tests/testthat/test_subset.R

In MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

data("data_fungi")
cond_taxa <- grepl("Endophyte", data_fungi@tax_table[, "Guild"])
names(cond_taxa) <- taxa_names(data_fungi)

test_that("subset_taxa_pq works fine", {
  expect_s4_class(
    subset_taxa_pq(
      data_fungi,
      data_fungi@tax_table[, "Phylum"] == "Ascomycota"
    ),
    "phyloseq"
  )
  skip_on_cran()
  expect_identical(
    ntaxa(subset_taxa_pq(
      data_fungi,
      data_fungi@tax_table[, "Phylum"] == "Ascomycota"
    )),
    1066L
  )
  expect_s4_class(subset_taxa_pq(data_fungi, cond_taxa), "phyloseq")
  expect_identical(ntaxa(subset_taxa_pq(data_fungi, cond_taxa)), 128L)
  expect_identical(
    ntaxa(subset_taxa_pq(data_fungi, cond_taxa, taxa_names_from_physeq = TRUE)),
    128L
  )
  expect_error(subset_taxa_pq(
    data_fungi,
    data_fungi@sam_data[["Height"]] == "Low"
  ))
})

cond_samp <- grepl("A1", data_fungi@sam_data[["Sample_names"]])
test_that("subset_samples_pq works fine", {
  expect_s4_class(
    subset_samples_pq(data_fungi, data_fungi@sam_data[["Height"]] == "Low"),
    "phyloseq"
  )
  skip_on_cran()
  expect_s4_class(subset_samples_pq(data_fungi, cond_samp), "phyloseq")
  expect_error(subset_samples_pq(
    data_fungi,
    data_fungi@tax_table[, "Phylum"] == "Ascomycota"
  ))
  data_fungi2 <- data_fungi
  data_fungi2@sam_data <- NULL
  expect_message(subset_samples_pq(data_fungi2, cond_samp))
  expect_s4_class(
    suppressMessages(subset_samples_pq(data_fungi2, cond_samp)),
    "phyloseq"
  )
})