tests/testthat/test_computeSpillmat.R

In CATALYST: Cytometry dATa anALYSis Tools

library(flowCore)

test_that("computeSpillmat()", {
    # generate some dummy testdata with ss_exp as a template
    data(ss_exp); set.seed(12345); n_cells <- 100

    # generate a known spillover matrix
    chs <- colnames(ss_exp)
    sm <- diag(n_chs <- ncol(ss_exp))
    colnames(sm) <- rownames(sm) <- chs
    # add isotope, +/-1, +16 specific spillover
    sm_ms <- .get_ms_from_chs(chs)
    sm_mets <- .get_mets_from_chs(chs)

    for (i in seq_along(sm_ms)){
        ch_i <- chs[i]
        curmass <- sm_ms[i]
        curmet <- sm_mets[i]
        iso <- sm_mets == sm_ms[i]
        p1 <- sm_ms == sm_ms[i] + 1
        m1 <- sm_ms == sm_ms[i] - 1
        ox <- sm_ms == sm_ms[i] + 16
        spill_cols <- chs[(iso | p1 | m1 | ox) & (chs != chs[i])]
        sm[chs[i], spill_cols] <- runif(length(spill_cols)) / 20
    }

    # generate 100 cells that are positive for each channel
    mat <- do.call(rbind, replicate(n_cells, diag(n_chs), simplify = FALSE))

    # add noise & spillover
    mat <- mat * (rnorm(n_chs * n_cells, 1, 0.01)) * 100
    mat_sm <- mat %*% sm

    # construct SCE & debarcode
    sce <- prepData(flowFrame(mat_sm), by_time = FALSE)
    sce <- assignPrelim(sce, sm_ms, verbose = FALSE)
    # set barcode IDs to constructed IDs
    sce$bc_id <- rep(as.character(sm_ms), n_cells)
    # estimate spillover matrix
    sce <- computeSpillmat(sce)
    sm_est <- metadata(sce)$spillover_matrix
    expect_equal(sm_est, sm, info = c(
        "test if spillover matrix can be reconstructed",
        "from simulated single cells without noise."))

    # repeat with a constant amount of background
    sce <- prepData(flowFrame(mat_sm + 20), by_time = FALSE)
    sce <- assignPrelim(sce, sm_ms, verbose = FALSE)
    sce$bc_id <- rep(as.character(sm_ms), n_cells)
    sce <- computeSpillmat(sce)
    sm_est <- metadata(sce)$spillover_matrix
    expect_equal(sm_est, sm, info = c(
        "test if spillover matrix can be reconstructed",
        "from simulated single cells without noise but with background."))

    noise <- rnorm(n_chs * n_cells, 5, 1)
    sce <- prepData(flowFrame(mat_sm * noise), by_time = FALSE)
    sce <- assignPrelim(sce, sm_ms, verbose = FALSE)
    sce$bc_id <- rep(as.character(sm_ms), n_cells)
    sce <- computeSpillmat(sce)
    sm_est <- metadata(sce)$spillover_matrix
    expect_equal(sm_est, sm, info = c(
        "test if spillover matrix can be reconstructed",
        "from simulated single cells without noise but with background."))
})