R/export.groups.R

In kridsadakorn/ipcaps2: Iterative Pruning to Capture Population Structure version 2

#' Export the IPCAPS2 result to a text file
#'
#' @description Export clustering result of
#' \code{\link{ipcaps2}} to text file called 'groups.txt'.
#'
#' @param result.dir A result directory as the \code{$output} object returned
#' from the \code{\link{ipcaps2}} function.
#' @param silence.mode To enable or disable silence mode. If silence mode is
#' enabled, the fuction is processed without printing any message on the
#' screen, and it is slightly faster. Default = TRUE.
#'
#' @return A data frame of exported data containing 4 columns; \code{group},
#' \code{node}, \code{label}, \code{row.number}, as described below for more
#' details:
#' \itemize{
#' \item \code{group} represents group membership of IPCAPS2 result.
#' \item \code{node} represents node numbers of IPCAPS2 result.
#' \item \code{label} represents labels of rows in orginal input data.
#' \item \code{row.number} represents row numbers of orginal input data.
#' }
#'
#' @details After running, this function exports the file called 'groups.txt' to the same result
#' directory. If 'groups.txt' already exists in the result directory, the
#' exported file is changed to 'groups1.txt', 'groups2.txt', 'groups3.txt', ...,
#' accordingly.
#'
#' @export
#'
#' @import utils
#'
#' @examples
#'
#' # Importantly, bed file, bim file, and fam file are required
#' # Use the example files embedded in the package
#'
#' BED.file <- system.file("extdata","ipcaps_example.bed",package="IPCAPS2")
#' LABEL.file <- system.file("extdata","ipcaps_example_individuals.txt.gz",package="IPCAPS2")
#'
#' my.cluster <- ipcaps2(bed=BED.file,
#'                       label.file=LABEL.file,
#'                       lab.col=2,
#'                       out=tempdir(),
#'                       silence=TRUE,
#'                       no.rep=1)
#'
#' #Here, to export the IPCAPS2 result to a text file
#' exported.data <- export.groups(my.cluster$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)
}