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index.php
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index.php
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<?php
// =============================================================================
// _____ _ _
// / ____(_) | |
// | | __ _ _ __ | | ____ _ ___
// | | |_ | | '_ \| |/ / _` |/ _ \
// | |__| | | | | | < (_| | (_) |
// \_____|_|_| |_|_|\_\__, |\___/
// __/ |
// |___/ 1.0
//
// =============================================================================
// =============================================================================
// == Configuration ============================================================
// =============================================================================
include "bootstrap.php";
// =============================================================================
// == Parse user query =========================================================
// =============================================================================
$query = explode("/", $_GET['q']);
// Extract page
$GINKGO_PAGE = $query[0];
if(!$GINKGO_PAGE)
$GINKGO_PAGE = 'home';
// Extract user ID
$GINKGO_USER_ID = $query[1];
if(!$GINKGO_USER_ID)
$GINKGO_USER_ID = generateID(20);
// Security patch: don't allow user IDs that aren't alphanumerical
// e.g. could use "a; echo b" as user ID; will create file "a" and write "b" to it
if(preg_match('/[^A-Za-z0-9_-]/', $GINKGO_USER_ID))
exit;
// Don't allow users to modify demo analyses
if($GINKGO_USER_ID[0] == '_' && ($GINKGO_PAGE == "home" || $GINKGO_PAGE == "dashboard")) {
header("Location: ?q=results/" . $GINKGO_USER_ID);
exit;
}
// =============================================================================
// == Page-specific configuration ==============================================
// =============================================================================
// Step 1 (choose cells), Step 2 (job name, genome, etc), Step 3 (specify email)
if($GINKGO_PAGE == "dashboard")
$MY_CELLS = getMyFiles($GINKGO_USER_ID);
// Step 4 (results)
if($GINKGO_PAGE == "results")
$CURR_CELL = $query[2];
// =============================================================================
// == Session management =======================================================
// =============================================================================
$_SESSION["user_id"] = $GINKGO_USER_ID;
// Define user directories
$userDir = DIR_UPLOADS . '/' . $GINKGO_USER_ID;
$userUrl = URL_ROOT . '/uploads/' . $GINKGO_USER_ID;
$permalink = URL_ROOT . '?q=results/' . $GINKGO_USER_ID;
if(file_exists($descFile = $userDir . '/description.txt'))
setcookie("ginkgo[$GINKGO_USER_ID]", file_get_contents($descFile), time()+36000000);
// =============================================================================
// == Template configuration ===================================================
// =============================================================================
// -- Panel for info -----------------------------------------------------------
if($GINKGO_PAGE == "results" || $GINKGO_PAGE == "analyze-subset")
{
$configFile = $userDir . "/config";
if(file_exists($configFile)) {
$f = file($configFile);
$config = array();
foreach($f as $index => $val) {
$values = explode("=", $val, 2);
$config[$values[0]] = str_replace("'", "", trim($values[1]));
}
}
}
$tmpBinMeth = split('_', $config['binMeth']);
$binInfo = $tmpBinMeth[0] . ' bins of ' . $tmpBinMeth[1]/1000 . 'kb size <small><small>(' . $tmpBinMeth[3] . '/' . $tmpBinMeth[2] . 'bp reads)</small></small>';
$clusteringInfo = $config['clustMeth'] . ' linkage, ' . str_replace('euclidian','euclidean',$config['distMeth']) . ' distance';
$segInfo = 'normalized read counts';
if($config['segMeth'] == '1')
$segInfo = 'sample with lowest IOD';
if($config['segMeth'] == '2')
$segInfo = 'uploaded reference sample';
$genome = $config['chosen_genome'];
$PANEL_INFO = <<<PANEL
<!-- Panel: Summary of parameters used -->
<div class="panel panel-primary">
<div class="panel-heading"><h3 class="panel-title"><span class="glyphicon glyphicon-list-alt"></span> Analysis Parameters</h3></div>
<div class="panel-body">
<b>Genome:</b> $genome<br/>
<b>Binning:</b> $binInfo<br/>
<b>Segmentation:</b> using $segInfo<br/>
<b>Clustering:</b> $clusteringInfo<br/>
</div>
</div>
PANEL;
// -- Panel for permalink ------------------------------------------------------
$PANEL_LATER = <<<PANEL
<!-- Panel: Save for later -->
<div class="panel panel-primary">
<div class="panel-heading"><h3 class="panel-title"><span class="glyphicon glyphicon-time"></span> View analysis later</h3></div>
<div class="panel-body">Access your results later at the following address:<br/><br/><textarea class="input-sm permalink">{$permalink}</textarea></div>
</div>
PANEL;
// -- Panel to show user's last analysis, if any -------------------------------
if(file_exists(DIR_UPLOADS . '/' . $GINKGO_USER_ID . '/status.xml'))
{
$PANEL_PREVIOUS = <<<PANEL
<!-- Panel: View previous analysis results -->
<div class="panel panel-primary">
<div class="panel-heading"><h3 class="panel-title"><span class="glyphicon glyphicon-stats"></span> Previous analysis results</h3></div>
<div class="panel-body">See your <a href="?q=results/$GINKGO_USER_ID">previous analysis results</a>.<br/><br/><strong>Note</strong>: Running another analysis will overwrite previous results.</div>
</div>
PANEL;
}
// -- Panel for downloading tree -----------------------------------------------
$dloadFileSizes = array(
'SegStats' => humanFileSize("{$userDir}/SegStats"),
'SegBreaks' => humanFileSize("{$userDir}/SegBreaks"),
'SegCopy' => humanFileSize("{$userDir}/SegCopy"),
'SegNorm' => humanFileSize("{$userDir}/SegNorm"),
'SegFixed' => humanFileSize("{$userDir}/SegFixed"),
'CNV1' => humanFileSize("{$userDir}/CNV1"),
'CNV2' => humanFileSize("{$userDir}/CNV2"),
);
$rnd = rand(1e6,2e6);
$PANEL_DOWNLOAD = <<<PANEL
<!-- Panel: Download results -->
<div id="results-download" class="panel panel-default" style="display:none;">
