view cluster.tools/cutree.R @ 2:b442996b66ae draft

Uploaded

#!/usr/bin/env Rscript
argspec <- c("tab.2.cdt.R converts a data matrix to cdt format

        Usage: 
                tab.2.cdt.R -d <data.file> 
        Optional:
                            -o <output_file>
                \n\n")
args <- commandArgs(TRUE)
if ( length( args ) == 1 && args =="--help") { 
  write(argspec, stderr())
  q();
}

lib.load.quiet <- function( package ) {
   package <- as.character(substitute(package))
   suppressPackageStartupMessages( do.call( "library", list( package=package ) ) )
}

lib.load.quiet( getopt )
lib.load.quiet( ctc )
if ( any( c( 'flashClust', 'fastcluster' ) %in% installed.packages() ) ) {
  if ( 'flashClust' %in% installed.packages() ) {
    lib.load.quiet( flashClust )
  } else {
    if ( 'fastcluster' %in% installed.packages() ) {
      lib.load.quiet( fastcluster )
    }
  }
}

spec <- matrix( c( "dataset",             "d", 1, "character",
                   "num.k",               "k", 1, "integer",
                   "output.fname",        "o", 2, "character"
                   ),
                nc=4,
                byrow=TRUE
               )


opt <- getopt( spec=spec )
if ( is.null( opt$output.fname ) ) { opt$output.fname <- file.path( opt$output.report.dir, paste( "data", opt$output.format, sep="." ) ) }


load( opt$dataset )  ## should load the cl, treecl.res (or partcl.res) and data
if ( exists( 'treecl.res' ) ) {
  cutree.res <- cutree( treecl.res, k=opt$num.k )
  cl <- cutree.res
  save( file=opt$output.name, treecl.res, cl, data )
} else {
}