tests/testthat/test-MultiAssayExperiment-helpers.R

In MultiAssayExperiment: Software for the integration of multi-omics experiments in Bioconductor

test_that("MultiAssayExperiment anyReplicated returns same order", {
    m <- matrix(0, 3, 3, dimnames=list(letters[1:3], letters[1:3]))
    m2 <- matrix(0, 0, 0)
    m3 <- matrix(0, 1, 1, dimnames=list("d", "d"))
    m4 <- matrix(0, 4, 4, dimnames=list(LETTERS[1:4], LETTERS[1:4]))
    obs <- MultiAssayExperiment(list(m=m, m2=m2, m3=m3))
    m4map <- DataFrame(
        assay = rep("m4", 4),
        primary = c("a", "a", "b", "d"),
        colname = LETTERS[1:4]
    )
    obs2 <- c(obs, m4 = m4, sampleMap = m4map)
    expect_true(
        length(replicated(obs2)[["m4"]]) == length(unique(m4map[["primary"]]))
    )
    expect_true(
        all.equal(
        vapply(replicated(obs2), function(x) unique(lengths(x)), integer(1L)),
        lengths(Filter(length, colnames(obs2)))
        )
    )

    expect_identical(
        lapply(replicated(obs), names),
        lapply(mapToList(sampleMap(obs)), function(x) x[["primary"]])
    )

    ## test primary is identical to colnames
    cnames <- lapply(mapToList(sampleMap(obs)), `[[`, "colname")
    expect_identical(
        IRanges::CharacterList(cnames), Filter(length, colnames(obs))
    )
})

test_that("getWithColData works", {
    Y1 <- matrix(rnorm(200), ncol=10)
    colnames(Y1) <- c("A.1", "A.2",
        "B.1", "B.2", "B.3",
        "C.1", "C.2",
        "D.1",
        "E.1", "E.2")

    # Making up some sample-level metadata, for some variety.
    df <- DataFrame(RIN=runif(10), sizeFactor=runif(10))
    rownames(df) <- colnames(Y1)
    se1 <- SummarizedExperiment(list(counts=Y1), colData=df)

    ### EXPERIMENT 2 ###
    Y2 <- matrix(rnorm(200), ncol=5)
    colnames(Y2) <- c("B", "C", "D", "E", "F")

    # Making up some more sample-level metadata.
    df <- DataFrame(FrIP=runif(5), NumPeaks=sample(1000, 5))
    rownames(df) <- colnames(Y2)
    se2 <- SummarizedExperiment(list(counts=Y2), colData=df)

    sampleMap <- rbind(
        DataFrame(assay="rnaseq",
            primary=sub("\\..*", "", colnames(se1)),
            colname=colnames(se1)
        ),
        DataFrame(assay="chipseq",
            primary=sub("\\..*", "", colnames(se2)),
            colname=colnames(se2)
        )
    )

    colData <- DataFrame(
        row.names=LETTERS[1:6],
        Sex=sample(c("M", "F"), 6, replace=TRUE),
        Age=sample(10:50, 6)
    )

    MAE <- MultiAssayExperiment(list(rnaseq=se1, chipseq=se2),
        sampleMap=sampleMap, colData=colData)

    expect_warning(
        getWithColData(MAE, 1L, "append")
    )

    expect_warning(
        getWithColData(MAE, 1L, "replace")
    )

    cData <- colData(getWithColData(MAE, 1L, "append"))
    cDataMatch <- cData[, names(colData), drop = FALSE]
    matchedData <- colData[
        match(mapToList(sampleMap)[[1]][["primary"]], rownames(colData)), ,
        drop = FALSE]
    testres <- unlist(
        Map(function(x, y) { identical(x, y) }, x = cDataMatch, y = matchedData)
    )
    expect_true( all(testres) )

    expect_identical(
        names(cData),
        c(names(colData(MAE[[1]])), names(colData))
    )
    expect_identical(
        colData(se1),
        cData[, names(colData(se1))]
    )
    testres <- unlist(
        Map(function(x, y) { identical(x, y) },
            x = colData(se1), y = cData[, names(colData(se1))])
    )
    expect_true( all(testres) )

    cData <- colData(getWithColData(MAE, 1L, "replace"))
    cDataMatch <- cData[, names(colData), drop = FALSE]
    matchedData <- colData[
        match(mapToList(sampleMap)[[1L]][["primary"]], rownames(colData)), ,
        drop = FALSE]
    expect_identical(cDataMatch, matchedData)

    ## Empty MAE colData return assay colData
    MAE0 <- MAE
    colData(MAE0) <- DataFrame(row.names = rownames(colData(MAE0)))
    cData <- colData(getWithColData(MAE0, 1L, "append"))
    expect_identical(
        cData,
        colData(se1)
    )

    MAE0 <- MAE
    colData(MAE0) <- DataFrame(row.names = rownames(colData(MAE0)))
    cData <- colData(getWithColData(MAE0, 1L, "replace"))

    expect_identical(
        cData,
        DataFrame(row.names = mapToList(sampleMap(MAE0))[[1]][["primary"]])
    )
    expect_true( isEmpty(cData) )

    ## Empty assay colData return MAE colData
    MAE0 <- MAE
    eCol <- DataFrame(row.names = rownames(colData(MAE0[["rnaseq"]])))
    colData(MAE0[["rnaseq"]]) <- eCol
    cData <- colData(getWithColData(MAE0, 1L, "replace"))
    matchedData <- colData(MAE0)[
        match(mapToList(sampleMap(MAE0))[["rnaseq"]][["primary"]],
            rownames(colData)), ,
        drop = FALSE]
    expect_identical(cData, matchedData)


    MAE0 <- MAE
    eCol <- DataFrame(row.names = rownames(colData(MAE0[["rnaseq"]])))
    colData(MAE0[["rnaseq"]]) <- eCol
    cData <- colData(getWithColData(MAE0, 1L, "append"))
    matchedData <- colData(MAE0)[
        match(mapToList(sampleMap(MAE0))[["rnaseq"]][["primary"]],
            rownames(colData)), ,
        drop = FALSE]
    expect_identical(cData, matchedData)
})