<div class="panel-heading"><span class="glyphicon glyphicon-tree-deciduous"></span> Tree display</div>
<!-- Table -->
<table class="table" style="font-size:12.5px;">
<tr class="active"><td><input type="radio" name="results-tree-view" onclick="javascript:drawTree('clust.xml');" checked> <strong>Normalized read counts</strong> (<a target="_blank" href="{$userUrl}/clust.newick">newick</a> | <a target="_blank" href="{$userUrl}/clust.xml">xml</a> | <a target="_blank" href="{$userUrl}/clust.pdf">pdf</a> | <a target="_blank" href="{$userUrl}/clust.jpeg">jpeg</a>)</td></tr>
<tr class="active"><td><input type="radio" name="results-tree-view" onclick="javascript:drawTree('clust2.xml');"> <strong>Copy-number</strong> (<a target="_blank" href="{$userUrl}/clust2.newick">newick</a> | <a target="_blank" href="{$userUrl}/clust2.xml">xml</a> | <a target="_blank" href="{$userUrl}/clust2.pdf">pdf</a> | <a target="_blank" href="{$userUrl}/clust2.jpeg">jpeg</a>)</td></tr>
<tr class="active"><td><input type="radio" name="results-tree-view" onclick="javascript:drawTree('clust3.xml');"> <strong>Correlations</strong> (<a target="_blank" href="{$userUrl}/clust3.newick">newick</a> | <a target="_blank" href="{$userUrl}/clust3.xml">xml</a> | <a target="_blank" href="{$userUrl}/clust3.pdf">pdf</a> | <a target="_blank" href="{$userUrl}/clust3.jpeg">jpeg</a>)</td></tr>
</table>
</div>
<div id="results-download2" class="panel panel-default" style="display:none;">
<div class="panel-heading"><span class="glyphicon glyphicon-file"></span> Download processed data</div>
<!-- Table -->
<table class="table" style="font-size:12.5px;">
<tr class="active"><td><a target="_blank" href="{$userUrl}/SegStats?uniq={$rnd}"><strong>Statistics</strong></a>: Bin count statistics for each cell <strong>({$dloadFileSizes['SegStats']})</strong>.</span></td></tr>
<tr class="active"><td><a target="_blank" href="{$userUrl}/SegBreaks?uniq={$rnd}"><strong>Breakpoints</strong></a>: Matrix that encodes whether a cell has a breakpoint at a bin position; 1 = breakpoint present, 0 = no breakpoint at that position; rows = bins, columns = cells <strong>({$dloadFileSizes['SegBreaks']}).</strong></span></td></tr>
<tr class="active"><td><a target="_blank" href="{$userUrl}/SegCopy?uniq={$rnd}"><strong>Copy Number</strong></a>: Integer coopy-number state for each cell at every bin position; rows = bins, columns = cells <strong>({$dloadFileSizes['SegCopy']}).</strong></span></td></tr>
<tr class="active"><td><a target="_blank" href="{$userUrl}/SegNorm?uniq={$rnd}"><strong>Normalized Counts</strong></a>: Normalized bin counts for each cell at every bin position; rows = bins, columns = cells <strong>({$dloadFileSizes['SegNorm']}).</strong></span></td></tr>
<tr class="active"><td><a target="_blank" href="{$userUrl}/SegFixed?uniq={$rnd}"><strong>Normalized and Segmented Counts</strong></a>: Normalized and segmented bin counts for each cell at every bin position; rows = bins, columns = cells <strong>({$dloadFileSizes['SegFixed']}).</strong></span></td></tr>
<tr class="active"><td><a target="_blank" href="{$userUrl}/CNV1?uniq={$rnd}"><strong>Copy number events</strong></a>: List of regions with copy number events <strong>({$dloadFileSizes['CNV1']}).</strong></span></td></tr>
<tr class="active"><td><a target="_blank" href="{$userUrl}/CNV2?uniq={$rnd}"><strong>Copy number regions</strong></a>: List of regions of amplifications (+1) and deletions (-1) <strong>({$dloadFileSizes['CNV2']}).</strong></span></td></tr>
</table>
</div>
PANEL;
// =============================================================================
// == Upload facs / binning file ===============================================
// =============================================================================
if($GINKGO_PAGE == 'admin-upload')
{
// Create user directory if doesn't exist
@mkdir($userDir);
$result = "";
// FACS file
if(!empty($_FILES['params-facs-file']))
// Upload facs file
if(is_uploaded_file($_FILES['params-facs-file']['tmp_name']))
{
move_uploaded_file($_FILES['params-facs-file']['tmp_name'], $userDir . "/user-facs.txt");
$result .= "facs";
}
// Segmentation file
if(!empty($_FILES['params-segmentation-file']))
// Upload binning file
if(is_uploaded_file($_FILES['params-segmentation-file']['tmp_name']))
{
move_uploaded_file($_FILES['params-segmentation-file']['tmp_name'], $userDir . "/user-segmentation.txt");
$result .= "segmentation";
}
die($result);
}
// =============================================================================
// == Launch analysis ==========================================================
// =============================================================================
if(isset($_POST['analyze']))
{
// Create user directory if doesn't exist
@mkdir($userDir);
// Sanitize user input (see bootstrap.php)
array_walk_recursive($_POST, 'sanitize');
$user = $GINKGO_USER_ID;
sanitize($user);
// Defaults for new analysis
$init = 1;
$process = 1;
$fix = 0;
// Did the user change the analysis parameters from the last time?
// Load previous configuration
$configFile = $userDir . "/config";
if(file_exists($configFile))
{
//
$f = file($configFile);
$oldParams = array();
foreach($f as $index => $val)
{
$values = explode("=", $val, 2);
$oldParams[$values[0]] = str_replace("", "", trim($values[1]));
}
// Defaults for old analysis (do nothing)
$init = 0;
$process = 0;
$fix = 0;
// Do we need to remap? This sets init to 1 if yes, 0 if not
$newBinParams = ($oldParams['binMeth'] != $_POST['binMeth']) ||
($oldParams['binList'] != $_POST['binList']) ||
($oldParams['rmbadbins']!= $_POST['rmbadbins']) ||
($oldParams['rmpseudoautosomal']!= $_POST['rmpseudoautosomal']);
$newFacs = ($oldParams['facs'] != $_POST['facs']);
$newSegParams = ($oldParams['segMeth'] != $_POST['segMeth']) || ($_POST['segMethCustom'] != '');
$newClustering = ($oldParams['clustMeth'] != $_POST['clustMeth']);
$newDistance = ($oldParams['distMeth'] != $_POST['distMeth']);
$newColor = ($oldParams['color'] != $_POST['color']);
$sexChange = ($oldParams['sex'] != $_POST['sex']);
// Different cells to analyze than last time?
