R/multiple_hexLen_count_TIPC_cat.R

In MPE-Lab/TIPC: Tumor-Immune Partitioning and Clustering (test)

#' A wrapper function of \code{\link[TIPC]{count_TIPC_cat}}
#'
#' A wrapper function to run \code{\link[TIPC]{count_TIPC_cat}} at various
#' hexagonal lengths.
#'
#' @param root_dir A directory path pointing to the parent directory of all the
#'   ouptput folders generated by \code{\link[TIPC]{tessellation}} at various
#'   hexagonal lengths.
#' @param hex_len_range A vector of 2 integer number indicating the range of
#'   hexagonal length. If unspecified (NULL), all found result folders generated
#'   by \code{\link[TIPC]{tessellation}} will be processed.
#' @param hex_len_stepsize An integer indicating the step size of hexagonal
#'   length. If unspecified (NULL), all found result folders generated
#'   by \code{\link[TIPC]{tessellation}} will be processed.
#' @export
multiple_hexLen_count_TIPC_cat <- function(root_dir = NULL,
                                         hex_len_range = NULL, hex_len_stepsize =  10){
  ## ======================
  ## identify all result folders generated by tessellation
  ## ======================
  subfolder_nms <- list.dirs(path = root_dir, full.names = TRUE, recursive = FALSE)
  ## subsetting for output folders from tessellation
  subfolder_nms <- grep(x= subfolder_nms, pattern = 'TIPC_hexLen', value = TRUE)

  ## ======================
  ## subsettting for result folders specified by users
  ## ======================
  if (!is.null(hex_len_range) & length(hex_len_range)>1) {
    hex_lens <- seq(from = min(hex_len_range), to = max(hex_len_range),
                    by = hex_len_stepsize)
    subfolder_nms <- grep(x = subfolder_nms, pattern = paste0(hex_lens,
                                                              collapse = "|"), value = TRUE)
  }else if(!is.null(hex_len_range) & length(hex_len_range)==1) {
    hex_lens <- hex_len_range
    subfolder_nms <- grep(x = subfolder_nms, pattern = paste0(hex_lens,
                                                              collapse = "|"), value = TRUE)
  }


  ## ======================
  ## calling count_TIPC_cat at individual hex_len
  ## ======================
  for (hex_lenX in subfolder_nms){
    count_TIPC_cat(root_dir =  hex_lenX)
  }
}