tests/testthat/testDroplets.R

In CRUKMI-ComputationalBiology/twoddpcr: Classify 2-d Droplet Digital PCR (ddPCR) data and quantify the number of starting molecules

context("Retrieving droplets")

testDir <- system.file("testdata", package = "twoddpcr")

test_that("Droplets can be retrieved in a data frame", {
  expect_s3_class(amplitudes(ddpcrWell()), "data.frame")
  expect_s3_class(amplitudes(ddpcrWell(file.path(testDir, "sample_B03_Amplitude.csv"))),
                  class="data.frame")
  expect_equal(class(amplitudes(ddpcrPlate())), "data.frame")
  expect_equal(class(amplitudes(ddpcrPlate(testDir))), "list")
  expect_equal(class(do.call(rbind, amplitudes(ddpcrPlate(testDir)))),
               "data.frame")
})

test_that("The wells names are loaded from filenames", {
  expect_equal(names(ddpcrPlate(testDir)), c("B03", "A04", "A05", "B06"))
})

test_that("There are the right number of droplets", {
  expect_equal(numDroplets(ddpcrWell()), 0)
  expect_equal(numDroplets(ddpcrWell(file.path(testDir, "sample_B03_Amplitude.csv"))), 6)
  expect_equal(numDroplets(ddpcrPlate()), c())
  expect_equivalent(numDroplets(ddpcrPlate(testDir)), c(6, 4, 4, 10))
  expect_equivalent(numDroplets(ddpcrPlate(list(A01=ddpcrWell()))), c(0),
                    info="Plate with an empty well")
})

test_that("isEmpty works as expected", {
  expect_true(isEmpty(ddpcrWell()))
  expect_true(isEmpty(ddpcrPlate()))
  expect_true(isEmpty(ddpcrPlate(list(A01=ddpcrWell()))),
              info="Plate with an empty well")

  expect_false(isEmpty(ddpcrWell(file.path(testDir, "sample_B03_Amplitude.csv"))))
  expect_false(isEmpty(ddpcrPlate(testDir)))
})