tests/testthat/test-diversity_functions.R

In SU-CompBio/SplicingFactory: Splicing Diversity Analysis for Transcriptome Data

context("Basic diversity calculations")

test_that("Basic diversity calculation is working", {

    read_counts <- c(0, 0, 5, 4, 1)

    naive_entropy <- calculate_entropy(read_counts)

    expect_true(is.numeric(naive_entropy))
    expect_length(naive_entropy, 1)

    naive_entropy_norm <- calculate_entropy(read_counts, norm = FALSE)

    expect_true(is.numeric(naive_entropy_norm))
    expect_length(naive_entropy_norm, 1)
    expect_equal(naive_entropy_norm, 1.360964, tolerance = 0.001, scale = 1)

    laplace_entropy <- calculate_entropy(read_counts, pseudocount = 1)

    expect_true(is.numeric(laplace_entropy))
    expect_length(laplace_entropy, 1)
    expect_equal(laplace_entropy, 0.8465362, tolerance = 0.001, scale = 1)

    laplace_entropy_norm <- calculate_entropy(read_counts, norm = FALSE,
                                              pseudocount = 1)

    expect_true(is.numeric(laplace_entropy_norm))
    expect_length(laplace_entropy_norm, 1)
    expect_equal(laplace_entropy_norm, 1.965596, tolerance = 0.001, scale = 1)

    gini_coef <- calculate_gini(read_counts)

    expect_true(is.numeric(gini_coef))
    expect_length(gini_coef, 1)
    expect_equal(gini_coef, 0.7, tolerance = 0.001, scale = 1)

    simpson_index <- calculate_simpson(read_counts)

    expect_true(is.numeric(simpson_index))
    expect_length(simpson_index, 1)
    expect_equal(simpson_index, 0.58, tolerance = 0.001, scale = 1)

    invsimpson_index <- calculate_inverse_simpson(read_counts)

    expect_true(is.numeric(invsimpson_index))
    expect_length(invsimpson_index, 1)
    expect_equal(invsimpson_index, 2.380952, tolerance = 0.001, scale = 1)

})

test_that("Diversity calculation of single isoforms", {

    read_counts_single <- c(1)

    naive_entropy_single <- calculate_entropy(read_counts_single)

    expect_true(is.nan(naive_entropy_single))

})

test_that("Diversity calculation of zero expression", {

    read_counts_zero <- c(0, 0)

    naive_entropy_zero <- calculate_entropy(read_counts_zero)

    expect_true(is.na(naive_entropy_zero))

})