diff abims_hclustering.r @ 0:2f7381ee5235 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/abims_hclustering.r	Tue Jun 30 06:36:09 2015 -0400
@@ -0,0 +1,38 @@
+#!/usr/local/public/bin/Rscript --verbose
+# version="1.1"
+
+# date: 04-06-2013
+# **Authors** Gildas Le Corguille  ABiMS - UPMC/CNRS - Station Biologique de Roscoff - gildas.lecorguille|at|sb-roscoff.fr 
+
+# abims_hclust.r version 20130604
+
+library(batch)
+library(ctc)
+
+hclust_metabolomics = function(file, method = "pearson", link = "ward", normalization=TRUE, keep.hclust=FALSE, sep=";", dec="."){
+
+    if (sep=="tabulation") sep="\t"
+    if (sep=="semicolon") sep=";"
+    if (sep=="comma") sep=","
+
+    # -- loading --
+    data=read.table(file, header = TRUE, row.names=1, sep = sep, quote="\"", dec = dec,
+		    fill = TRUE, comment.char="",na.strings = "NA")
+
+    # -- Normalization: logratio --
+    if (normalization) {
+	#meandata = apply(data,1,mean, na.rm=T)
+	#data = log2(data/meandata)
+	data=t(scale(t(data)))
+    }
+
+    # -- hclust / output files for TreeView --
+    file="hclust.cdt"
+    hclust2treeview(data,file=file, method = method, link = link, keep.hclust= keep.hclust)
+    
+    # -- output / return --
+    system("zip -r hclust.zip hclust.*", ignore.stdout = TRUE)
+}
+
+listArguments = parseCommandArgs(evaluate=FALSE)
+do.call(hclust_metabolomics, listArguments)