tests/testthat/test-utils.R

In insightsengineering/hermes: Preprocessing, analyzing, and reporting of RNA-seq data

# h_df_factors_with_explicit_na ----

test_that("h_df_factors_with_explicit_na works as expected with default settings", {
  dat <- data.frame(
    a = c(NA, "B", "C"),
    b = c(3, 1, NA),
    c = c(TRUE, FALSE, NA),
    d = factor(c("X", "Y", NA)),
    e = c("U", "V", NA)
  )
  result <- h_df_factors_with_explicit_na(dat)
  expected <- data.frame(
    a = factor(c("<Missing>", "B", "C"), levels = c("B", "C", "<Missing>")),
    b = c(3, 1, NA),
    c = factor(c(TRUE, FALSE, "<Missing>"), levels = c("FALSE", "TRUE", "<Missing>")),
    d = factor(c("X", "Y", "<Missing>"), levels = c("X", "Y", "<Missing>")),
    e = factor(c("U", "V", "<Missing>"), levels = c("U", "V", "<Missing>"))
  )
  expect_identical(result, expected)
})

test_that("h_df_factors_with_explicit_na works as expected without missing values", {
  dat <- data.frame(
    a = c("B", "C"),
    b = c(3, NA),
    c = c(TRUE, FALSE),
    d = factor(c("X", "Y")),
    e = c("U", "V")
  )
  result <- h_df_factors_with_explicit_na(dat)
  expected <- data.frame(
    a = factor(c("B", "C"), levels = c("B", "C")),
    b = c(3, NA),
    c = factor(c(TRUE, FALSE), levels = c("FALSE", "TRUE")),
    d = factor(c("X", "Y")),
    e = factor(c("U", "V"), levels = c("U", "V"))
  )
  expect_identical(result, expected)
})

test_that("h_df_factors_with_explicit_na works with mixed complete and incomplete variables", {
  dat <- data.frame(
    a = c(NA, "B", "C"),
    b = c(3, 1, NA),
    c = c(TRUE, FALSE, NA),
    d = factor(c("X", "Y", NA)),
    e = c("U", "V", "W")
  )
  result <- h_df_factors_with_explicit_na(dat)
  expected <- data.frame(
    a = factor(c("<Missing>", "B", "C"), levels = c("B", "C", "<Missing>")),
    b = c(3, 1, NA),
    c = factor(c(TRUE, FALSE, "<Missing>"), levels = c("FALSE", "TRUE", "<Missing>")),
    d = factor(c("X", "Y", "<Missing>"), levels = c("X", "Y", "<Missing>")),
    e = factor(c("U", "V", "W"))
  )
  expect_identical(result, expected)
})

test_that("h_df_factors_with_explicit_na works as expected with custom settings", {
  dat <- data.frame(
    a = c(NA, "B"),
    b = c(3, NA),
    c = c(TRUE, FALSE),
    d = factor(c("X", NA)),
    e = c("U", NA)
  )
  result <- h_df_factors_with_explicit_na(dat, na_level = "Misses")
  expected <- data.frame(
    a = factor(c("Misses", "B"), levels = c("B", "Misses")),
    b = c(3, NA),
    c = factor(c(TRUE, FALSE)),
    d = factor(c("X", "Misses"), levels = c("X", "Misses")),
    e = factor(c("U", "Misses"), levels = c("U", "Misses"))
  )
  expect_identical(result, expected)
})

test_that("h_df_factors_with_explicit_na works with a single character variable only", {
  dat <- data.frame(
    e = c("U", NA)
  )
  result <- h_df_factors_with_explicit_na(dat)
  expected <- data.frame(
    e = factor(c("U", "<Missing>"), levels = c("U", "<Missing>"))
  )
  expect_identical(result, expected)
})

test_that("h_df_factors_with_explicit_na converts empty strings to explicit missings", {
  dat <- data.frame(
    a = c("", "B", "C"),
    d = factor(c("X", "Y", ""))
  )
  result <- h_df_factors_with_explicit_na(dat)
  expected <- data.frame(
    a = factor(c("<Missing>", "B", "C"), levels = c("B", "C", "<Missing>")),
    d = factor(c("X", "Y", "<Missing>"), levels = c("X", "Y", "<Missing>"))
  )
  expect_identical(result, expected)
})

test_that("h_df_factors_with_explicit_na fails as expected when no columns in data", {
  dat <- data.frame(a = 1)[, NULL]
  expect_error(
    h_df_factors_with_explicit_na(dat),
    "Must have at least 1 cols"
  )
})

test_that("h_df_factors_with_explicit_na works without any rows", {
  dat <- data.frame(a = "5")[NULL, , drop = FALSE]
  result <- h_df_factors_with_explicit_na(dat)
  expected <- data.frame(a = factor())
  expect_identical(result, expected)
})

