This demo makes hierarchical clustering on your data
Upload your data (text-tabulated file)
$MAX_FILE)
exit("File size: $taillefichier; max allowed: $MAX_FILE");
}
/* ================================== */
/* We write R code in file $ID/prog.R */
/* ================================== */
$fp=fopen("$ID/prog.R",'w');
fwrite($fp,"library(ctc)\n");
/* Read Data */
fwrite($fp,"data <- read.delim('$ID/data.txt',header=$HEADER,row.names=$ROWNAMES) \n" );
fwrite($fp,"data \n");
/* Hierarchical clustering */
fwrite($fp,"hr <- hclust(dist(data)) \n");
fwrite($fp,"hc <- hclust(dist(t(data))) \n");
fwrite($fp,"dr <- as.dendrogram(hr) \n");
fwrite($fp,"dc <- as.dendrogram(hc) \n");
/* A pdf file */
fwrite($fp,"pdf(file='$ID/Rplots.pdf') \n");
fwrite($fp,"heatmap(as.matrix(data),Colv=dc,Rowv=dr) \n");
fwrite($fp,"dev.off() \n");
/* Some png images */
fwrite($fp,"bitmap(file='$ID/heatmap.png') \n");
fwrite($fp,"heatmap(as.matrix(data),Colv=dc,Rowv=dr) \n");
fwrite($fp,"dev.off() \n");
fwrite($fp,"r2atr(hc,file='$ID/cluster.atr') \n");
fwrite($fp,"r2gtr(hr,file='$ID/cluster.gtr') \n");
fwrite($fp,"r2cdt(hr,hc,data ,file='$ID/cluster.cdt') \n");
fclose($fp);
/* ===================== */
/* Send command (R batch)*/
/* ===================== */
system("$R_BIN --no-save < $ID/prog.R > $ID/prog.R.out 2> $ID/prog.R.warnings");
/* ===================================== */
/* We create html page including results */
/* ===================================== */
echo "Ctc Demo results
";
echo "A pdf file";
echo "3 files for Freeview";
echo " or Treeview: ";
echo "cdt ";
echo "atr ";
echo "gtr ";
echo "
";
echo "
";
/* Signature */
echo "
This results made by ctc
package. Code use: prog.R,
Out: prog.R.out,
Warnings: prog.R.warnings.";
}
?>
ctc/demo/ 0000755 0001750 0001750 00000000000 14136046747 012115 5 ustar nilesh nilesh ctc/demo/00Index 0000644 0001750 0001750 00000000024 14136046747 013243 0 ustar nilesh nilesh ctc Ctc demo file
ctc/demo/ctc.R 0000755 0001750 0001750 00000002655 14136046747 013024 0 ustar nilesh nilesh cat ("\n\n C T C \n D E M O \n\n")
cat("\n------ Standard clustering with R (not ctc): -------\n")
data(USArrests)
h = hclust(dist(USArrests))
plot(h)
readline("Next")
cat("\n------ Get the ``heatmap'': -------\n")
heatmap(as.matrix(USArrests))
readline("Next")
cat("\n------ BUILDING HIERARCHICAL CLUSTERING WITH ANOTHER SOFTWARE -------\n")
cat("\n------ Write data table to Xcluster file format -------\n")
r2xcluster(USArrests,file='USArrests_xcluster.txt')
readline("Next")
cat("\n------ Write data table to cluster file format -------\n")
r2cluster(USArrests,file='USArrests_cluster.txt')
readline("Next")
cat("\n------ Hierarchical clustering (need Xcluster tool by Gavin Sherlock) -------\ntry:\n\nh.xcl=xcluster(USArrests)\nplot(h.xcl)
")
readline("Next")
hr = hclust(dist(USArrests))
hc = hclust(dist(t(USArrests)))
cat("\n------ USING OTHER VISUALIZATION SOFTWARES -------\n")
cat("\n------ Export hclust objects to Newick format files -------\n")
write(hc2Newick(hr),file='hclust.newick')
readline("Next")
cat("\n------ Export hclust objects to Freeview or Treeview
visualization softwares -------\n")
r2atr(hc,file="cluster.atr")
r2gtr(hr,file="cluster.gtr")
r2cdt(hr,hc,USArrests ,file="cluster.cdt")
readline("Next")
cat("\n------ Clustering and Export hclust objects to Freeview or Treeview
visualization softwares -------\n")
hclust2treeview(USArrests,file="cluster.cdt")
ctc/DESCRIPTION 0000644 0001750 0001750 00000001263 14136067410 012667 0 ustar nilesh nilesh Package: ctc
Version: 1.68.0
Date: 2005-11-16
Depends: amap
Title: Cluster and Tree Conversion.
Author: Antoine Lucas