$cells = '';
foreach($_POST['cells'] as $cell)
$cells .= str_replace("'", "", $cell) . "\n";
if($cells != file_get_contents($userDir . '/list'))
$newBinParams = 1;
// -- Set new variable values
// Redo the mapping for all files
if($newBinParams)
$init = 1;
// Redo binning stuff
if($newBinParams || $newSegParams || $newColor || $newFacs)
$process = 1;
// Redraw dendrogams
// Only need to run fix when not running process.R
if(!$process && !$init && ($newClustering || $newDistance || $sexChange))
$fix = 1;
// When redirect, if status file isn't changed quickly enough, will show up as 100% completed
// However, only delete status file if we need to redo at least 1 part of the analysis
if($init || $process || $fix) {
$statusFile = DIR_UPLOADS . '/' . $GINKGO_USER_ID . '/status.xml';
unlink($statusFile);
}
}
// Make sure have enough cells for analysis
if(count($_POST['cells']) < $GINKGO_MIN_NB_CELLS)
die("Please select at least " . $GINKGO_MIN_NB_CELLS . " cells for your analysis.");
// Create list-of-cells-to-analyze file
$cells = '';
foreach($_POST['cells'] as $cell)
$cells .= str_replace("'", "", $cell) . "\n";
file_put_contents($userDir . '/list', $cells);
// Create config file
$config = '#!/bin/bash' . "\n";
$config.= 'user=' . $user . "\n";
$config.= 'email=' . $_POST['email'] . "\n";
$config.= 'permalink=\'' . URL_ROOT . '/?q=results/' . str_replace("'", "", $user) . "'\n";
//
$config.= 'segMeth=' . $_POST['segMeth'] . "\n";
$config.= 'binMeth=' . $_POST['binMeth'] . "\n";
$config.= 'clustMeth=' . $_POST['clustMeth'] . "\n";
$config.= 'distMeth=' . $_POST['distMeth'] . "\n";
//
$config.= 'b=' . $_POST['b'] . "\n";
$config.= 'binList=' . $_POST['binList'] . "\n";
$config.= 'f=' . $_POST['f'] . "\n";
$config.= 'facs=' . $_POST['facs'] . "\n";
$config.= 'q=' . $_POST['g'] . "\n";
$config.= 'chosen_genome=' . $_POST['chosen_genome'] . "\n";
//
$config.= 'init=' . $init . "\n";
$config.= 'process=' . $process . "\n";
$config.= 'fix=' . $fix . "\n";
//
$config.= 'ref=' . $_POST['segMethCustom'] . "\n";
//
$config.= 'color=' . $_POST['color'] . "\n";
$config.= 'sex=' . $_POST['sex'] . "\n";
$config.= 'rmbadbins=' . $_POST['rmbadbins'] . "\n";
$config.= 'rmpseudoautosomal=' . $_POST['rmpseudoautosomal'] . "\n";
//
file_put_contents($userDir . '/config', $config);
// Start analysis
$cmd = "./scripts/analyze $GINKGO_USER_ID >> $userDir/ginkgo.out 2>&1 &";
session_regenerate_id(TRUE);
$handle = popen($cmd, 'r');
pclose($handle);
// Save to cookie and file
setcookie("ginkgo[$GINKGO_USER_ID]", $_POST['job_name'], time()+36000000);
file_put_contents($userDir . '/description.txt', $_POST['job_name']);
// Return OK status
echo "OK";
exit;
}
// =============================================================================
// == Launch analysis **on subset of cells** ===================================
// =============================================================================
if(isset($_POST['analyze-subset']))
{
// Job settings
$selectedCells = $_POST['selectedCells'];
$analysisType = $_POST['analysisType'];
//
$analysisID = generateID(10);
// Save job settings
$configTxt = $analysisType . "\n";
foreach($selectedCells as $cell)
$configTxt .= $cell . "\n";
file_put_contents($userDir . '/' . $analysisID . '.config', $configTxt);
// Start analysis
$PAR = 'original';
if($config['rmpseudoautosomal'] == '1')
$PAR = 'pseudoautosomal';
$cmd = "./scripts/analyze-subset.R $GINKGO_USER_ID $analysisID $genome {$config['binMeth']} $PAR >> $userDir/ginkgo-" . $analysisID . ".out 2>&1 &";
session_regenerate_id(TRUE);
$handle = popen($cmd, 'r');
pclose($handle);
echo $analysisID;
exit;
}
if($GINKGO_PAGE == "results-subset")
{
if(file_exists('uploads/' . $GINKGO_USER_ID . '/' . $query[2] . '.done'))
echo '<img src="./uploads/' . $GINKGO_USER_ID . '/' . $query[2] . '.jpeg?uniq=' . rand(1e6,2e6) . '">';
else
echo 'Generating figure...<meta http-equiv="refresh" content="1">';
exit;
}
// =============================================================================
// == Prepare file for UCSC custom track =======================================
// =============================================================================
if(isset($_POST['ucsc']))
{
// Job settings
$cell = $_POST['cell'];
$range = $_POST['range'];
//
$analysisID = generateID(10);
// Save job settings
$configTxt = "browser position {$range}\n";
$CMD = <<<CM
awk -v CELL='"{$cell}"' 'BEGIN{ print "track name=Amplifications description="CELL" color=0,0,255,"; }{ if(NR==1){ for(i=1;i<=NF;i++){if(\$i==CELL)cellID=i;} }else{ if(\$cellID>2)print \$1"\t"\$2"\t"\$3; } }' ./uploads/{$GINKGO_USER_ID}/SegCopy;
awk -v CELL='"{$cell}"' 'BEGIN{ print "track name=Deletions description="CELL" color=255,0,0,"; }{ if(NR==1){ for(i=1;i<=NF;i++){if(\$i==CELL)cellID=i;} }else{ if(\$cellID<2)print \$1"\t"\$2"\t"\$3; } }' ./uploads/{$GINKGO_USER_ID}/SegCopy;
CM;
file_put_contents($userDir . '/' . $analysisID . '.ucsc', "browser position {$range}\n".shell_exec($CMD));
echo $analysisID;