# df_cols_to_factor ----

test_that("df_cols_to_factor works as expected with default settings", {
  dat <- S4Vectors::DataFrame(
    a = c(NA, "B"),
    b = array(1:4, c(2, 1, 2)),
    c = c(TRUE, FALSE),
    d = factor(c("X", NA)),
    e = c("U", NA),
    chromosome = c("a", "b"),
    low_depth_flag = c(TRUE, FALSE)
  )
  result <- df_cols_to_factor(dat)
  expected <- S4Vectors::DataFrame(
    a = factor(c("<Missing>", "B"), levels = c("B", "<Missing>")),
    b = array(1:4, c(2, 1, 2)),
    c = factor(c(TRUE, FALSE)),
    d = factor(c("X", "<Missing>"), levels = c("X", "<Missing>")),
    e = factor(c("U", "<Missing>"), levels = c("U", "<Missing>")),
    chromosome = c("a", "b"),
    low_depth_flag = c(TRUE, FALSE)
  )
  expect_identical(result, expected)
})

test_that("df_cols_to_factor works as expected with custom settings", {
  dat <- S4Vectors::DataFrame(
    a = c(NA, "B"),
    b = array(1:4, c(2, 1, 2)),
    c = c(TRUE, NA),
    d = factor(c("X", NA)),
    e = c("U", NA),
    chromosome = c("a", "b"),
    low_depth_flag = c(TRUE, FALSE)
  )
  result <- df_cols_to_factor(dat, omit_columns = c("a", "b"), na_level = "Misses")
  expected <- S4Vectors::DataFrame(
    a = c(NA, "B"),
    b = array(1:4, c(2, 1, 2)),
    c = factor(c(TRUE, "Misses"), levels = c("TRUE", "Misses")),
    d = factor(c("X", "Misses"), levels = c("X", "Misses")),
    e = factor(c("U", "Misses"), levels = c("U", "Misses")),
    chromosome = c("a", "b"),
    low_depth_flag = c(TRUE, FALSE)
  )
  expect_identical(result, expected)
})

# h_short_list ----

test_that("h_short_list works as expected with default arguments", {
  expect_identical(
    h_short_list(letters),
    "a, b, ..., z"
  )
  expect_identical(
    h_short_list(letters[1:3]),
    "a, b, c"
  )
  expect_identical(
    h_short_list(letters[1:2]),
    "a, b"
  )
  expect_identical(
    h_short_list(letters[1]),
    "a"
  )
})

test_that("h_short_list works as expected with custom arguments", {
  expect_identical(
    h_short_list(letters, sep = "; "),
    "a; b; ...; z"
  )
  expect_identical(
    h_short_list(letters[1:4], thresh = 4L),
    "a, b, c, d"
  )
  expect_identical(
    h_short_list(letters[1:5], thresh = 5L, sep = "-"),
    "a-b-c-d-e"
  )
  expect_error(h_short_list(letters[1:3], thresh = 2L))
  expect_error(h_short_list(letters[1:3], sep = ""))
})

# h_parens ----

test_that("h_parens works as expected for strings", {
  expect_identical(
    h_parens("bla"),
    "(bla)"
  )
  expect_identical(
    h_parens(""),
    ""
  )
  expect_error(h_parens(123))
  expect_error(h_parens(NULL))
})

test_that("h_parens works as expected for character vectors", {
  expect_identical(
    h_parens(c("bla", "bli")),
    c("(bla)", "(bli)")
  )
  expect_identical(
    h_parens(c("", "bla")),
    c("", "(bla)")
  )
  expect_error(h_parens(c(NA, "")))
})

# colPrinComp1 ----

test_that("colPrinComp1 function works as expected for standard matrix input", {
  set.seed(123)
  cnts <- matrix(data = rpois(30, 5), nrow = 3, ncol = 10)
  cnts[2L, ] <- 5 # Constant gene.
  result <- expect_silent(colPrinComp1(cnts))
  expect_numeric(result)
  expect_length(result, 10L)
  expect_lt(mean(result), 1e-10)
})

test_that("colPrinComp1 function returns an error when data are not numeric", {
  cnts <- expect_silent(matrix(as.character(1:20), 4, 5))
  expect_error(colPrinComp1(cnts))
})

