R/postprocess.R

In kridsadakorn/ipcaps.bioc: 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
    silence.mode <- 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, silence.mode = silence.mode)
    save.html(result.dir)
    if (no.plot == FALSE)
    {
        save.plots(result.dir)
    }
    if (!silence.mode)
        cat("The result files were saved at: ", result.dir, "\n")
    return(cluster.tab)

}