exit;
}
// =============================================================================
// == If analysis under way, redirect to status page ===========================
// =============================================================================
// Load status.xml if exists and check if analysis under way
if($GINKGO_PAGE == "" || $GINKGO_PAGE == "home" || $GINKGO_PAGE == "dashboard") {
$statusFile = DIR_UPLOADS . '/' . $GINKGO_USER_ID . '/status.xml';
if(file_exists($statusFile)) {
$status = simplexml_load_file($statusFile);
if($status->step < 3 && $status->percentdone < 100) {
header("Location: ?q=results/" . $GINKGO_USER_ID);
exit;
}
}
}
// Load current settings
$configFile = $userDir . "/config";
if(file_exists($configFile)) {
$f = file($configFile);
$config = array();
foreach($f as $index => $val) {
$values = explode("=", $val, 2);
$config[$values[0]] = str_replace("'", "", trim($values[1]));
}
}
//
if($GINKGO_PAGE == 'admin-search')
{
$file = DIR_ROOT . '/genomes/' . $config['chosen_genome'] . '/' . ($config['rmpseudoautosomal'] == '1' ? 'pseudoautosomal' : 'original') . '/genes_' . $config['binMeth'];
$gene = escapeshellarg($_GET['gene']);
$bin = escapeshellarg($_GET['binNumber']);
//
if(isset($_GET['gene']))
die(`grep -i -w $gene $file | head -n 1 | cut -f3`);
//
if(isset($_GET['binNumber']))
die(`awk '{if($3==$bin) print $2}' $file | sort | uniq`);
}
// =============================================================================
// == HTML template ============================================================
// =============================================================================
?><!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<meta name="description" content="">
<meta name="author" content="">
<title>Ginkgo</title>
<!-- Bootstrap core CSS -->
<link rel="stylesheet" href="//netdna.bootstrapcdn.com/bootstrap/3.0.0/css/bootstrap.min.css">
<link rel="stylesheet" href="//netdna.bootstrapcdn.com/bootstrap/3.0.0/css/bootstrap-theme.min.css">
<!-- Custom styles -->
<style>
html, body { height:100%; }
td { vertical-align:middle !important; }
code input { border:none; color:#c7254e; background-color:#f9f2f4; width:100%; }
code textarea { border:none; color:#c7254e; background-color:#f9f2f4; width:100%; resize:none; }
svgCanvas { fill:none; pointer-events:all; }
.jumbotron { padding:50px 30px 15px 30px; }
.glyphicon { vertical-align:top; }
.badge { vertical-align:top; margin-top:5px; }
.permalink { border:1px solid #DDD; width:100%; color:#666; background:transparent; font-family:"courier"; resize:none; height:50px; }
.sorting_asc { background: url('includes/datatables/images/sort_asc.png') no-repeat center right; }
.sorting_desc { background: url('includes/datatables/images/sort_desc.png') no-repeat center right; }
.sorting { background: url('includes/datatables/images/sort_both.png') no-repeat center right; }
.sorting_asc_disabled { background: url('includes/datatables/images/sort_asc_disabled.png') no-repeat center right; }
.sorting_desc_disabled { background: url('includes/datatables/images/sort_desc_disabled.png') no-repeat center right; }
/* callout */
.bs-callout { margin:20px 0; padding:15px 30px 15px 15px; border-left:5px solid #eee; }
.bs-callout h4 { margin-top:0; }
.bs-callout p:last-child { margin-bottom:0; }
.bs-callout code, .bs-callout .highlight { background-color:#fff; }
/* */
.bs-callout-danger { background-color:#fcf2f2; border-color:#dFb5b4; }
.bs-callout-warning { background-color:#fefbed; border-color:#f1e7bc; }
.bs-callout-info { background-color:#f0f7fd; border-color:#d0e3f0; }
/* */
#results-QA-table tr td:first-child { text-align: center; }
#results-QA-table tr td:first-child:before { content: "\f096"; font-family: FontAwesome; }
#results-QA-table tr.selected td:first-child:before { content: "\f046"; }
/* */
.codesample { background-color:#f9f2f4; font-family:Monaco, monospace, serif; font-size:90%; color:#C7254E; padding:10px; }
</style>
<!-- Tinycon styles/javascript -->
<script type="text/javascript" src="includes/tinycon/tinycon.min.js"></script>
<link rel="icon" href="includes/tinycon/ginkgo.ico" />
<script>
(function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
(i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
})(window,document,'script','//www.google-analytics.com/analytics.js','ga');
ga('create', 'UA-31249083-2', 'auto');
ga('send', 'pageview');
</script>
</head>
<body>
<!-- Navigation bar -->
<div class="navbar navbar-inverse navbar-fixed-top">
<div class="container">
<div class="navbar-header">
<button type="button" class="navbar-toggle" data-toggle="collapse" data-target=".navbar-collapse">
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<ul class="nav navbar-nav">
<li>
<a class="navbar-brand dropdown-toggle" data-toggle="dropdown" href="#"><span class="glyphicon glyphicon-tree-deciduous"></span> Ginkgo <span class="caret" style="border-top-color:#ccc !important; border-bottom-color:#ccc !important;"></span></a>
