Test and plot multipatt result — multipatt

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()
...: Additional arguments passed on to indicspecies::multipatt() function

Value

A ggplot2 object

Details

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

Author

Adrien Taudière

Examples

# \donttest{
if (requireNamespace("indicspecies")) {
  multipatt_pq(subset_samples(data_fungi_mini, !is.na(Time)),
    fact = "Time", control = permute::how(nperm = 99))
  multipatt_pq(subset_samples(data_fungi_mini, !is.na(Time)),
    fact = "Time",
    max.order = 1, control = permute::how(nperm = 99)
  )
}
#> Taxa are now in columns.
#> Taxa are now in columns.

# }