tests/testthat/test-clinical_outcomes_functions.R

In CRI-iAtlas/iatlas-app: What the Package Does (One Line, Title Case)

test_that("build_co_survival_list", {
    res1 <- build_co_survival_list(iatlas.modules2::tcga_immune_subtype_cohort_obj_small$feature_tbl)
    expect_named(res1)
    expect_vector(res1)
    res2 <- build_co_survival_list(iatlas.modules2::tcga_bin_cohort_obj_small$feature_tbl)
    expect_named(res2)
    expect_vector(res2)
})

test_that("get_co_status_feature", {
    expect_equal(get_co_status_feature("PFI_time_1"), "PFI_1")
    expect_equal(get_co_status_feature("OS_time"), "OS")
    expect_error(get_co_status_feature("not_a_feature"), "Unknown time feature")
})

survival_tbl1 <- build_co_survival_value_tbl(iatlas.modules2::tcga_immune_subtype_cohort_obj_small, "OS_time", "OS")
survival_tbl2 <- build_co_survival_value_tbl(iatlas.modules2::tcga_bin_cohort_obj_small, "OS_time", "OS")

test_that("Build Survival Values Tibble", {
    expect_named(survival_tbl1, c("sample", "group", "time", "status"))
    expect_named(survival_tbl2, c("sample", "group", "time", "status"))
})

feature_tbl1 <- build_co_feature_tbl(
    iatlas.modules2::tcga_immune_subtype_cohort_obj_small, "DNA Alteration"
)
feature_tbl2 <- build_co_feature_tbl(
    iatlas.modules2::tcga_bin_cohort_obj_small, "DNA Alteration"
)

test_that("build_co_feature_tbl", {
    expected_columns <- c(
        "sample",
        "feature_display",
        "feature_value",
        "feature_order"
    )
    expect_named(feature_tbl1, expected_columns)
    expect_named(feature_tbl2, expected_columns)
})

heatmap_tbl1 <- build_co_heatmap_tbl(survival_tbl1, feature_tbl1)
heatmap_tbl2 <- build_co_heatmap_tbl(survival_tbl2, feature_tbl2)

test_that("build_co_heatmap_tbl", {
    expected_columns <- c(
        "sample",
        "group",
        "time",
        "status",
        "feature_display",
        "feature_value",
        "feature_order"
    )
    expect_named(heatmap_tbl1, expected_columns)
    expect_named(heatmap_tbl2, expected_columns)
})

heatmap_matrix1 <- build_co_heatmap_matrix(heatmap_tbl1)

test_that("Build Heatmap Matrix", {
    expect_type(heatmap_matrix1, "double")
    expected_rownames <- c(
        "Nonsilent Mutation Rate",
        "SNV Neoantigen",
        "Indel Neoantigen",
        "Intratumor Heterogeneity",
        "Aneuploidy Score",
        "Number of Segments",
        "Fraction Altered",
        "Homologous Recombination Deficiency",
        "Number of Segments with LOH",
        "Fraction of Segments with LOH",
        "Silent Mutation Rate"
    )
    expect_equal(rownames(heatmap_matrix1), expected_rownames)

    expected_colnames <- c("C4", "C5", "C6")
    expect_equal(colnames(heatmap_matrix1), expected_colnames)
})