multipatt_pq {MiscMetabar} | R Documentation |
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 |
fact |
(required) Name of the factor in |
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 |
... |
Others arguments passed on to |
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)
)
}
[Package MiscMetabar version 0.9.1 Index]