diff cluster.tools/cutree.R @ 0:0decf3fd54bc draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cluster.tools/cutree.R	Thu Feb 28 01:45:39 2013 -0500
@@ -0,0 +1,52 @@
+#!/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.fname, treecl.res, cl, data )
+} else {
+  stop( "no hierarchical clustering result found!\n" )
+}