tests/testthat/test-transformations.R

In villegar/MetaPipe: A High-Performance Computing Pipeline for QTL Mapping of Large Ionomic and Metabolomic Datasets

test_that("check alpha level works", {
  expect_error(check_alpha(0.5), NA)
  expect_error(check_alpha(-0.5), "alpha must be*")
  expect_error(check_alpha(1.5), "alpha must be*")
  expect_error(check_alpha("1.5"), "alpha must be*")
  expect_error(check_alpha("One"), "alpha must be*")
})

test_that("log transformation works", {
  set.seed(123)
  data <- rnorm(100, 5)
  
  # # Expected transformation
  # expected_df <- data.frame(
  #   flag = "Normal",
  #   transf = "log",
  #   transf_val = 2,
  #   stringsAsFactors = FALSE
  # )
  
  expect_message(result_df <- log_transformation(2 ^ data, "EXP_2"))
  expect_equivalent(data, result_df)
  expect_warning(result_df <- log_transformation(data, "EXP_2"))
  # expect_null(result_df)
  filename <- "HIST_LOG_2_EXP_2.png"
  expect_true(file.exists(filename))
  expect_false(dir.exists(filename))
  expect_gt(file.size(filename), 0)
  file.remove(filename)
  expect_false(file.exists(filename))
})

test_that("power transformation works", {
  set.seed(123)
  data <- rnorm(100, 5)
  
  # # Expected transformation
  # expected_df <- data.frame(
  #   flag = "Normal",
  #   transf = "power",
  #   transf_val = 2,
  #   stringsAsFactors = FALSE
  # )
  
  expect_message(result_df <- power_transformation(sqrt(data), "ROOT_2"))
  expect_equivalent(data, result_df)
  expect_warning(result_df <- power_transformation(data, "ROOT_2"))
  # expect_null(result_df)
  filename <- "HIST_POW_2_ROOT_2.png"
  expect_true(file.exists(filename))
  expect_false(dir.exists(filename))
  expect_gt(file.size(filename), 0)
  file.remove(filename)
  expect_false(file.exists(filename))
})

test_that("root transformation works", {
  set.seed(123)
  data <- rnorm(100, 5)
  
  # # Expected transformation
  # expected_df <- data.frame(
  #   flag = "Normal",
  #   transf = "root",
  #   transf_val = "e",
  #   stringsAsFactors = FALSE
  # )
  
  expect_message(result_df <- root_transformation(data ^ 2, "POW_2"))
  expect_equivalent((data ^ 2) ^ (1/exp(1)), result_df)
  expect_warning(result_df <- root_transformation(data, "POW_2"))
  # expect_null(result_df)
  filename <- "HIST_ROOT_e_POW_2.png"
  expect_true(file.exists(filename))
  expect_false(dir.exists(filename))
  expect_gt(file.size(filename), 0)
  file.remove(filename)
  expect_false(file.exists(filename))
})

test_that("pareto scale works", {
  set.seed(123)
  data <- matrix(rnorm(100, 5), ncol = 2)
  data_new <- paretoscale(data)
  expect_equal(mean(data_new), 0)
})

test_that("data transform works", {
  set.seed(123)
  data <- rnorm(100, 5)
  
  # Expected transformation
  ## Exponential data -> Log transformation
  expected_df_log_2 <- data.frame(
    index = "",
    trait  = "EXP_2",
    values = log(2 ^ data, 2),
    flag = "Normal",
    transf = "log",
    transf_val = 2,
    stringsAsFactors = FALSE
  )
  
  ## Squared data -> Power transformation
  expected_df_power_2 <- data.frame(
    index = "",
    trait = "ROOT_2",
    values = (sqrt(data)) ^ 2,
    flag = "Normal",
    transf = "power",
    transf_val = 2,
    stringsAsFactors = FALSE
  )
  
  ## Powered data -> Root transformation
  expected_df_root_2 <- data.frame(
    index = "",
    trait = "POW_2",
    values = (data ^ 2) ^ (1 / exp(1)),
    flag = "Normal",
    transf = "root",
    transf_val = "e",
    stringsAsFactors = FALSE
  )
  
  expect_message(result_df <- transform_data(data))
  expect_null(result_df)
  
  result_df_log_2 <- transform_data(2 ^ data, "EXP_2")
  result_df_power_2 <- transform_data(sqrt(data), "ROOT_2")
  result_df_root_2 <- transform_data(data ^ 2, "POW_2")
  
  expect_identical(expected_df_log_2, result_df_log_2)
  expect_identical(expected_df_power_2, result_df_power_2)
  expect_identical(expected_df_root_2, result_df_root_2)
  
  filenames <- c("HIST_LOG_2_EXP_2.png", "HIST_POW_2_ROOT_2.png", "HIST_ROOT_e_POW_2.png")
  for (f in filenames) {
    expect_true(file.exists(f))
    expect_false(dir.exists(f))
    expect_gt(file.size(f), 0)
    file.remove(f)
    expect_false(file.exists(f))
  }
})