R/BASiCSParams-methods.R

In Oshlack/splatter: Simple Simulation of Single-cell RNA Sequencing Data

#' @rdname newParams
#' @importFrom methods new
#' @export
newBASiCSParams <- function(...) {
    checkDependencies("BASiCS")

    params <- new("BASiCSParams")
    params <- setParams(params, ...)

    return(params)
}

#' @importFrom checkmate checkInt checkDataFrame checkNumeric
setValidity("BASiCSParams", function(object) {
    object <- expandParams(object)
    v <- getParams(object, slotNames(object))

    nCells <- v$nCells
    nGenes <- v$nGenes
    nBatches <- v$nBatches
    checks <- c(
        seed = checkInt(v$seed, lower = 0),
        nGenes = checkInt(v$nGenes, lower = 1),
        nCells = checkInt(v$nCells, lower = 1),
        nBatches = checkInt(v$nBatches, lower = 1),
        batchCells = checkIntegerish(
            v$batchCells,
            lower = 1,
            len = nBatches
        ),
        gene.params = checkDataFrame(
            v$gene.params,
            types = "numeric",
            any.missing = FALSE,
            min.rows = 1,
            ncols = 2
        ),
        nSpikes = checkNumber(v$nSpikes, lower = 0, finite = TRUE),
        spike.means = checkNumeric(v$spike.means,
            lower = 0,
            finite = TRUE
        ),
        cell.params = checkDataFrame(
            v$cell.params,
            types = "numeric",
            any.missing = FALSE,
            min.rows = 1,
            ncols = 2
        ),
        theta = checkNumeric(
            v$theta,
            lower = 0,
            len = nBatches,
            finite = TRUE
        )
    )

    if (!all(colnames(v$gene.params) == c("Mean", "Delta"))) {
        checks <- c(checks, gene.params = "Incorrect column names")
    }

    if (!all(colnames(v$cell.params) == c("Phi", "S"))) {
        checks <- c(checks, cell.params = "Incorrect column names")
    }

    # Check batchCells matches nCells, nBatches
    if (nCells != sum(v$batchCells) || nBatches != length(v$batchCells)) {
        checks <- c(
            checks,
            "nCells, nBatches and batchCells are not consistent"
        )
    }

    if (all(checks == TRUE)) {
        valid <- TRUE
    } else {
        valid <- checks[checks != TRUE]
        valid <- paste(names(valid), valid, sep = ": ")
    }

    return(valid)
})

#' @rdname setParam
setMethod("setParam", "BASiCSParams", function(object, name, value) {
    checkmate::assertString(name)

    if (name == "nCells" || name == "nBatches") {
        stop(name, " cannot be set directly, set batchCells instead")
    }

    if (name == "batchCells") {
        object <- setParamUnchecked(object, "nCells", sum(value))
        object <- setParamUnchecked(object, "nBatches", length(value))
    }

    object <- callNextMethod()

    return(object)
})

setMethod("show", "BASiCSParams", function(object) {
    pp <- list(
        "Genes:" = c("(Params)" = "gene.params"),
        "Cells:" = c("(Params)" = "cell.params"),
        "Batches:" = c(
            "(Batches)" = "nBatches",
            "(Batch Cells)" = "batchCells"
        ),
        "Spike-ins:" = c(
            "(Number)" = "nSpikes",
            "(Means)" = "spike.means"
        ),
        "Variability:" = c("(Theta)" = "theta")
    )

    callNextMethod()

    showPP(object, pp)
})

#' @rdname expandParams
setMethod("expandParams", "BASiCSParams", function(object) {
    n <- getParam(object, "nBatches")

    vectors <- c("theta")

    object <- paramsExpander(object, vectors, n)

    return(object)
})