<ul class="dropdown-menu" role="menu">
<li><a href="?q=">Home</a></li>
<li><a href="https://github.com/robertaboukhalil/ginkgo">Code on Github</a></li>
<li><a href="http://biorxiv.org/content/early/2015/03/06/011346">Paper on bioRxiv</a></li>
<li class="divider"></li>
<li><a href="?q=results/_t10breast_navin"><small><small style="color:#bdc3c7">DOP-PCR</small></small> Polygenomic breast tumor — <i>Navin et al, 2011</i></a></li>
<li><a href="?q=results/_t16breast_liver_met_navin"><small><small style="color:#bdc3c7">DOP-PCR</small></small> Breast cancer + liver metastasis — <i>Navin et al, 2011</i></a></li>
<li><a href="?q=results/_neuron_mcconnell"><small><small style="color:#bdc3c7">DOP-PCR</small></small> Neurons — <i>McConnell et al, 2013</i></a></li>
<li><a href="?q=results/_ctc_ni"><small><small style="color:#bdc3c7">MALBAC </small></small> Circulating lung tumor cells — <i>Ni et al, 2013</i></a></li>
<li><a href="?q=results/_oocyte_hou"><small><small style="color:#bdc3c7">MALBAC </small></small> Oocytes — <i>Hou et al, 2013</i></a></li>
<li><a href="?q=results/_sperm_lu"><small><small style="color:#bdc3c7">MALBAC </small></small> Sperm — <i>Lu et al, 2012</i></a></li>
<li><a href="?q=results/_sperm_kirkness"><small><small style="color:#bdc3c7">MDA </small></small> Sperm — <i>Kirkness et al, 2013</i></a></li>
<li><a href="?q=results/_sperm_wang"><small><small style="color:#bdc3c7">MDA </small></small> Sperm — <i>Wang et al, 2012</i></a></li>
<li><a href="?q=results/_neuron_evrony"><small><small style="color:#bdc3c7">MDA </small></small> Neurons — <i>Evrony et al, 2012</i></a></li>
<?php if(count($_COOKIE['ginkgo']) > 0): ?>
<li class="divider"></li>
<?php foreach($_COOKIE['ginkgo'] as $id => $name): ?>
<?php if($id != "sample"): ?>
<li><a href="?q=dashboard/<?php echo $id;?>"><?php echo str_replace("'", "", $name);?></a></li>
<?php endif; ?>
<?php endforeach; ?>
<?php endif; ?>
</ul>
</li>
</ul>
</div>
</div>
</div>
<!-- Welcome message -->
<div class="jumbotron">
<div class="container">
<h1><a style="text-decoration:none; color:#000" href="?q=/<?php echo $GINKGO_USER_ID; ?>">Ginkgo</a> <small><?php echo str_replace("'", "", @file_get_contents($userDir.'/description.txt')); ?></small></h1>
<div id="status" style="margin-top:20px;">
<?php if($GINKGO_PAGE == 'home'): ?>
A web tool for analyzing single-cell sequencing data.
<br>
<div class="btn-group">
<button type="button" class="btn btn-primary dropdown-toggle" data-toggle="dropdown">Sample analyses <span class="caret"></span></button>
<ul class="dropdown-menu" role="menu">
<li><a href="?q=results/_t10breast_navin"><small><small style="color:#bdc3c7">DOP-PCR</small></small> Polygenomic breast tumor — <i>Navin et al, 2011</i></a></li>
<li><a href="?q=results/_t16breast_liver_met_navin"><small><small style="color:#bdc3c7">DOP-PCR</small></small> Breast cancer + liver metastasis — <i>Navin et al, 2011</i></a></li>
<li><a href="?q=results/_neuron_mcconnell"><small><small style="color:#bdc3c7">DOP-PCR</small></small> Neurons — <i>McConnell et al, 2013</i></a></li>
<li><a href="?q=results/_ctc_ni"><small><small style="color:#bdc3c7">MALBAC </small></small> Circulating lung tumor cells — <i>Ni et al, 2013</i></a></li>
<li><a href="?q=results/_oocyte_hou"><small><small style="color:#bdc3c7">MALBAC </small></small> Oocytes — <i>Hou et al, 2013</i></a></li>
<li><a href="?q=results/_sperm_lu"><small><small style="color:#bdc3c7">MALBAC </small></small> Sperm — <i>Lu et al, 2012</i></a></li>
<li><a href="?q=results/_bonemarrow_hou"><small><small style="color:#bdc3c7">MDA </small></small> Bone marrow — <i>Hou et al, 2012</i></a></li>
<li><a href="?q=results/_kidney_xu"><small><small style="color:#bdc3c7">MDA </small></small> Kidney — <i>Xu et al, 2012</i></a></li>
<li><a href="?q=results/_neuron_evrony"><small><small style="color:#bdc3c7">MDA </small></small> Neurons — <i>Evrony et al, 2012</i></a></li>
</ul>
</div>
<?php if(count($_COOKIE['ginkgo']) > 0): ?>
<div class="btn-group">
<button type="button" class="btn btn-primary dropdown-toggle" data-toggle="dropdown">Load previous analysis <span class="caret"></span></button>
<ul class="dropdown-menu" role="menu">
<li class="divider"></li>
<?php foreach($_COOKIE['ginkgo'] as $id => $name): ?>
<?php if($id != "sample"): ?>
<li><a href="?q=dashboard/<?php echo $id;?>"><?php echo str_replace("'", "", $name);?></a></li>
<?php endif; ?>
<?php endforeach; ?>
</ul>
</div>
<?php endif; ?>
<?php elseif($GINKGO_PAGE == 'dashboard'): ?>
<div class="status-box">Your files are uploaded. Now let's do some analysis:</div>
<?php elseif($GINKGO_PAGE == 'results'): ?>
<div class="status-box" id="results-status">
<span id="results-status-text">Updating status...</span><br />
<div class="progress progress-striped active"><div id="results-progress" class="progress-bar" role="progressbar" style="width: 0%"></div></div>
</div>
<?php endif; ?>
</div>
</div>
</div>
<!-- Main container -->
<div class="container">
