Performs graph-based permutation tests on phyloseq object

A wrapper of phyloseqGraphTest::graph_perm_test() for quick plot with important statistics

Usage

graph_test_pq(
  physeq,
  fact,
  merge_sample_by = NULL,
  nperm = 999,
  return_plot = TRUE,
  title = "Graph Test",
  na_remove = FALSE,
  ...
)

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. This should be a factor with two or more levels.

merge_sample_by

a vector to determine which samples to merge using merge_samples2() function. Need to be in physeq@sam_data

nperm

(int) The number of permutations to perform.

return_plot

(logical) Do we return only the result of the test or do we plot the result?

title

The title of the Graph.

na_remove

(logical, default FALSE) If set to TRUE, remove samples with NA in the variables set in formula.

...

Other params for be passed on to phyloseqGraphTest::graph_perm_test() function

Value

A ggplot2 plot with a subtitle indicating the pvalue and the number of permutations

Details

This function is mainly a wrapper of the work of others. Please cite phyloseqGraphTest package.

Author

Adrien Taudière

Examples

# \donttest{
if (requireNamespace("phyloseqGraphTest")) {
  data(enterotype)
  graph_test_pq(enterotype, fact = "SeqTech")
  graph_test_pq(enterotype, fact = "Enterotype", na_remove = TRUE)
}
#> 9 were discarded due to NA in variables present in formula.

# }