tests/testthat/test-0utilites.R

In FelixErnst/mia: Microbiome analysis

context("meltSE")
test_that("meltSE", {
    # .norm_add_row_data
    expect_error(
        mia:::.norm_add_row_data(), 'argument "add.row" is missing')
    expect_error(
        mia:::.norm_add_row_data(TRUE), 'argument "x" is missing')
    expect_error(
        mia:::.norm_add_row_data(.internal_MARGIN = "col"),
        'argument "add.row" is missing')
    expect_error(
        mia:::.norm_add_row_data(TRUE, .internal_MARGIN = "col"),
        'argument "x" is missing')
    #
    data(GlobalPatterns, package="mia")
    x <- GlobalPatterns
    actual <- mia:::.norm_add_row_data(TRUE, x, "FeatureID")
    expect_equal(actual, colnames(rowData(x)))
    actual <- mia:::.norm_add_row_data(
        TRUE, x, "SampleID", .internal_MARGIN = "col")
    expect_equal(actual, colnames(colData(x)))
    expect_error(
        mia:::.norm_add_row_data("test", x),
        paste0("All columns specified by 'add.row' must match with columns ",
            "in rowData()"))
    expect_error(
        mia:::.norm_add_row_data("test", x, .internal_MARGIN = "col"),
        paste0("All columns specified by 'add.col' must match with columns in ",
            "colData()"))
    x2 <- x
    rowData(x2)$FeatureID <- rownames(x2)
    colData(x2)$SampleID <- colnames(x2)
    expect_error(
        mia:::.norm_add_row_data(NA, x, "FeatureID"), "'add.row' contains NA")
    expect_error(
        mia:::.norm_add_row_data(NA, x, "SampleID", .internal_MARGIN = "col"),
        "'add.col' contains NA")
    #
    # Check that melting works correctly
    se <- GlobalPatterns
    molten_assay <- meltSE(
        se,
        add.row = TRUE,
        add.col = c("X.SampleID", "Primer"),
        assay.type = "counts")
    expect_s3_class(molten_assay, c("tbl_df","tbl","data.frame"))
    expect_equal(
        colnames(molten_assay)[c(1:4,11)],
        c("FeatureID","SampleID","counts","Kingdom","X.SampleID"))
    expect_equal(is.numeric(molten_assay$counts), TRUE)
    #
    only_assay <- meltSE(se, assay.type = "counts")
    expect_equal(colnames(only_assay)[1:3], c("FeatureID","SampleID","counts"))
    expect_equal(is.numeric(only_assay$counts), TRUE)
    # Check that adding row/colData works
    assay_taxa <- mia:::.add_row_data_to_molten_assay(
        only_assay,
        se,
        add.row = taxonomyRanks(se),
        "FeatureID")
    expect_equal(
        colnames(assay_taxa)[1:4],
        c("FeatureID","SampleID","counts","Kingdom"))
    expect_equal(is.numeric(assay_taxa$counts), TRUE)
    #
    assay_taxa_coldata <- mia:::.add_row_data_to_molten_assay(
        assay_taxa,
        se, FALSE,
        "SampleID", .internal_MARGIN = "col")
    expect_equal(
        colnames(molten_assay)[c(1:4,11)],
        c("FeatureID","SampleID","counts","Kingdom","X.SampleID"))
    expect_equal(is.numeric(assay_taxa_coldata$counts), TRUE)
    #
    # Test melting with different options
    actual <- meltSE(x, add.row = TRUE, add.col = TRUE)
    # Should give warning that FeatureID and SampleID columns are renamed
    expect_warning(actual2 <- meltSE(x2, add.row = TRUE, add.col = TRUE))
    # Should not give warning since row/colData are not added
    expect_no_warning(meltSE(x2, add.row = FALSE, add.col = FALSE))
    expect_false("FeatureID_row" %in% colnames(actual))
    expect_true("FeatureID_row" %in% colnames(actual2))
    expect_false("SampleID_col" %in% colnames(actual))
    expect_true("SampleID_col" %in% colnames(actual2))
    x3 <- x2
    rownames(x3) <- NULL
    colnames(x3) <- NULL
    # Should give warning that col/rownames are added and that FeatureID and
    # SampleID columns are renamed
    expect_warning(
        actual3 <- meltSE(x3, add.row = TRUE, add.col = TRUE)
    )
    expect_false("FeatureID_row" %in% colnames(actual))
    expect_false("SampleID_col" %in% colnames(actual))
    #
    x4 <- se
    # Change names to 1, 2, 3... format
    colnames(x4) <- seq_along(colnames(x4))
    melted <- meltSE(x4, assay.type = "counts", add.col = TRUE)
    melted2 <- meltSE(
        x4, assay.type = "counts", add.col = TRUE, check_names = TRUE)
    # There should not be any NAs
    expect_true(any(!(is.na(melted))))
    expect_true(any(!(is.na(melted2))))
    # Remove prefix from sample names
    melted2$SampleID <- as.factor(
        gsub(pattern = "X", replacement = "", x = melted2$SampleID))
    expect_equal(melted, melted2)
})

context("getTop")
test_that("", {
    #
    expect_error(mia:::.check_max_taxa(),
                 'argument "top" is missing')
    expect_error(mia:::.check_max_taxa(GlobalPatterns),
                 'argument "top" is missing')
    expect_error(mia:::.check_max_taxa(GlobalPatterns, 5L),
                 'argument "assay.type" is missing')
    expect_null(mia:::.check_max_taxa(GlobalPatterns, 5L, "counts"))
    expect_error(mia:::.check_max_taxa(GlobalPatterns, 100000000, "counts"),
                 "'top' must be <= nrow(x)",fixed=TRUE)
    #
    data(GlobalPatterns, package="mia")
    mean.taxa <- c("549656", "331820", "279599", "360229", "317182")
    sum.taxa <- c("549656", "331820", "279599", "360229", "317182")
    median.taxa <- c("549656", "331820", "317182", "94166",  "279599")
    top_mean <- getTop(GlobalPatterns, method="mean", top=5,
                           assay.type="counts")
    top_sum <- getTop(GlobalPatterns, method="sum", top=5,
                          assay.type="counts")
    top_median <- getTop(GlobalPatterns, method="median", top=5,
                             assay.type="counts")
    expect_equal(top_mean, mean.taxa)
    expect_equal(top_sum, sum.taxa)
    expect_equal(top_median, median.taxa)
})