upset_test_pq: Test for differences between intersections

In MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

Test for differences between intersections

Description

See upset_pq() to plot upset.

Usage

upset_test_pq(
  physeq,
  fact,
  var_to_test = "OTU",
  min_nb_seq = 0,
  na_remove = TRUE,
  numeric_fonction = sum,
  ...
)

Arguments

physeq	(required): a phyloseq-class object obtained using the phyloseq package.
fact	(required): Name of the factor to cluster samples by modalities. Need to be in physeq@sam_data.
var_to_test	(default c("OTU")) : a vector of column present in the tax_table slot from the physeq object
min_nb_seq	minimum number of sequences by OTUs by samples to take into count this OTUs in this sample. For example, if min_nb_seq=2,each value of 2 or less in the OTU table will not count in the venn diagram
na_remove	: if TRUE (the default), NA values in fact are removed if FALSE, NA values are set to "NA"
numeric_fonction	(default : sum) the function for numeric vector useful only for complex plot (see examples)
...	Other arguments passed on to the ComplexUpset::upset_test()

Value

A ggplot2 plot

Author(s)

Adrien Taudière

See Also

upset_pq()

Examples

data(data_fungi)
if (requireNamespace("ComplexUpset")) {
  upset_test_pq(data_fungi, "Height", var_to_test = c("OTU", "Class", "Guild"))
  upset_test_pq(data_fungi, "Time")
}

MiscMetabar documentation built on Oct. 8, 2024, 1:07 a.m.