inst/scripts/run_make_multiplex.R

In dkainer/RWRtoolkit: Random Walk with Restart Tool Suite

library(RWRtoolkit)

## Parse args function
parse_arguments <- function() {
  suppressPackageStartupMessages(library(optparse))
  option_list <- list(
    make_option(
      c("-f", "--flist"),
      action = "store",
      default = NULL,
      type = "character",
      help = "Table describing network files to use.  File columns: <path
            to file> <short name of network> <group>.  'groups' are either 1,
            2, or 3.  All 1's will form one multiplex network (e.g.
            gene-to-gene), All 2's will form a separate multiplex network (e.g.
            disease-to-disease), And all 3's will be used to join the 1's and 2's
            together (e.g. gene-to-disease) You don't have to have both 1's and
            2's.  But if you do have 1's and 2's, you SHOULD have at least one
            3 to join them up."
    ),
    make_option(
      c("-d", "--delta"),
      action = "store",
      default = 0.5,
      type = "numeric",
      help = "The parameter delta sets the probability to change between
            layers at the next step. If delta = 0, the particle will always
            remain in the same layer after a non-restart iteration.  If delta = 1,
            the particle will always change between layers, therefore not following
            the specific edges of each layer. Default is 0.5.  Note delta must
            be greater than 0 and less than or equal to 1."
    ),
    make_option(
      c("-t", "--test"),
      action = "store_true",
      default = FALSE,
      type = "character",
      help = "Run example to test script."
    ),
    make_option(
      c("-o", "--out"),
      action = "store",
      default = "network.Rdata",
      type = "character",
      help = 'Output file name (default "network.Rdata")'
    ),
    make_option(
      c("-v", "--verbose"),
      action = "store_true",
      default = TRUE,
      help = "Print extra output [default]"
    )
  )

  opt <- parse_args(OptionParser(option_list = option_list))
  return(opt)
}

## Processing arguments
opt <- parse_arguments()

if (is.null(opt$flist)) {
  stop("Error. \n - Input file \"flist\" parameter not included.\n", file = stderr())
}

if (opt$verbose) {
  # you can use either the long or short name. opt$a and opt$avar are the same.
  cat("Network files table:           ")
  cat(opt$flist)
}

print("Running RWR Make Multiplex with options: ")
print(opt)

RWRtoolkit::RWR_make_multiplex(
    flist = opt$flist,
    delta = opt$delta,
    output = opt$out,
    verbose = opt$verbose
  )