multipatt_pq: Test and plot multipatt result

In adrientaudiere/MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

Test and plot multipatt result

Description

A wrapper for the indicspecies::multipatt() function in the case of physeq object.

Usage

multipatt_pq(
  physeq,
  fact,
  p_adjust_method = "BH",
  pval = 0.05,
  control = permute::how(nperm = 999),
  ...
)

Arguments

physeq	(required): a phyloseq-class object obtained using the phyloseq package.
fact	(required) Name of the factor in physeq@sam_data used to plot different lines
p_adjust_method	(chr, default "BH"): the method used to adjust p-value
pval	(int, default 0.05): the value to determine the significance of LCBD
control	see ?indicspecies::multipatt()
...	Other arguments passed on to indicspecies::multipatt() function

Details

This function is mainly a wrapper of the work of others. Please make a reference to indicspecies::multipatt() if you use this function.

Value

A ggplot2 object

Author(s)

Adrien Taudière

Examples

if (requireNamespace("indicspecies")) {
  data(data_fungi)
  data_fungi_ab <- subset_taxa_pq(data_fungi, taxa_sums(data_fungi) > 10000)
  multipatt_pq(subset_samples(data_fungi_ab, !is.na(Time)), fact = "Time")
}

if (requireNamespace("indicspecies")) {
  multipatt_pq(subset_samples(data_fungi_ab, !is.na(Time)),
    fact = "Time",
    max.order = 1, control = permute::how(nperm = 99)
  )
}

adrientaudiere/MiscMetabar documentation built on Oct. 13, 2024, 9:42 p.m.