diff cluster.tools/extract.cons.cluster.from.result.R @ 2:b442996b66ae draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cluster.tools/extract.cons.cluster.from.result.R	Wed Feb 27 20:17:04 2013 -0500
@@ -0,0 +1,62 @@
+#!/usr/bin/env Rscript
+# Extract k cluster assignment from consensus clustering result Script by Peter Waltman
+# Nov. 12, 2012
+# License under Creative Commons Attribution 3.0 Unported (CC BY 3.0)
+#
+##usage, options and doc goes here
+argspec <- c("galaxy.extract.cons.clustering.from.result.R extracts a cluster assignment for a specified
+value of K from a specified consensus cluster result file.
+
+
+        Usage: 
+                galaxy.extract.cons.cluster.from.result.R -r <results_file> -k <k_select>
+        Optional:
+                -o consensus class output file # tab-delimitted file format
+\n\n")
+args <- commandArgs(TRUE)
+if ( length( args ) == 1 && args =="--help") { 
+  write( argspec, stderr() )
+  q();
+}
+
+library(getopt)
+
+spec <- matrix( c( "results.file",   "r", 1, "character",
+                   "k.select",       "k", 1, "integer",
+                   "cluster.class.out",   "o", 2, "character",
+                   "output.select.rdata", "d", 2, "character"
+                  ),
+                nc=4,
+                byrow=T
+               )
+opt <- getopt( spec=spec )
+if ( is.null( opt$output.select.rdata ) ) { opt$output.select.rdata <- "select.RData" }
+##if ( is.null( opt$cluster.class.out) ) { opt$cluster.class.out <- "select.cls" }
+
+load( opt$results.file )
+cons.matrices <- lapply( results[ 2:length(results) ], '[[', 'consensusMatrix' )
+cls <- lapply( results[ 2:length(results) ], '[[', 'consensusClass' )
+names( cons.matrices ) <- names( cls ) <- 2:length( results )
+
+ch.k.select <- as.character( opt$k.select )
+if ( ch.k.select %in% names( cls ) ) {
+  ## get the consensusClass file that's associated with the k.select
+  cl <- cls[[ ch.k.select  ]] 
+
+  if ( ! is.null( opt$cluster.class.out ) ) {
+    cl <- cbind( names( cl ), as.integer(cl) )
+    colnames( cl ) <- c( "ID", "class" )
+    write.table( cl, opt$cluster.class.out, sep="\t", row.names=FALSE, quote=FALSE )
+  } else if ( ! is.null( opt$output.select.rdata ) ) {
+    ## re-order the samples to follow the cluster assignment
+    treecl.res <- results[[ opt$k.select ]]$consensusTree
+    select.result <- results[[ opt$k.select ]]
+    save( file=opt$output.select.rdata, treecl.res, cl, select.result, data )
+  } else {
+    stop( 'no valid output format specified\n' )
+  }
+} else {
+  out.string <- paste( "choice of k =", ch.k.select, "not available in this result file. Max k = ", max( as.numeric( names(cls) ) ), "\n" )
+  cat( out.string, file=opt$cluster.class.out )
+}
+