Perform compositional differential abundance analysis

add_codifab() performs a differential abundance test for all pairwise ratios between taxa.Taxa that have a relatively high number of significantly different ratios, can be considered more abundant in one condition versus the other. The tacoplot_codifab() function allows better interpretation of these results.

Usage

add_codifab(ta, condition, conditions = NULL, max_taxa = 30)

Arguments

ta

A tidytacos object.

condition

A binary variable in the sample table (unquoted).

conditions

A character vector with exactly two categories of the condition variable.

max_taxa

The maximum number of taxa to use.

Value

A tidytacos object with an extra table taxon_pairs

Details

A table called taxon_pairs will be added to the tidytacos object, with for each pair of a taxon and a reference taxon, the differential abundance of the taxon between the two conditions (with respect to the reference taxon). The test that is performed is a Wilcoxon rank sum test and the test statistic that is reported is the two-sample Hodges–Lehmann estimator (the median of all pairwise differences between the samples).

It is possible to supply the conditions to compare through the conditions argument. Other conditions than the two supplied will be removed from the data.

This method is based on the principle introduced by Aitchison in "The statistical analysis of compositional data." Journal of the Royal Statistical Society: Series B (Methodological) 44.2 (1982): 139-16