<?php // ================================================================ ?>
<?php // == Home: Upload files ========================================== ?>
<?php // ================================================================ ?>
<?php if($GINKGO_PAGE == 'home'): ?>
<!-- Upload files -->
<?php if($GINKGO_USER_ID != 'sample' && $GINKGO_USER_ID != 'sample2'): ?>
<div class="row" style="height:100%;">
<div class="col-lg-8">
<h3 style="margin-top:-5px;"><span class="badge">STEP 0</span> Upload your .bed files <small><strong>(We accept *.bed and *.bed.gz, max 1GB/file, min 3 cells)</strong></small></h3>
<iframe id="upload-iframe" style="width:100%; height:100%; border:0;" src="includes/fileupload/?user_id=<?php echo $GINKGO_USER_ID; ?>"></iframe>
<p>
<div style="float:right">
<a id="fileupload-next-step" class="btn btn-lg btn-primary" href="?q=dashboard/<?php echo $GINKGO_USER_ID; ?>">Next step <span class="glyphicon glyphicon-chevron-right"></span></a>
</div>
</p>
</div>
<div class="col-lg-4">
<?php echo $PANEL_PREVIOUS; ?>
<?php echo $PANEL_LATER; ?>
<!-- Panel: Help -->
<div class="panel panel-primary">
<div class="panel-heading"><h3 class="panel-title"><span class="glyphicon glyphicon-question-sign"></span> Help</h3></div>
<div class="panel-body">
<div class="panel-group" id="help-bedfmt">
<div class="panel panel-default">
<div class="panel-heading"><h4 class="panel-title"><a class="accordion-toggle" data-toggle="collapse" data-parent="#help-bedfmt" href="#help-bedfmt-content">Sample .bed file</a></h4></div>
<div id="help-bedfmt-content" class="panel-collapse collapse in"><div class="panel-body">
<table class="table">
<thead><tr><th>chrom</th><th>chromStart</th><th>chromEnd</th></tr></thead>
<tbody><tr><td>chr1</td><td>555485</td><td>555533</td></tr><tr><td>chr1</td><td>676584</td><td>676632</td></tr><tr><td>chr1</td><td>745136</td><td>745184</td></tr></tbody>
</table>
</div></div>
</div>
</div>
<br/>
<div class="panel-group" id="help-makebed">
<div class="panel panel-default">
<div class="panel-heading"><h4 class="panel-title"><a class="accordion-toggle" data-toggle="collapse" data-parent="#help-makebed" href="#help-makebed-content">How to make .bed files</a></h4></div>
<div id="help-makebed-content" class="panel-collapse collapse in">
<div class="panel-body">
<p>If your mapped reads are saved in the file <strong>reads.bam</strong>:</p>
<div class="codesample">bamToBed -i reads.bam > reads.bed</div>
</div>
</div>
</div>
</div>
<br/>
<div class="panel-group" id="help-details">
<div class="panel panel-default">
<div class="panel-heading"><h4 class="panel-title"><a class="accordion-toggle" data-toggle="collapse" data-parent="#help-details" href="#help-details-content">Detailed instructions</a></h4></div>
<div id="help-details-content" class="panel-collapse collapse out">
<div class="panel-body">
<p>
<strong>Step 1</strong><br/>
If you do not have a reference genome index (e.g. hg19), download it from the <a href="http://bowtie-bio.sourceforge.net/bowtie2/index.shtml" target="_blank">Bowtie2 website</a> (menu on right, under <i>Indexes</i>).
Then, map your reads (in <strong>reads.fastq</strong>) to the genome, and output the results to <strong>reads.sam</strong>:</p>
<div class="codesample">bowtie2 -x hg19 -U reads.fastq -S reads.sam</div>
<br/>
<p>If you have paired-end reads, use the following command instead:</p>
<div class="codesample">bowtie2 -x hg19 -1 reads_r1.fastq -2 reads_r2.fastq -S reads.sam</div>
<br/>
<p>
<strong>Step 2</strong><br/>
Convert <strong>reads.sam</strong> to <strong>reads.bam</strong>:</p>
<div class="codesample">samtools view -Sb reads.sam -q 20 -o reads.bam</div>
<br/><p>
<strong>Step 3</strong><br/>
Convert <strong>reads.bam</strong> to <strong>reads.bed</strong>:</p>
<div class="codesample">bamToBed -i reads.bam > reads.bed</div>
</div>
</div>
</div>
</div>
</div>
<?php else: ?>
<script>
window.location = '?q=results/<?php echo $GINKGO_USER_ID; ?>';
</script>
<?php endif; ?>
<?php // ================================================================ ?>
<?php // == Dashboard: Analysis settings ================================ ?>
<?php // ================================================================ ?>
<?php elseif($GINKGO_PAGE == 'dashboard'): ?>
<!-- Dashboard -->
<div class="row">
<div id="dashboard" class="col-lg-8">
<form id="form-dashboard">
<!-- Choose cells of interest -->
<h3 style="margin-top:-5px;"><span class="badge">STEP 1</span> Choose cells for analysis</h3>
<?php if($GINKGO_USER_ID != 'sample' && $GINKGO_USER_ID != 'sample2'): ?>
<button id="dashboard-toggle-cells" class="btn btn-info" style="margin:20px;">Select all cells</button>
<br/>
<div id="params-cells" style="max-height:200px; overflow:auto">
<?php $previouslySelected = file(DIR_UPLOADS . '/' . $GINKGO_USER_ID . '/list', FILE_IGNORE_NEW_LINES | FILE_SKIP_EMPTY_LINES); ?>
<?php $selected = array(); ?>
<?php foreach($MY_CELLS as $currCell): ?>
<?php
// Was the current cell previously selected in an analysis?
