tests/testthat/test-external_indices.R

In selinj/chromswitch: An R package to detect chromatin state switches from epigenomic data

context("External cluster validity functions")


test_that("External cluster validity indices are correct", {

    metadata <- data.frame(Sample = c("A", "B", "C", "D"),
                           Condition = c(1, 1, 2, 2),
                           stringsAsFactors = FALSE)

    exp <- data.frame(Var1 = c("1", "2", "1", "2"),
                      Var2 = c("0", "0", "1", "1"),
                      Freq = c(0, 2, 2, 0),
                      stringsAsFactors = FALSE)
    exp$Var1 <- factor(exp$Var1)
    exp$Var2 <- factor(exp$Var2)

    clusters <- c(A = 1, B = 1, C = 0, D = 0)

    expect_equal(data.frame(contingencyTable(clusters, metadata),
                            stringsAsFactors = FALSE),
                 exp)

    clusters <- c(0, 0, 2, 1, 1, 0, 1)
    classes <- c("A", "A", "A", "B", "B", "A", "B")
    ct <- table(classes, clusters)

    expect_equal(purity(contingency = ct), 1)
    expect_equal(purity(c = classes, k = clusters), 1)

    expect_equal(classEntropy(ct), 0.6829081)
    expect_equal(clusterEntropy(ct), 1.004242, tolerance = 1e-6)

    expect_equal(conditionalClassEntropy(ct), 0)
    expect_equal(conditionalClusterEntropy(ct), 0.3213344, tolerance = 1e-6)

    expect_equal(homogeneity(ct), 1)
    expect_equal(completeness(ct), 0.6800231, tolerance = 1e-6)
    expect_equal(vMeasure(ct), 0.8095402)

    expect_equal(NMI(clusters, classes), 0.8246351, tolerance = 1e-6)

})