tests/testthat/test_krona.R

In MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

data("GlobalPatterns", package = "phyloseq")
GA <- subset_taxa(GlobalPatterns, Phylum == "Acidobacteria")

krona_error_or_not <- try(system("ktImportText 2>&1", intern = TRUE))

if (class(krona_error_or_not) == "try-error") {
  skip_on_cran()
  skip_on_os("windows")
  test_that("krona send an error when krona is not installed", {
    expect_warning(krona(GA, "Number.of.sequences.html"))
    expect_warning(krona(GA, "Number.of.ASVs.html", nb_seq = FALSE))
    expect_warning(merge_krona(c(
      "Number.of.sequences.html",
      "Number.of.ASVs.html"
    )))
  })
} else {
  test_that("krona function works fine with GlobalPatterns dataset", {
    skip_on_cran()
    skip_on_os("windows")
    testFolder <- tempdir()
    suppressWarnings(unlink(
      list.files(testFolder, full.names = TRUE),
      recursive = TRUE
    ))
    expect_message(krona(
      GA,
      file = paste0(testFolder, "/Number.of.sequences.html")
    ))
    expect_message(krona(
      GA,
      file = paste0(testFolder, "/Number.of.ASVs.html"),
      nb_seq = FALSE
    ))
    expect_silent(merge_krona(
      c(
        paste0(testFolder, "/Number.of.sequences.html"),
        paste0(testFolder, "/Number.of.ASVs.html")
      ),
      output = paste0(testFolder, "/mergeKrona.html")
    ))
    unlink(list.files(testFolder, full.names = TRUE), recursive = TRUE)
  })
}