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Test for differences between intersections

Source: R/plot_functions.R
upset_test_pq.Rd

lifecycle-experimental

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

See also

upset_pq()

Author

Adrien Taudière

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")
}
#> Cleaning suppress 0 taxa (  ) and 0 sample(s) (  ).
#> Number of non-matching ASV 0
#> Number of matching ASV 1420
#> Number of filtered-out ASV 0
#> Number of kept ASV 1420
#> Number of kept samples 185
#> [1] "OTU, Class, Guild differ significantly between intersections"
#> Cleaning suppress 0 taxa (  ) and 0 sample(s) (  ).
#> Number of non-matching ASV 0
#> Number of matching ASV 1420
#> Number of filtered-out ASV 0
#> Number of kept ASV 1420
#> Number of kept samples 185
#> [1] "OTU differ significantly between intersections"
#>     variable     p.value statistic                         test         fdr
#> OTU      OTU 0.002217898   33.7837 Kruskal-Wallis rank sum test 0.002217898