tests/testthat/test-set_reference_spectra.R

In maldipickr: Dereplicate and Cherry-Pick Mass Spectrometry Spectra

# WARNING - Generated by {fusen} from dev/dereplicate-spectra.Rmd: do not edit by hand

processed <- system.file("toy-species-spectra", package = "maldipickr") %>%
  import_biotyper_spectra() %>%
  process_spectra()
cosine_similarity <- matrix(
  c(
    1, 0.79, 0.77, 0.99, 0.98, 0.98,
    0.79, 1, 0.98, 0.79, 0.8, 0.8,
    0.77, 0.98, 1, 0.77, 0.77, 0.77,
    0.99, 0.79, 0.77, 1, 1, 0.99,
    0.98, 0.8, 0.77, 1, 1, 1,
    0.98, 0.8, 0.77, 0.99, 1, 1
  ),
  nrow = 6,
  dimnames = list(
    c(
      "species1_G2", "species2_E11", "species2_E12",
      "species3_F7", "species3_F8", "species3_F9"
    ),
    c(
      "species1_G2", "species2_E11", "species2_E12",
      "species3_F7", "species3_F8", "species3_F9"
    )
  )
)
clusters <- delineate_with_similarity(cosine_similarity, threshold = 0.92)
test_that("set_reference_spectra works", {
  expect_equal(
    set_reference_spectra(clusters, processed$metadata)$is_reference,
    c(FALSE, FALSE, TRUE, FALSE, TRUE, FALSE)
  )
})
test_that("set_reference_spectra fails with inadequate metadata", {
  expect_error(
    set_reference_spectra(clusters, processed$metadata[1:2, ]),
    "The tibbles do not have the same number of rows!"
  )
  expect_error(
    set_reference_spectra(clusters[, -2], processed$metadata),
    "lacks one of the following columns"
  )
  expect_error(
    set_reference_spectra(clusters, processed$metadata[, -2]),
    "lacks one of the following columns"
  )
})