tests/testthat/test-transforms.R

In rafalab/smallcount: Methods for Small Counts Stored in a Sparse Matrix

test_that("Identity transformation succeeds", {
    data <- rbind(
        c(1, 2, 3),
        c(4, 5, 6),
        c(7, 8, 9)
    )
    sparse_data <- as(data, "SparseMatrix")

    tmatrix <- TransformedMatrix(sparse_data, identity_transform())
    expect_equal(as.matrix(tmatrix), data)
})

test_that("Row centering succeeds", {
    data <- rbind(
        c(1, 2, 3),
        c(2, 4, 6),
        c(3, 6, 9)
    )
    sparse_data <- as(data, "SparseMatrix")

    row_centered_data <- rbind(
        c(-1, 0, 1),
        c(-2, 0, 2),
        c(-3, 0, 3)
    )

    row_center_transform <- identity_transform(center = TRUE)
    tmatrix <- TransformedMatrix(sparse_data, row_center_transform)
    expect_equal(as.matrix(tmatrix), row_centered_data)
})

test_that("Row normalization succeeds", {
    data <- rbind(
        c(1, 0, -1),
        c(3, 1, -1),
        c(6, 1, -4)
    )
    sparse_data <- as(data, "SparseMatrix")

    row_normalized_data <- rbind(
        c(1, 0, -1),
        c(1, 0, -1),
        c(1, 0, -1)
    )

    row_normalize_transform <- identity_transform(center = TRUE, scale = TRUE)
    tmatrix <- TransformedMatrix(sparse_data, row_normalize_transform)
    expect_equal(as.matrix(tmatrix), row_normalized_data)
})

test_that("Column centering succeeds", {
    data <- rbind(
        c(1, 2, 3),
        c(2, 4, 6),
        c(3, 6, 9)
    )
    sparse_data <- as(data, "SparseMatrix")

    col_centered_data <- rbind(
        c(-1, -2, -3),
        c(0, 0, 0),
        c(1, 2, 3)
    )

    col_center_transform <- identity_transform(center = c(FALSE, TRUE))
    tmatrix <- TransformedMatrix(sparse_data, col_center_transform)
    expect_equal(as.matrix(tmatrix), col_centered_data)
})

test_that("Log1p transformations succeed", {
    data <- rbind(
        c(1, 2, 3),
        c(4, 5, 6),
        c(7, 8, 9)
    )
    sparse_data <- as(data, "SparseMatrix")

    tmatrix1 <- TransformedMatrix(sparse_data, log1p_transform())
    expect_equal(as.matrix(tmatrix1), log(data + 1))

    tmatrix2 <- TransformedMatrix(sparse_data, cpm_log1p_transform())
    expect_equal(as.matrix(tmatrix2), log(data / 1000000 + 1))

    tmatrix3 <- TransformedMatrix(sparse_data, scaled_log1p_transform(3))
    expect_equal(as.matrix(tmatrix3), log(3 * data + 1))
})