R/depecheAllData.R

In DepecheR: Determination of essential phenotypic elements of clusters in high-dimensional entities

# This function is used by depecheCoFunction.
# It is only used for datasets with less than 10 000 total observations.
# "Unique" parameters
# inDataFrameUsed: the scaled version of inDataFrame. See initial part of
# depeche function for details.
# firstClusterNumber: this defines if the first number for the cluster
# definitions.
# For information on the other parameters, see depeche.
#' @importFrom parallel detectCores makeCluster stopCluster
#' @importFrom doSNOW registerDoSNOW
#' @importFrom foreach foreach %dopar%
#' @importFrom moments kurtosis
#' @importFrom foreach foreach %dopar%
#' @importFrom gplots heatmap.2
#' @importFrom dplyr sample_n
depecheAllData <- function(inDataFrameUsed, penalty, k, nCores) {
    penaltyForRightSize <- penalty * ((nrow(inDataFrameUsed) *
        sqrt(ncol(inDataFrameUsed))) / 1450)

    dataMat <- data.matrix(inDataFrameUsed)

    if (nCores == "default") {
        nCores <- floor(detectCores() * 0.875)
        if (nCores > 10) {
            nCores <- 10
        }
    }

    i <- 1
    cl <- makeCluster(nCores, type = "SOCK")
    registerDoSNOW(cl)
    return_all <- foreach(i = seq_len(21), .packages = "DepecheR") %dopar%
        sparse_k_means(dataMat, round(k * 3), penaltyForRightSize, 1, i)
    stopCluster(cl)

    # Here, the best iteration is retrieved,
    # if this is not one with only 1 cluster

    logMaxLik <- as.vector(do.call("rbind", lapply(return_all, "[[", 5)))
    nClust <- vapply(return_all,
        FUN.VALUE = 1,
        function(x) sum(rowSums(x[[3]] != 0) != 0)
    )
    logMaxLikNotOne <- logMaxLik[which(nClust > 1)]
    maxN <- max(logMaxLikNotOne)
    returnLowest <- return_all[[which(logMaxLik == maxN)[1]]]

    # And here, the optimal results are retrieved
    clusterVector <- returnLowest$i
    clusterCenters <- returnLowest$c

    # And here, the optimal results are made
    # more dense by removing empty rows and
    # columns, etc.

    colnames(clusterCenters) <- colnames(inDataFrameUsed)

    # Remove all rows and columns that do not
    # contain any information
    reducedClusterCenters <- clusterCenters[
        which(rowSums(clusterCenters) != 0),
        which(colSums(clusterCenters) != 0)
    ]

    # In the specific case that only one row
    # is left, due to a high penalty, the
    # data needs to be converted back to a
    # matrix from a vector. The same is done
    # if the number of informative variables
    # is just one.
    if (length(which(rowSums(clusterCenters) != 0)) == 1) {
        reducedClusterCenters <- t(reducedClusterCenters)
    } else if (length(which(colSums(clusterCenters) != 0) == 1)) {
        reducedClusterCenters <- as.matrix(reducedClusterCenters)
    }

    # Here, the results are combined
    dClustResult <- list(clusterVector, reducedClusterCenters)
    names(dClustResult) <- c("clusterVector", "clusterCenters")
    return(dClustResult)
}