa to the data argument of dist_calc() and specify dist = "aitchison".

is it ok to subset the resulting psExtra object, i-e remove certain low abundance taxa, before running dist_permanova ? I thought it would, but I realise that this procedure doesnt rcclr transform the data. I thought aitchison distance calculations were based on log-ratio transformed compositions, so I'm a bit confused. I was counting on subcompositional coherence to subset, but my (very basic) understanding of the underlying maths of compositional data may be causing my confusion.

Looking forward to your input