tests/testthat/test-S3-transform.R

In SomaDataIO: Input/Output 'SomaScan' Data

# this is to ensure the S3 method is available and dispatched
# otherwise the base::transform.data.frame() method will not
# transform the analytes inside scaleAnalytes()

test_that("the transform S3 method exists in the namespace", {
  expect_error(getS3method("transform", "soma_adat"), NA)  # expect no error
})

test_that("the transform S3 method is listed in methods", {
  methods <- unclass(methods("transform", "soma_adat"))
  expect_true("transform.soma_adat" %in% methods)
})

# dummy ADAT:
# double seq1; half seq2
v  <- c(2, 0.5)
df <- data.frame(
  sample      = paste0("sample_", 1:3),
  seq.1234.56 = c(1, 2, 3),
  seq.9999.88 = c(4, 5, 6) * 10
  ) |>  # `soma_adat` to invoke S3 method dispatch
  addClass("soma_adat")

test_that("`transform()` dispatches the `soma_adat` method and correctly scales (cols)", {
  trans <- transform(df, v)
  expect_s3_class(trans, "soma_adat")
  expect_equal(trans$seq.1234.56, df$seq.1234.56 * 2)
  expect_equal(trans$seq.9999.88, df$seq.9999.88 * 0.5)
  expect_named(trans, names(df))
})

test_that("`transform()` dispatches the `soma_adat` method and correctly scales (rows)", {
  vec <- c(1, 2, 3)
  trans <- transform(df, vec, 1L)
  expect_s3_class(trans, "soma_adat")
  expect_equal(trans$seq.1234.56, df$seq.1234.56 * vec)
  expect_equal(trans$seq.9999.88, df$seq.9999.88 * vec)
})