tests/testthat/test-combine.R

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

context("c function expands ExperimentList and modifies sampleMap")

test_that("combine c function works", {
    mat <- matrix(rnorm(20), ncol = 4, dimnames = list(NULL, LETTERS[1:4]))
    myMulti <- MultiAssayExperiment(list(express = mat))
    mat2 <- matrix(rnorm(20), ncol = 4, dimnames = list(NULL, letters[1:4]))
    expect_error(c(myMulti, mat2)) # Unnamed list element
    # no sampleMap or mapFrom arg
    expect_error(c(myMulti, express2 = mat2))
    expect_true(validObject(c(myMulti, express2 = mat2, mapFrom = 1L)))
    expect_true(is(c(myMulti, express2 = mat2, mapFrom = 1L),
        "MultiAssayExperiment"))
})

test_that("combine c function works on multiple objects", {
    nrows <- 200
    ncols <- 6
    counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows)
    rowRanges <- GRanges(rep(c("chr1", "chr2"), c(50, 150)),
        IRanges(floor(runif(200, 1e5, 1e6)), width=100),
        strand=sample(c("+", "-"), 200, TRUE),
        feature_id=sprintf("ID%03d", 1:200))
    colData <- DataFrame(Treatment=rep(c("ChIP", "Input"), 3),
        row.names=LETTERS[1:6])
    rse <- SummarizedExperiment(assays=SimpleList(counts=counts),
        rowRanges=rowRanges, colData=colData)
    rse <- rse[, 1:4]

    library(RaggedExperiment)
    sample1 <- GRanges(c(a = "chr1:1-10:-", b = "chr1:11-18:+"), score = 1:2)
    sample2 <- GRanges(c(c = "chr2:1-10:-", d = "chr2:11-18:+"), score = 3:4)
    colDat <- DataFrame(id = 1:2)
    grl <- GRangesList(sample1 = sample1, sample2 = sample2)
    re <- RaggedExperiment(grl, colData = colDat)

    addMap <- DataFrame(assay = "RExp",
        primary = c("Jack", "Jill"),
        colname = c("sample1", "sample2"))
    addMap <- rbind(addMap, DataFrame(assay = "myRSE",
        primary = c("Jack", "Jill", "Bob", "Barbara"),
        colname = LETTERS[1:4]))
    expect_true(validObject(c(mae, RExp = re, myRSE = rse, sampleMap = addMap)))
})

test_that("concatenate two MultiAssayExperiment objects works", {
    ex3 <- experiments(mae)
    newasn <- paste0(names(mae), seq_along(mae))
    names(ex3) <- newasn

    cd3 <- colData(mae)
    newrns <- paste0(rownames(cd3), seq_along(rownames(cd3)))
    rownames(cd3) <- newrns

    maprn <- .setNames(newrns, rownames(colData(mae)))
    mapassay <- .setNames(newasn, names(mae))

    sm3 <- sampleMap(mae)
    sm3[["primary"]] <- maprn[sampleMap(mae)[["primary"]]]
    sm3[["assay"]] <- mapassay[sampleMap(mae)[["assay"]]]

    mae3 <- MultiAssayExperiment(ex3, cd3, sm3)
    combinedmae <- c(mae, mae3)

    expect_true(all(c(names(mae), names(mae3)) %in% names(combinedmae)))
    expect_true(all(unique(c(rownames(colData(mae)), newrns))
        %in% rownames(colData(combinedmae))))
})

test_that("concatenation of regular named list works", {
    elist <- ExpList
    names(elist) <- paste0(names(elist), seq_along(elist))

    expect_true(validObject(c(mae, as.list(elist))))
})

test_that("colData concatenation works with one column", {
    arraydat <- matrix(
        data = seq(101, length.out = 20),
        ncol = 4, dimnames = list(NULL, letters[1:4])
    )
    mae1 <- MultiAssayExperiment(
        ExperimentList(
            exp1 = SummarizedExperiment(arraydat),
            exp2 = SummarizedExperiment(arraydat)
        )
    )
    newcd <- DataFrame(foo = rep("bar", 4), row.names = letters[1:4])
    colData(mae1) <- newcd
    mae2 <- MultiAssayExperiment(
        ExperimentList(exp3 = SummarizedExperiment(arraydat))
    )
    expect_silent(
        mae <- c(mae1, mae2)
    )
    expect_true(validObject(mae))
    expect_identical(
        colData(mae),
        newcd
    )
})