Test for differences between intersections

See upset_pq() to plot upset. There is a bug with ggplot2 >= 4.0.0. See issue https://github.com/krassowski/complex-upset/issues/213 for more details.

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)

...

Additional arguments passed on to the ComplexUpset::upset_test()

Value

A ggplot2 plot

See also

upset_pq()

Author

Adrien Taudière

Examples

if (requireNamespace("ComplexUpset")) {
  upset_test_pq(data_fungi_mini, "Height",
    var_to_test = c("OTU", "Class", "Guild"))
  upset_test_pq(data_fungi_mini, "Time")
}
#> Loading required namespace: ComplexUpset
#> Cleaning suppress 0 taxa (  ) and 0 sample(s) (  ).
#> Number of non-matching ASV 0
#> Number of matching ASV 45
#> Number of filtered-out ASV 0
#> Number of kept ASV 45
#> Number of kept samples 137
#> Cleaning suppress 0 taxa (  ) and 0 sample(s) (  ).
#> Number of non-matching ASV 0
#> Number of matching ASV 45
#> Number of filtered-out ASV 0
#> Number of kept ASV 45
#> Number of kept samples 137
#>     variable   p.value statistic                         test       fdr
#> OTU      OTU 0.3847389  12.78662 Kruskal-Wallis rank sum test 0.3847389