tests/testthat/test_purehoney_utils.R

In hemoshear/assayr2: Tools for analyzing assay data

### make_c3c2() -----------------------------------------------------
context("Test make_c3c2()")

file <- system.file("extdata", "PureHoney_Carnitines.RDS", package = "assayr2")
samps <- readRDS(file)

test_that("inputs of NULL fail", {
  expect_error(make_c3c2(NULL))
})
test_that("missing required columns will fail", {
  bad <- samps
  bad["plate_id"] <- NULL
  expect_error(make_c3c2(bad))
})
test_that("NA sample IDs will fail", {
  bad <- samps
  bad$sample_id[1] <- NA
  expect_error(make_c3c2(bad))
})
test_that("requred analytes are present", {
  bad <- samps
  bad$target <- "12C-Acetyl-Car"
  expect_error(make_c3c2(bad))
})
test_that("samples are uniquely identified", {
  bad <- samps
  bad$row <- "A"
  bad$sample_id <- 1
  expect_error(make_c3c2(bad))
})
test_that("it works", {
  result <- make_c3c2(samps)
  expect_true(is.data.frame(result))
  expect_true("12C-C3-C2-ratio-Car" %in% unique(result$target))
  expect_true("C3-C2-ratio-Car" %in% unique(result$curve_plot))
})
test_that("it works with 13C-Propionyl", {
  result <- make_c3c2(samps, propionyl_species = "13C")
  expect_true(is.data.frame(result))
  expect_true("13C-C3-C2-ratio-Car" %in% unique(result$target))
  expect_true("C3-C2-ratio-Car" %in% unique(result$curve_plot))
})


# apply_curve_pairs -------------------------------------------------------
samps$curve_id <- NULL
samps$plate_run <- NULL
curve_pairs <- c("12C-Acetyl-Car" = "13C-Acetyl-Car",
                 "12C-Propionyl-Car" = "13C-Propionyl-Car")

test_that("inputs of NULL to 'data' fail", {
  expect_error(apply_curve_matches(NULL, curve_pairs))
})

test_that("inputs of NULL to 'curve_pairs' work", {
  expect_silent(apply_curve_matches(samps, NULL))
})

result <- apply_curve_matches(samps, curve_pairs)

test_that("New columns are added", {
  expect_true(all(c("curve_id", "plate_run") %in% names(result)))
})

test_that("New values are correct", {
  expect_true(all(c("2042_ONE_13C-Acetyl-Car", "2042_ONE_13C-Propionyl-Car") %in% unique(result$curve_id)))
  expect_true(all(c("2042_ONE", "2042_ONE") %in% unique(result$plate_run)))
})

test_that("Specifying 'plate_id' works", {
  result <- apply_curve_matches(samps, curve_pairs, plate_id = 1)
  expect_true(all(c("1_ONE_13C-Acetyl-Car", "1_ONE_13C-Propionyl-Car") %in% unique(result$curve_id)))
  expect_true(all(c("1_ONE") %in% unique(result$plate_run)))
})

test_that("Specifying 'prun' works", {
  result <- apply_curve_matches(samps, curve_pairs, prun = "FOO")
  expect_true(all(c("2042_FOO_13C-Acetyl-Car", "2042_FOO_13C-Propionyl-Car") %in% unique(result$curve_id)))
  expect_true(all(c("2042_FOO") %in% unique(result$plate_run)))
})

rm(samps, file)