R/export.groups.R

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

#' Export the ipcaps result to a text file
#'
#' @description Export clustering result of
#' \code{\link{ipcaps}} to text file called 'groups.txt'.
#'
#' @param result.dir A result directory as the \code{$output} object returned
#' from the \code{\link{ipcaps}} function.
#' @param silence.mode To enable or disable silence mode. If silence mode is
#' enabled, the fuction is processed without printing any message on the
#' screen, and it is slightly faster. Default = TRUE.
#'
#' @return A data frame of exported data containing 4 columns; \code{group},
#' \code{node}, \code{label}, \code{row.number}, as described below for more
#' details:
#' \itemize{
#' \item \code{group} represents group membership of ipcaps result.
#' \item \code{node} represents node numbers of ipcaps result.
#' \item \code{label} represents labels of rows in orginal input data.
#' \item \code{row.number} represents row numbers of orginal input data.
#' }
#'
#' @details After running, this function exports the file called 'groups.txt'
#' to the same result directory. If 'groups.txt' already exists in the result
#' directory, the exported file is changed to 'groups1.txt', 'groups2.txt',
#' 'groups3.txt', ..., accordingly.
#'
#' @export
#'
#' @import utils
#'
#' @examples
#'
#' # Importantly, bed file, bim file, and fam file are required
#' # Use the example files embedded in the package
#'
#' BED.file <- system.file('extdata',
#'                         'ipcaps_example.bed',
#'                         package = 'IPCAPS.BIOC')
#'
#' LABEL.file <- system.file('extdata',
#'                           'ipcaps_example_individuals.txt.gz',
#'                           package = 'IPCAPS.BIOC')
#'
#' my.cluster <- ipcaps(bed = BED.file,
#'                      label.file = LABEL.file,
#'                      lab.col = 2,
#'                      out = tempdir(),
#'                      max.thread = 1,
#'                      seed = 1234)
#'
#' #Here, to export the ipcaps result to a text file
#' exported.data <- export.groups(my.cluster$output.dir)
#' print(dim(exported.data))
#' head(exported.data)


export.groups <- function(result.dir, silence.mode = FALSE)
{
    leaf.node <- NULL
    index <- NULL
    label <- NULL

    load(file.path(result.dir, "RData", "leafnode.RData"))
    export.data <- NULL
    for (i in seq(1, length(leaf.node)))
    {
        assigned_group <- which(leaf.node == leaf.node[i])
        if (!silence.mode)
            cat(paste0(
                "Exporting node ",
                leaf.node[i],
                " as group ",
                assigned_group,
                "\n"
            ))
        load(file.path(
            result.dir,
            "RData",
            paste0("node", leaf.node[i],
                    ".RData")
        ))
        groups <- rep(assigned_group, length(index))
        nodes <- rep(leaf.node[i], length(index))
        node.data <- data.frame(groups, nodes, label, index)
        export.data <- rbind(export.data, node.data)
    }
    colnames(export.data) <- c("group", "node", "label", "row.number")
    file.name <- file.path(result.dir, "groups.txt")
    if (file.exists(file.name))
    {
        i <- 1
        file.name <- file.path(result.dir, paste0("groups", i, ".txt"))
        while (file.exists(file.name))
        {
            i <- i + 1
            file.name <-
                file.path(result.dir, paste0("groups", i, ".txt"))
        }
    }
    if (!silence.mode)
        cat(paste0("Note: save as ", file.name, "\n"))
    write.table(
        export.data,
        file = file.name,
        quote = FALSE,
        sep = "\t",
        row.names = FALSE,
        col.names = TRUE
    )
    return(export.data)
}