# colMeanZScores ----

test_that("colMeanZScores function works as expected for standard matrix input", {
  set.seed(123)
  cnts <- matrix(data = rpois(30, 5), nrow = 3, ncol = 10)
  cnts[2L, ] <- 5 # Constant gene.
  result <- expect_silent(colMeanZscores(cnts))
  expect_numeric(result)
  expect_length(result, 10L)
  expect_lt(mean(result), 1e-10)
})

test_that("colMeanZScores function returns an error when data are not numeric", {
  result <- expect_silent(matrix(as.character(1:20), 4, 5))
  expect_error(colMeanZScores(result))
})

# wrap_in_mae ----

test_that("wrap_in_mae function works as expected for standard SummarizedExperiment object", {
  object <- summarized_experiment
  result <- expect_silent(wrap_in_mae(object))
  expect_s4_class(result, "MultiAssayExperiment")
  expect_identical(result[[1]], object)
})

test_that("wrap_in_mae function uses the correct default name for the experiment", {
  result <- expect_silent(wrap_in_mae(summarized_experiment))
  expect_named(result, "summarized_experiment")
})

test_that("wrap_in_mae function uses the custom name for the experiment", {
  result <- expect_silent(wrap_in_mae(
    summarized_experiment,
    name = "bla"
  ))
  expect_named(result, "bla")
})

# h_all_duplicated ----

test_that("h_all_duplicated works as expected for numerics", {
  result <- expect_silent(h_all_duplicated(c(1, 1, 2, 3, 3, 4)))
  expected <- c(TRUE, TRUE, FALSE, TRUE, TRUE, FALSE)
  expect_identical(result, expected)
})

test_that("h_all_duplicated works as expected for character", {
  result <- expect_silent(h_all_duplicated(c("a", "", "", "a", "c")))
  expected <- c(TRUE, TRUE, TRUE, TRUE, FALSE)
  expect_identical(result, expected)
})

# cut_quantile ----

test_that("cut_quantile works as expected with default settings", {
  x <- c(4, 6, -10, 2.2, 0)
  result <- cut_quantile(x)
  expected_char <- c("(67%,100%]", "(67%,100%]", "[0%,33%]", "(33%,67%]", "[0%,33%]")
  expect_identical(as.character(result), expected_char)
  expect_factor(result, levels = c("[0%,33%]", "(33%,67%]", "(67%,100%]"))
})

test_that("cut_quantile works as expected with custom settings", {
  x <- c(4, 6, -10, 2.2, 0)
  result <- cut_quantile(x, c(0.33333333, 0.6666666, 0.8), digits = 3)
  expected_char <- c("(66.667%,80%]", "(80%,100%]", "[0%,33.333%]", "(33.333%,66.667%]", "[0%,33.333%]")
  expect_identical(as.character(result), expected_char)
  expect_factor(result, levels = c("[0%,33.333%]", "(33.333%,66.667%]", "(66.667%,80%]", "(80%,100%]"))
})

test_that("cut_quantile preserves NAs in result", {
  x <- c(4, 6, -10, 2.2, 0)
  x[c(1, 4)] <- NA
  result <- cut_quantile(x)
  expect_identical(is.na(x), is.na(result))
  result2 <- cut_quantile(x, percentiles = c(0.2, 0.7, 0.8))
  expect_identical(is.na(x), is.na(result2))
})

test_that("cut_quantile works without percentiles", {
  x <- c(4, 6, -10, 2.2, 0)
  result <- cut_quantile(x, numeric())
  expect_true(all(result == "[0%,100%]"))
  expect_identical(levels(result), "[0%,100%]")
})

test_that("cut_quantile works without percentiles when there is only 1 number", {
  x <- 4
  result <- cut_quantile(x, numeric())
  expect_identical(result, factor("[0%,100%]"))
})

test_that("cut_quantile works without percentiles when there are only 2 numbers", {
  x <- c(2, 4)
  result <- cut_quantile(x, numeric())
  expect_identical(result, factor(c("[0%,100%]", "[0%,100%]")))
})

test_that("cut_quantile produces an error if quantile boundaries are not unique", {
  x <- rep(1, 10)
  expect_error(
    cut_quantile(x),
    "Duplicate quantiles produced, please use a coarser `percentiles` vector"
  )
})

# cat_with_newline ----

test_that("cat_with_newline works as expected", {
  expect_equal(
    capture.output({
      cat_with_newline("hello")
      cat_with_newline("world", append = TRUE)
    }),
    c("hello", "world")
  )
  expect_equal(
    cat_with_newline(),
    NULL
  )
})