R/process.each.node.R

In kridsadakorn/ipcaps.bioc: Iterative Pruning to Capture Population Structure

#' (Internal function) Perform the iterative process for each node
#'
#' @param node An integer representing the current node number which is being
#' analyzed.
#' @param work.dir A working directory.
#'
#' @return \code{NULL}
#'
#' @include clustering.R
#'
#'
process.each.node <- function(node, work.dir)
{
    start.time <- Sys.time()

    label <- NULL
    raw.data <- NULL
    threshold <- NULL
    min.fst <- NULL
    method <- NULL
    min.in.group <- NULL
    datatype <- NULL
    nonlinear <- NULL
    result.dir <- NULL
    silence.mode <- NULL

    # load tree list, no need to lock file, just reading info from the file
    file.name <- file.path(work.dir, "RData", "condition.RData")
    load(file = file.name)
    file.name <- file.path(work.dir, "RData", "tree.RData")
    if (!silence.mode)
        cat(paste0("Node ", node, ": Loading ", file.name, "\n"))

    e <- globalenv()$myenv

    if (isTRUE(e$global.lock))
    {
        Sys.sleep(runif(1, min = 0, max = 2))
    } else
    {
        e$global.lock <- TRUE
        load(file = file.name)
        e$global.lock <- FALSE
    }

    if (!silence.mode)
        cat(paste0("Node ", node, ": Start the process\n"))

    which.row <- which(tree$node == node)
    # Status -1 = deleted node due to error
    if (tree$status[which.row[1]] != -1)
    {
        # load experiment condition
        file.name <- file.path(work.dir, "RData", "condition.RData")
        if (!silence.mode)
            cat(paste0("Node ", node, ": Loading ", file.name, "\n"))
        load(file = file.name)


        # load raw data
        file.name <- file.path(work.dir, "RData", "rawdata.RData")
        if (!silence.mode)
            cat(paste0("Node ", node, ": Loading ", file.name, "\n"))
        load(file = file.name)
        ref.label <- label

        # load node data
        file.name <-
            file.path(work.dir, "RData", paste0("node", node,
                                                ".RData"))
        if (!silence.mode)
            cat(paste0("Node ", node, ": Loading ", file.name, "\n"))
        load(file = file.name)
        ref.index <- index

        dataframe <- list(raw.data = raw.data[ref.index, ],
                        label = ref.label[ref.index],
                        index = ref.index)

        if (!silence.mode)
            cat(paste0("Node ", node, ": Check for splitting\n"))
        res <- clustering(
            dataframe,
            node,
            work.dir,
            threshold,
            min.fst,
            method,
            min.in.group,
            datatype,
            nonlinear
        )
        # list.new.node = data.frame()
        if (!silence.mode)
            cat(paste0("Node ", node, ": Return status ", res$status, "\n"))
        if (res$status == 0)
        {
            if (!silence.mode)
                cat(paste0("Node ", node, ": Split to sub-nodes\n"))

            # serial loop
            for (i in seq(1, length(res$new.index)))
            {
                file.name <- file.path(work.dir, "RData", "tree.RData")
                load(file = file.name)
                new.node <- max(tree$node) + 1

                tree <- rbind(tree,
                            c(
                                node = new.node,
                                parent.node = node,
                                status = 0
                            ))

                if (isTRUE(e$global.lock))
                {
                    Sys.sleep(runif(1, min = 0, max = 2))
                } else
                {
                    e$global.lock <- TRUE
                    save(tree,
                        file = file.name,
                        compress = "bzip2")
                    e$global.lock <- FALSE
                }

                index <- res$new.index[[i]]
                file.name <- file.path(result.dir,
                                        "RData",
                                        paste0("node",
                                            new.node, ".RData"))
                if (!silence.mode)
                    cat(paste0("Node ", node, ": Saving ", file.name, "\n"))
                save(index, file = file.name, compress = "bzip2")
            }


            # load tree list
            file.name <- file.path(work.dir, "RData", "tree.RData")
            if (!silence.mode)
                cat(paste0("Node ", node, ": Loading ", file.name, "\n"))
            load(file = file.name)

            which.row <- which(tree$node == node)
            # Status -1 = deleted node due to error
            if (tree$status[which.row[1]] != -1)
            {
                tree$status[which.row[1]] <- 2

                # colnames(list.new.node) = c('node','parent.node','status')
                # tree =
                # rbind(tree,list.new.node)

                file.name <-
                    file.path(result.dir, "RData", "tree.RData")
                if (!silence.mode)
                    cat(paste0("Node ", node, ": Updating ", file.name, "\n"))

                if (isTRUE(e$global.lock))
                {
                    Sys.sleep(runif(1, min = 0, max = 2))
                } else
                {
                    e$global.lock <- TRUE
                    save(tree,
                        file = file.name,
                        compress = "bzip2")
                    e$global.lock <- FALSE
                }

            }


        } else if (res$status == 1)
        {
            # case of status = 5, no split, stopping criteria are met
            if (!silence.mode)
                cat(paste0("Node ", node,
                            ": No split was performed, Status=1\n"))

            file.name <-
                file.path(result.dir, "RData", "leafnode.RData")
            load(file = file.name)
            leaf.node <- c(leaf.node, node)
            if (!silence.mode)
                cat(paste0("Node ", node, ": Updating ", file.name, "\n"))
            save(leaf.node, file = file.name, compress = "bzip2")


            # load tree
            file.name <- file.path(work.dir, "RData", "tree.RData")
            if (!silence.mode)
                cat(paste0("Node ", node, ": Loading ", file.name, "\n"))
            load(file = file.name)

            which.row <- which(tree$node == node)
            tree$status[which.row[1]] <- 2

            file.name <-
                file.path(result.dir, "RData", "tree.RData")
            if (!silence.mode)
                cat(paste0("Node ", node, ": Updating ", file.name, "\n"))

            if (isTRUE(e$global.lock))
            {
                Sys.sleep(runif(1, min = 0, max = 2))
            } else
            {
                e$global.lock <- TRUE
                save(tree, file = file.name, compress = "bzip2")
                e$global.lock <- FALSE
            }
        }
    }

    end.time <- Sys.time()
    if (!silence.mode)
        cat(paste0("Node ", node, ": Done!\n"))
    if (!silence.mode)
        cat(paste0("Node ", node, ": processed in ", format(end.time -
                                                                start.time)))

    invisible(NULL)
}