$selected[$currCell] = "";
if(in_array($currCell, $previouslySelected))
$selected[$currCell] = " checked";
?>
<label><div class="input-group" style="margin:20px;"><span class="input-group-addon"><input type="checkbox" name="dashboard_cells[]" value="<?php echo $currCell; ?>"<?php echo $selected[$currCell];?>></span><span class="form-control"><?php echo $currCell; ?></span></div></label>
<?php endforeach; ?>
</div>
<!-- Which genome? -->
<br/><br/><h3 style="margin-top:-5px;"><span class="badge">STEP 2</span> Set analysis options <small></small></h3>
<div id="params-genome" style="margin:20px;">
<table class="table table-striped">
<tr>
<td width="20%">Job name:</td>
<td>
<input id="param-job-name" class="form-control" type="text" placeholder="Single-cells from tissue X" value="<?php echo str_replace("'", "", file_get_contents($userDir . '/description.txt')); ?>">
</td>
</tr>
<tr>
<td width="20%">Genome:</td>
<td>
<select id="param-genome" class="input-mini" style="margin-top:8px; font-size:11px; padding-top:3px; padding-bottom:0; height:25px; ">
<optgroup label="Latest genomes">
<!--<option value="hg20">Human (hg20)</option>-->
<?php $selected = array(); $selected[$config['chosen_genome']] = ' selected'; ?>
<option value="hg19"<?php echo $selected['hg19']; ?>>Human (hg19)</option>
<option value="panTro4"<?php echo $selected['panTro4']; ?>>Chimpanzee (panTro4)</option>
<option value="mm10"<?php echo $selected['mm10']; ?>>Mus musculus (mm10)</option>
<option value="rn5"<?php echo $selected['rn5']; ?>>R. norvegicus (rn5)</option>
<option value="dm3"<?php echo $selected['dm3']; ?>>D. Melanogaster (dm3)</option>
</optgroup>
<optgroup label="Older genomes">
<option value="hg18"<?php echo $selected['hg18']; ?>>Human (hg18)</option>
<option value="panTro3"<?php echo $selected['panTro3']; ?>>Chimpanzee (panTro3)</option>
</optgroup>
</select>
</td>
</tr>
</table>
</div>
<!-- Get informed by email when done? -->
<br/><br/><h3 style="margin-top:-5px;"><span class="badge">STEP 3</span> E-mail notification <small></small></h3>
<div id="params-email" style="margin:20px;">
<p>If you want to be notified once the analysis is done, enter your e-mail here:<br/></p>
<div class="input-group">
<?php if($config['email'] != '') $email = $config['email']; ?>
<span class="input-group-addon"><span class="glyphicon glyphicon-envelope"></span></span>
<input id="email" class="form-control" type="text" placeholder="my@email.com" value="<?php echo $email; ?>">
</div>
</div>
<br/><br/>
<!-- Set parameters -->
<h3 style="margin-top:-5px;"><span class="badge">OPTIONAL</span> <a href="#parameters" onClick="javascript:$('#params-table').toggle();">Advanced parameters</a></h3>
<table class="table" id="params-table">
<tbody>
<tr class="active"><td colspan="2"><strong>Sample Parameters</strong></td></tr>
<tr>
<td>CNV Profile Color Scheme</td>
<?php $selected = array(); $selected[$config['color']] = ' selected'; ?>
<td>
Use <select id="param-color-scheme" class="input-mini" style="margin-top:8px; font-size:11px; padding-top:3px; padding-bottom:0; height:25px; ">
<option value="3"<?php echo $selected['3']; ?>>dark blue / red</option>
<option value="1"<?php echo $selected['1']; ?>>light blue / orange</option>
<option value="2"<?php echo $selected['2']; ?>>magenta / gold</option>
</select> color scheme.
</td>
</tr>
<tr>
<td>General Binning Options</td>
<?php
if(empty($config))
$config['binMeth'] = 'variable_500000_101_bowtie';
$binMeth = split('_', $config['binMeth']);
?>
<td>
<?php $selected = array(); $selected[$binMeth[0]] = ' selected'; ?>
Use a <select id="param-bins-type" class="input-mini" style="margin-top:8px; font-size:11px; padding-top:3px; padding-bottom:0; height:25px; ">
<option value="variable_"<?php echo $selected['variable']; ?>>variable</option>
<option value="fixed_"<?php echo $selected['fixed']; ?>>fixed</option>
</select> bin size of
<?php $selected = array(); $selected[$binMeth[1]] = ' selected'; ?>
<select id="param-bins-value" class="input-mini" style="margin-top:8px; font-size:11px; padding-top:3px; padding-bottom:0; height:25px; ">
<option value="500000_"<?php echo $selected['500000']; ?>>500kb</option>
<option value="250000_"<?php echo $selected['250000']; ?>>250kb</option>
<option value="175000_"<?php echo $selected['175000']; ?>>175kb</option>
<option value="100000_"<?php echo $selected['100000']; ?>>100kb</option>
<option value="50000_"<?php echo $selected['50000']; ?>>50kb</option>
<!-- <option value="40000_"<?php echo $selected['40000']; ?>>40kb</option> -->
<option value="25000_"<?php echo $selected['25000']; ?>>25kb</option>
<option value="10000_"<?php echo $selected['10000']; ?>>10kb</option>
<!-- <option value="5000_"<?php echo $selected['5000']; ?>>5kb</option> -->
</select> size.
</td>
</tr>
<tr id="param-binning-sim-options">
<td>Binning Simulation Options</td>
<td>
<?php $selected = array(); $selected[$binMeth[2]] = ' selected'; ?>
Bins based on simulations of <select id="param-bins-sim-rlen" class="input-mini" style="margin-top:8px; font-size:11px; padding-top:3px; padding-bottom:0; height:25px; ">
<option value="150_"<?php echo $selected['150']; ?>>150</option>
<option value="101_"<?php echo $selected['101']; ?>>101</option>
<option value="76_"<?php echo $selected['76']; ?>>76</option>
<option value="48_"<?php echo $selected['48']; ?>>48</option>
</select> bp reads, mapped with
<?php $selected = array(); $selected[$binMeth[3]] = ' selected'; ?>
<select id="param-bins-sim-mapper" class="input-mini" style="margin-top:8px; font-size:11px; padding-top:3px; padding-bottom:0; height:25px; ">
<option value="bowtie"<?php echo $selected['bowtie']; ?>>bowtie</option>
<option value="bwa"<?php echo $selected['bwa']; ?>>bwa</option>
</select>.
