tests/testthat/test_custom_sampnames.R

In pmartR/pmartR: Panomics Marketplace - Quality Control and Statistical Analysis for Panomics Data

context("custom_sampnames")

test_that("sample names are properly abridged", {
  # Load the data and create a pepData object ----------------------------------

  load(system.file('testdata',
    'little_pdata.RData',
    package = 'pmartR'
  ))

  # Construct a pepData object.
  pdata <- as.pepData(
    e_data = edata,
    f_data = fdata,
    e_meta = emeta,
    edata_cname = 'Mass_Tag_ID',
    fdata_cname = 'SampleID',
    emeta_cname = 'Protein'
  )

  # Make long sample names that can be used to test each method for reducing the
  # length of the sample names.
  names(pdata$e_data) <- c(
    "Mass_Tag_ID",
    "qwerty_one_infection1_asdf",
    "qwerty_two_infection2_asdf",
    "qwerty_three_infection3_asdf",
    "qwerty_four_infection4_asdf",
    "qwerty_five_infection5_asdf",
    "qwerty_six_infection6_asdf",
    "qwerty_seven_infection7_asdf",
    "qwerty_eight_infection8_asdf",
    "qwerty_nine_infection9_asdf",
    "qwerty_one_mock1_asdf",
    "qwerty_two_mock2_asdf",
    "qwerty_three_mock3_asdf"
  )

  # Change to the new long names in f_data
  pdata$f_data$SampleID <- c(
    "qwerty_one_infection1_asdf",
    "qwerty_two_infection2_asdf",
    "qwerty_three_infection3_asdf",
    "qwerty_four_infection4_asdf",
    "qwerty_five_infection5_asdf",
    "qwerty_six_infection6_asdf",
    "qwerty_seven_infection7_asdf",
    "qwerty_eight_infection8_asdf",
    "qwerty_nine_infection9_asdf",
    "qwerty_one_mock1_asdf",
    "qwerty_two_mock2_asdf",
    "qwerty_three_mock3_asdf"
  )

  # Holy short sample names, Batman! -------------------------------------------

  # firstn ---------------

  # Create short sample names with firstn that are not unique
  expect_error(
    custom_sampnames(pdata, firstn = 6),
    paste("The input used does not produce a unique sample name",
      "for each sample.",
      sep = " "
    )
  )

  # Create short names with the first four characters of the sample names using
  # the firstn argument.
  firstn_16 <- custom_sampnames(pdata, firstn = 16)

  # Make sure attributes have not been changed after adding short names.
  expect_identical(attributes(pdata), attributes(firstn_16))
  # Make sure the short sample names are present and correct.
  expect_equal(
    dim(firstn_16$f_data),
    c(12, 3)
  )
  expect_equal(
    firstn_16$f_data$VizSampNames,
    c(
      "qwerty_one_infec",
      "qwerty_two_infec",
      "qwerty_three_inf",
      "qwerty_four_infe",
      "qwerty_five_infe",
      "qwerty_six_infec",
      "qwerty_seven_inf",
      "qwerty_eight_inf",
      "qwerty_nine_infe",
      "qwerty_one_mock1",
      "qwerty_two_mock2",
      "qwerty_three_moc"
    )
  )

  # Create not so short sample names (the input to firstn is larger than the
  # longest sample name).
  expect_warning(firstn_35 <- custom_sampnames(pdata, firstn = 35))

  # Make sure nothing changes if firstn is larger than largest sample name.
  expect_identical(
    as.character(firstn_35$f_data$SampleID),
    firstn_35$f_data$VizSampNames
  )

  # from to ---------------

  # Range completely excludes some or all sample names.
  expect_error(custom_sampnames(pdata, from = 16, to = 22))
  expect_error(custom_sampnames(pdata, from = 30, to = 33))

  # Non-numeric inputs for from and to.
  expect_error(custom_sampnames(pdata, from = "2", to = "10"))

  # The value for to is less than from.
  expect_error(custom_sampnames(pdata, from = 3, to = 2))

  # Create short names using the from/to combo.
  from_to <- custom_sampnames(pdata, from = 8, to = 16)

  # Make sure attributes have not been changed after adding short names.
  expect_identical(attributes(pdata), attributes(from_to))
  # Make sure the short sample names are present and correct.
  expect_equal(
    dim(from_to$f_data),
    c(12, 3)
  )
  expect_equal(
    from_to$f_data$VizSampNames,
    c(
      "one_infec",
      "two_infec",
      "three_inf",
      "four_infe",
      "five_infe",
      "six_infec",
      "seven_inf",
      "eight_inf",
      "nine_infe",
      "one_mock1",
      "two_mock2",
      "three_moc"
    )
  )

  # delim ---------------

  # Use delim and components to make tiny sample names.
  delim_u <- custom_sampnames(pdata, delim = "_", components = 3)
  delim_empty <- custom_sampnames(pdata, delim = "", components = 8:16)

  # Make sure attributes have not been changed after adding short names.
  expect_identical(attributes(pdata), attributes(delim_u))
  # Make sure the short sample names are present and correct.
  expect_equal(
    dim(delim_u$f_data),
    c(12, 3)
  )
  expect_equal(
    delim_u$f_data$VizSampNames,
    c(paste0("infection", 1:9), paste0("mock", 1:3))
  )
  expect_equal(
    dim(delim_empty$f_data),
    c(12, 3)
  )
  expect_equal(
    delim_empty$f_data$VizSampNames,
    c(
      "one_infec",
      "two_infec",
      "three_inf",
      "four_infe",
      "five_infe",
      "six_infec",
      "seven_inf",
      "eight_inf",
      "nine_infe",
      "one_mock1",
      "two_mock2",
      "three_moc"
    )
  )

  # Components does not specify an index created by delim that exists.
  expect_error(
    custom_sampnames(pdata, delim = "_", components = 20),
    paste("none of the indices specified in 'components' match",
      "indices of the split sample name",
      sep = " "
    )
  )


  load(system.file('testdata',
    'little_seqdata.RData',
    package = 'pmartR'
  ))

  myseqData <- as.seqData(
    e_data = edata,
    f_data = fdata,
    edata_cname = 'ID_REF',
    fdata_cname = 'Samples'
  )

  err_1 <- "Please specify both 'from' and 'to' if either argument is used."
  err_2 <- "Please specify both 'delim' and 'components' if either argument is used."

  expect_identical(
    strtrim(myseqData$f_data$Samples, 13),
    suppressWarnings(custom_sampnames(myseqData, firstn = 13)$f_data$VizSampNames)
    ## Might wanna think about a lastn as well
  )

  testthat::expect_error(custom_sampnames(myseqData, from = 1), err_1)
  testthat::expect_error(custom_sampnames(myseqData, to = 13), err_1)

  expect_identical(
    substring(myseqData$f_data$Samples, first = 3, last = 13),
    custom_sampnames(myseqData, from = 3, to = 13)$f_data$VizSampNames
  )

  testthat::expect_error(custom_sampnames(myseqData, delim = "_"), err_2)
  testthat::expect_error(custom_sampnames(myseqData, components = c(1, 2, 3)), err_2)

  ## No changes actually happening here, demo of arg use
  expect_identical(
    myseqData$f_data$Samples,
    custom_sampnames(myseqData, delim = "_", components = c(1, 2, 3))$f_data$VizSampNames,
    custom_sampnames(myseqData, pattern = ".+")$f_data$VizSampNames
  )
})