R/SparseDCParams-methods.R

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

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

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

    return(params)
}

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

    checks <- c(
        nGenes = checkmate::checkInt(v$nGenes, lower = 1),
        nCells = checkmate::checkInt(v$nCells, lower = 1),
        markers.n = checkmate::checkInt(
            v$markers.n,
            lower = 0,
            upper = v$nGenes
        ),
        markers.shared = checkmate::checkInt(
            v$markers.shared,
            lower = 0,
            upper = v$markers.n
        ),
        markers.same = checkmate::checkFlag(v$markers.same),
        clusts.c1 = checkmate::checkIntegerish(
            v$clusts.c1,
            lower = 1,
            any.missing = FALSE,
            min.len = 1
        ),
        clusts.c2 = checkmate::checkIntegerish(
            v$clusts.c2,
            lower = 1,
            any.missing = FALSE,
            min.len = 1
        ),
        mean.lower = checkmate::checkNumber(v$mean.lower, finite = TRUE),
        mean.upper = checkmate::checkNumber(v$mean.upper, finite = TRUE),
        seed = checkmate::checkInt(v$seed, lower = 0)
    )

    if (length(v$clusts.c1) == 1) {
        if (v$clusts.c1 > 1) {
            checks <- c(
                checks,
                clusts.c1 = "If clusts.c1 is length 1 it must equal 1"
            )
        }
    }

    if (length(v$clusts.c2) == 1) {
        if (v$clusts.c2 > 1) {
            checks <- c(
                checks,
                clusts.c2 = "If clusts.c2 is length 1 it must equal 1"
            )
        }
    }

    clusts.combined <- c(v$clusts.c1, v$clusts.c2)
    if (!all(seq_len(max(clusts.combined)) %in% clusts.combined)) {
        checks <- c(checks, clusts = "Cluster labels must be sequential")
    }

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

    return(valid)
})

setMethod("show", "SparseDCParams", function(object) {
    pp <- list(
        "Markers:" = c(
            "(Number)" = "markers.n",
            "(Shared)" = "markers.shared",
            "[Same]" = "markers.same"
        ),
        "Clusters:" = c(
            "(Condition 1)" = "clusts.c1",
            "(Condition 2)" = "clusts.c2"
        ),
        "Means:" = c(
            "[Lower]" = "mean.lower",
            "[Upper]" = "mean.upper"
        )
    )

    callNextMethod()
    showPP(object, pp)
})