PERMANOVA analysis on each phyloseq object in a list_phyloseq

Performs a PERMANOVA analysis using MiscMetabar::adonis_pq() on each phyloseq object in a list_phyloseq and returns a summary table with the results.

Usage

adonis_lpq(
  x,
  formula,
  dist_method = "bray",
  na_remove = FALSE,
  correction_for_sample_size = FALSE,
  rarefy_nb_seqs = FALSE,
  by = "margin",
  verbose = TRUE,
  ...
)

Arguments

x: (required) A list_phyloseq object.
formula: (character, required) The right part of a formula for vegan::adonis2(). Variables must be present in the sample_data slot of all phyloseq objects. The formula should contain variables that are in the shared modalities.
dist_method: (character, default "bray") The distance method to use. See phyloseq::distance() for available methods.
na_remove: (logical, default FALSE) If TRUE, samples with NA values in the formula variables are removed before analysis.
correction_for_sample_size: (logical, default FALSE) If TRUE, adds library size to the formula following Weiss et al. 2017 recommendations.
rarefy_nb_seqs: (logical, default FALSE) If TRUE, rarefy each sample before computing distances.
by: (character, default "margin") The by argument passed to vegan::adonis2(). Options are "terms", "margin", or NULL.
verbose: (logical, default TRUE) If TRUE, print progress messages.
...: Additional arguments passed to MiscMetabar::adonis_pq().

Value

A tibble with one row per phyloseq object and the following columns:

name: Name of the phyloseq object
term: The term(s) from the formula (one row per term if multiple)
Df: Degrees of freedom
SumOfSqs: Sum of squares
R2: R-squared value
F: F statistic
Pr(>F): P-value
partial_R2: Partial R-squared (if available)

Details

This function requires that the list_phyloseq type is NOT SEPARATE_ANALYSIS, as the formula must contain variables that are common across all phyloseq objects.

The function is a wrapper around MiscMetabar::adonis_pq(), which itself wraps vegan::adonis2().

Examples

if (FALSE) { # \dontrun{
lpq <- list_phyloseq(
  list(
    fungi = data_fungi,
    fungi_clust = postcluster_pq(data_fungi)
  ),
  same_bioinfo_pipeline = FALSE
)

# Run PERMANOVA on each phyloseq object
results <- adonis_lpq(lpq, formula = "Height+Time", na_remove = TRUE)
results

# With Jaccard distance
results_jaccard <- adonis_lpq(lpq, formula = "Height", dist_method = "jaccard")
} # }