R/MFAParams-methods.R

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

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

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

    return(params)
}

setValidity("MFAParams", function(object) {
    v <- getParams(object, slotNames(object))

    checks <- c(
        nGenes = checkmate::checkInt(v$nGenes, lower = 1),
        nCells = checkmate::checkInt(v$nCells, lower = 1),
        trans.prop = checkmate::checkNumber(
            v$trans.prop,
            lower = 0,
            upper = 1
        ),
        zero.neg = checkmate::checkLogical(
            v$zero.neg,
            any.missing = FALSE,
            len = 1
        ),
        dropout.present = checkmate::checkLogical(
            v$dropout.present,
            any.missing = FALSE,
            len = 1
        ),
        dropout.lambda = checkmate::checkNumber(v$dropout.lambda),
        seed = checkmate::checkInt(v$seed, lower = 0)
    )

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

    return(valid)
})

setMethod("show", "MFAParams", function(object) {
    pp <- list(
        "Transient:" = c("[Proportion]" = "trans.prop"),
        "Negative:" = c("[Zero]" = "zero.neg"),
        "Dropout:" = c(
            "[Present]" = "dropout.present",
            "(Lambda)" = "dropout.lambda"
        )
    )

    callNextMethod()
    showPP(object, pp)
})