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<?php
/*
This program is a sample to use R and amap and ctc as a web application.
ctc package is available on bioconductor.org
Standard setup:
put amap.php in your public_html directory
check that webserver user (apache, or www) is able
to write in public_html (chmod 'a+w' ~/public_html)
Change global variable R_BIN below
That's all.
Example working:
http://bioinfo.genopole-toulouse.prd.fr/~lucas/amap.php
Note:
Variable include_path in php.ini should includes path to gs binary.
*/
/* Some globals variables */
$R_BIN = "/usr/local/bin/R";
$MAX_FILE = 307200; // 300 Ko
/* End of personalization */
?>
<html>
<header>
<title>AMAP Demo Web application V0-3</title>
</header>
<body>
<center>
<?php
/* and ID made by TIME + Process_ID */
$ID = "tmp_".time().getmypid();
/* Print form */
if ($_POST[page] != "Exec")
{
?>
<p>
Upload your data (text-tabulated file)
<form
action="amap.php"
enctype="multipart/form-data"
method="POST"
>
<INPUT TYPE = hidden NAME=page value="Exec"></input>
<INPUT type="file" name="FileData" />
<p>
File Description:
<table><tr>
<td>A first Column</td><td>
<SELECT NAME=rownames>
<OPTION SELECTED VALUE = "1">with labels
<OPTION VALUE = "NULL">with data
</SELECT>
</td></tr>
<tr><td>
A first line</td><td>
<SELECT NAME=header>
<OPTION SELECTED VALUE = TRUE>with columns header
<OPTION VALUE = FALSE>with data
</SELECT>
</td></tr>
<tr><td>
Separator</td><td>
<SELECT NAME=sep>
<OPTION SELECTED VALUE = "t">tabulation</option>
<OPTION VALUE = "s">space</option>
<OPTION VALUE = "c">comma</option>
<OPTION VALUE = 'sc'>semicolon</option>
</SELECT>
</td></tr></table>
<INPUT TYPE=SUBMIT VALUE="Submit" name="GO">
</form>
<?php
}
else
{
mkdir($ID,0777);
$HEADER = $_POST[header];
$ROWNAMES = $_POST[rownames];
$SEP = $_POST[sep];
if($SEP == 't')
$SEP = "\t";
if($SEP == 'c')
$SEP = ",";
if($SEP == 'sc')
$SEP = ";";
if($SEP == 's')
$SEP = " ";
/* Get upload data */
if(is_uploaded_file ($_FILES['FileData']['tmp_name'] ))
{
move_uploaded_file ($_FILES['FileData']['tmp_name'],$ID."/data.txt");
$taillefichier = filesize($ID."/data.txt");
if($taillefichier>$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> $ID/prog.R.warnings");
/* ===================================== */
/* We create html page including results */
/* ===================================== */
echo "<h3>Amap Demo results </h3>";
echo "<a href=$ID/Rplots.pdf>A pdf file</a><p>";
echo "<img src=$ID/pcaplot.png></img><p>";
echo "<img src=$ID/pcabiplot.png></img><p>";
echo "<img src=$ID/pcaplot2.png></img><p>";
echo "<img src=$ID/heatmap.png></img><p>";
echo "3 files for <a href=http://magix.fri.uni-lj.si/freeview/>Freeview</a>";
echo " or <a href=http://rana.lbl.gov/>Treeview</a>: ";
echo "<a href=$ID/cluster.cdt>cdt</a> ";
echo "<a href=$ID/cluster.atr>atr</a> ";
echo "<a href=$ID/cluster.gtr>gtr</a> ";
echo "<p>";
/* Signature */
echo "<p>This results made by amap,
Code use: <a href='$ID/prog.R'>prog.R</a>,
Out: <a href='$ID/prog.R.out'>prog.R.out</a>,
Warnings: <a href='$ID/prog.R.warnings'>prog.R.warnings</a>.";
}
?>
</center>
</body>
</html>
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