tests/testthat/test-normalization.R

In sipss/AlpsNMR: Automated spectraL Processing System for NMR

test_that("nmr_normalize & nmr_normalize_extra_info work", {
    dataset <- new_nmr_dataset_1D(
        ppm_axis = 1:10,
        data_1r = matrix(sample(0:99, replace = TRUE), nrow = 10),
        metadata = list(external = data.frame(
            NMRExperiment = c("10", "20", "30", "40", "50", "60", "70", "80", "90", "100")
        ))
    )
    dataset <- nmr_normalize(dataset, method = "pqn")
    diagnostic <- nmr_normalize_extra_info(dataset)
    expect_true(is.matrix(dataset[["data_1r"]]))
    expect_true(is.numeric(dataset[["data_1r"]][[1]]))
    expect_true(is.list(diagnostic))
    expect_true(is.data.frame(diagnostic[["norm_factor"]]))
    expect_true(is.character(diagnostic[["norm_factor"]][[1, 1]]))
})

test_that("nmr_normalize with negative values and below 10 samples work", {
    dataset <- new_nmr_dataset_1D(
        ppm_axis = 1:10,
        data_1r = matrix(sample(-1:88, replace = FALSE), nrow = 9),
        metadata = list(external = data.frame(NMRExperiment = c("10", "20", "30", "40", "50", "60", "70", "80", "90")))
    )
    expect_warning(nmr_normalize(dataset, method = "pqn"))
})

test_that("nmr_normalize works with unknown method", {
    dataset <- new_nmr_dataset_1D(
        ppm_axis = 1:10,
        data_1r = matrix(sample(-1:88, replace = FALSE), nrow = 9),
        metadata = list(external = data.frame(NMRExperiment = c("10", "20", "30", "40", "50", "60", "70", "80", "90")))
    )
    dataset_none <- nmr_normalize(dataset, method = "none")
    dataset_area <- nmr_normalize(dataset, method = "area")
    dataset_max <- nmr_normalize(dataset, method = "max")
    dataset_ <- nmr_normalize(dataset)

    expect_true(is.matrix(dataset_none[["data_1r"]]))
    expect_true(is.matrix(dataset_area[["data_1r"]]))
    expect_true(is.matrix(dataset_max[["data_1r"]]))
    expect_true(is.matrix(dataset_[["data_1r"]]))
})