tidy_pcoa: PCoA on a 'long' (tidy) tibble, and a long tibble is returned
In leylabmpi/LeyLabRMisc: Ley Lab misc R functions, rmd templates, etc.

tidy_pcoa

R Documentation

PCoA on a 'long' (tidy) tibble, and a long tibble is returned

Description

Perform PCoA in a "tidy" way. If multiple diversity metrics are provided (eg., "bray" and "jaccard"), all PCoA results will be combined into one data.frame.

Usage

tidy_pcoa(
  df,
  taxon_col,
  sample_col,
  abundance_col,
  dists = c("bray", "jaccard", "wunifrac", "unifrac"),
  tree = NULL,
  threads = 1,
  threads_unifrac = 1,
  k = 2,
  dist_mtx_file = NULL,
  pcoa_file = NULL
)

Arguments

`df`	data.frame or tibble
`taxon_col`	the column specifying taxa or OTUs (no quotes needed)
`sample_col`	the column specifying sample names (no quotes needed)
`abundance_col`	the column specifying the taxon abundances in each sample (no quotes needed)
`dists`	vector of beta-diversity distances ('wunifrac' = weighted UniFrac, 'unifrac' = unweighted Unifrac; see vegan::vegsist for others)
`tree`	phylogeny for UniFrac calculations. It can have more tips that what is in the data.frame
`threads`	number of parallel calculations of each distance metric (1 thread per distance)
`threads_unifrac`	number of threads to use for wunifrac & unifrac calculations
`k`	passed to cmdscale
`dist_mtx_file`	file name for saving the distance matrices (qs serialization; use ".qs" for the file extension)
`pcoa_file`	file name for saving the raw pcoa results