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($fp,"library(amap)\n"); fwrite($fp,"library(ctc)\n"); /* Read Data */ fwrite($fp,"data <- read.delim('$ID/data.txt',header=$HEADER,row.names=$ROWNAMES,sep='$SEP') \n" ); fwrite($fp,"data <- scale(data) \n"); fwrite($fp,"pca <- acprob(data,h=1) \n"); /* Number of columns to keep ( number of column to keep 90 % of * variance)*/ fwrite($fp,"cumVarNorm <- cumsum(pca\$sdev ^ 2) / sum(pca\$sdev ^ 2)\n"); fwrite($fp,"ncol <- max(which( cumVarNorm< 0.9)) +1 \n"); fwrite($fp,"ncol \n"); fwrite($fp,"data <- pca\$scores[,1:ncol] \n"); /* Hierarchical clustering */ fwrite($fp,"hr0 <- hclusterpar(data) \n"); fwrite($fp,"hc0 <- hclusterpar(t(data)) \n"); fwrite($fp,"hr <- as.dendrogram(hr0) \n"); fwrite($fp,"hc <- as.dendrogram(hc0) \n"); /* A pdf file */ fwrite($fp,"pdf(file='$ID/Rplots.pdf') \n"); fwrite($fp,"plot(pca) \n"); fwrite($fp,"biplot(pca) \n"); fwrite($fp,"plot2.acp(pca) \n"); fwrite($fp,"heatmap(as.matrix(data),Colv=hc,Rowv=hr) \n"); fwrite($fp,"dev.off() \n"); /* Some png images */ fwrite($fp,"bitmap(file='$ID/pcaplot.png') \n"); fwrite($fp,"plot(pca) \n"); fwrite($fp,"dev.off() \n"); fwrite($fp,"bitmap(file='$ID/pcabiplot.png') \n"); fwrite($fp,"biplot(pca) \n"); fwrite($fp,"dev.off() \n"); fwrite($fp,"bitmap(file='$ID/pcaplot2.png') \n"); fwrite($fp,"plot2.acp(pca) \n"); fwrite($fp,"dev.off() \n"); fwrite($fp,"bitmap(file='$ID/heatmap.png') \n"); fwrite($fp,"heatmap(as.matrix(data),Colv=hc,Rowv=hr) \n"); fwrite($fp,"dev.off() \n"); fwrite($fp,"r2atr(hc0,file='$ID/cluster.atr') \n"); fwrite($fp,"r2gtr(hr0,file='$ID/cluster.gtr') \n"); fwrite($fp,"r2cdt(hr0,hc0,data ,file='$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 "Amap Demo results
"; echo "A pdf file";
echo "
";
echo "
";
echo "
";
echo "
"; echo "3 files for Freeview"; echo " or Treeview: "; echo "cdt "; echo "atr "; echo "gtr "; echo "
"; /* Signature */ echo "
This results made by amap package. Code use: prog.R, Out: prog.R.out, Warnings: prog.R.warnings."; } ?>