R/postprocess.R

In IPCAPS: Iterative Pruning to Capture Population Structure

#' (Internal function) Perform the post-processing step of IPCAPS
#'
#' @param result.dir A result directory as the \code{$output} object returned
#' from the \code{\link{ipcaps}} function.
#' @param reanalysis (Unimplemented) To specify whether it is re-analysis or not. If TRUE, it is
#' re-analysis, otherwise it is not. Default = FALSE.
#'
#' @return A data frame of clustering result 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.
#' }
#'
#' @include export.groups.R
#' @include save.plots.R
#' @include save.html.R
#'
postprocess <- function( result.dir, reanalysis=FALSE){

  no.plot <- NULL

  file.name = file.path(result.dir,"RData","leafnode.RData")
  load(file=file.name)
  file.name = file.path(result.dir,"RData","condition.RData")
  load(file=file.name)

  if (length(leaf.node) == 0){
    leaf.node = c(1)
    save(leaf.node,file=file.name, compress = 'bzip2')
  }

  #Generate HTML output file
  cluster.tab = export.groups(result.dir)
  save.html(result.dir)
  if (no.plot == FALSE){
    save.plots(result.dir)
  }
  cat("The result files were saved at: ",result.dir,"\n")
  return (cluster.tab)

}