</td>
</tr>
<tr>
<td>Segmentation</td>
<?php $selected = array(); $selected[$config['segMeth']] = ' selected'; ?>
<td>Use <select id="param-segmentation" class="input-medium" style="margin-top:8px; font-size:11px; padding-top:3px; padding-bottom:0; height:25px; ">
<option value="0"<?php echo $selected[0]; ?>>Independent (normalized read counts)</option>
<option value="1"<?php echo $selected[1]; ?>>Global (sample with lowest IOD)</option>
<option value="2"<?php echo $selected[2]; ?>>Custom (using uploaded reference sample)</option>
</select> method to segment.</td>
</tr>
<tr style="display:none" id="param-segmentation-custom">
<td>Custom segmentation<br/><i><small>Upload the .bed file of a cell to normalize your data by</small></i></td>
<td style="height:45px;">
<div class="fileupload fileupload-new" data-provides="fileupload">
<div class="input-append">
<div class="uneditable-input span3">
<i class="glyphicon glyphicon-upload"></i>
<span class="fileupload-preview"></span>
</div>
<span class="btn btn-file">
<span class="fileupload-new btn btn-success">Select .bed file</span>
<span class="fileupload-exists btn btn-success">Change</span>
<input type="file" name="params-segmentation-file" />
</span>
<a href="#" class="btn btn-danger fileupload-exists" data-dismiss="fileupload">Remove</a>
</div>
</div>
</td>
</tr>
<tr id="param-segmentation-maskbadbins" style="display:none">
<td>Mask bad bins <i><small>(experimental)</small></i><br/><i><small>Removes bins with consistent read pileups from the analysis (e.g. at chromosome boundaries)</small></i></td>
<td>
<?php /* Uncomment this later */ $checked = " "; if($config['rmbadbins'] == '0') $checked=""; ?>
<input type="checkbox" id="dashboard-rmbadbins"<?php echo $checked;?>>
</td>
</tr>
<tr id="param-segmentation-pseudoautosomal" style="display:none">
<td>Mask Y-chr pseudoautosomal regions <i><small>(experimental)</small></i><br/><i><small>Description</small></i></td>
<td>
<?php /* Uncomment this later */ $checked = " "; if($config['rmpseudoautosomal'] == '0') $checked=""; ?>
<input type="checkbox" id="dashboard-rmpseudoautosomal"<?php echo $checked;?>>
</td>
</tr>
<tr class="active"><td colspan="2"><strong>Clustering Parameters</strong></td></tr>
<tr>
<td>Clustering</td>
<td>
<?php $selected = array(); $selected[$config['clustMeth']] = ' selected'; ?>
Use <select id="param-clustering" class="input-small" style="margin-top:8px; font-size:11px; padding-top:3px; padding-bottom:0; height:25px; ">
<option value="ward"<?php echo $selected['ward']; ?>>ward linkage</option>
<option value="single"<?php echo $selected['single']; ?>>single linkage</option>
<option value="complete"<?php echo $selected['complete']; ?>>complete linkage</option>
<option value="average"<?php echo $selected['average']; ?>>average linkage</option>
<option value="NJ"<?php echo $selected['NJ']; ?>>neighbor-joining</option>
</select>.
</td>
</tr>
<tr>
<td>Distance metric</td>
<td>
<?php $selected = array(); $selected[$config['distMeth']] = ' selected'; ?>
Use <select id="param-distance" class="input-small" style="margin-top:8px; font-size:11px; padding-top:3px; padding-bottom:0; height:25px; ">
<option value="euclidian"<?php echo $selected['euclidian']; ?>>Euclidean</option>
<option value="maximum"<?php echo $selected['maximum']; ?>>maximum</option>
<option value="manhattan"<?php echo $selected['manhattan']; ?>>Manhattan</option>
<option value="canberra"<?php echo $selected['canberra']; ?>>Canberra</option>
<option value="binary"<?php echo $selected['binary']; ?>>binary</option>
<option value="minkowski"<?php echo $selected['minkowski']; ?>>Minkowski</option>
</select> distance.
</td>
</tr>
<tr>
<td>Include sex chromosomes?<br/><i><small>Uncheck this box for mixed-gender samples</small></i></td>
<td>
<?php $checked = " checked"; if($config['sex'] == '0') $checked=""; ?>
<input type="checkbox" id="dashboard-include-sex"<?php echo $checked;?>>
</td>
</tr>
<tr class="active"><td colspan="2"><strong>FACS File</strong></td></tr>
<tr>
<td>FACS file:<br/><i><small>Upload a file with 2 columns: first column is cell name, second column is estimated ploidy by FACS (by DAPI stain)</small></i></td>
<td>
<div class="fileupload fileupload-new" data-provides="fileupload">
<div class="input-append">
<div class="uneditable-input span3">
<i class="glyphicon glyphicon-upload"></i>
<span class="fileupload-preview"></span>
</div>
<span class="btn btn-file">
<span class="fileupload-new btn btn-success">Select .txt file</span>
<span class="fileupload-exists btn btn-success">Change</span>
<input type="file" name="params-facs-file" />
</span>
<a href="#" class="btn btn-danger fileupload-exists" data-dismiss="fileupload">Remove</a>
</div>
</div>
</td>
</tr>
</tbody>
</table>
<?php else: ?>
<script>
window.location = '?q=results/<?php echo $GINKGO_USER_ID; ?>';
</script>
<?php endif; ?>
<br/>
<a name="parameters"></a>
<!-- Buttons: back or next -->
<?php
$btnCaption = 'Start Analysis';
if(file_exists($configFile))
$btnCaption = 'View Results';
?>
<hr><br/>
<div style="float:left"><a class="btn btn-lg btn-primary" href="?q=/<?php echo $GINKGO_USER_ID; ?>"><span class="glyphicon glyphicon-chevron-left"></span> Manage Files </a></div>
<div style="float:right"><a id="analyze" class="btn btn-lg btn-primary" href="javascript:void(0);"><?php echo $btnCaption; ?> <span class="glyphicon glyphicon-chevron-right"></span></a></div><br/><br/><br/>
</form>
</div>
<div class="col-lg-4">
<?php echo $PANEL_PREVIOUS; ?>
<?php echo $PANEL_LATER; ?>
</div>
</div>
<?php // ================================================================ ?>
<?php // == Dashboard: Results/Main ===================================== ?>
<?php // ================================================================ ?>
<?php elseif($GINKGO_PAGE == 'results' && $CURR_CELL == ""): ?>
<!-- Results -->
<div class="row">
<div id="results" class="col-lg-8">
<h3 style="margin-top:-5px;"><span class="badge">STEP 3</span> View results</h3>
<div id="results-tree" class="panel panel-info">
<div class="panel-heading"><h3 class="panel-title"><span class="glyphicon glyphicon-tree-deciduous"></span> Tree</h3></div>
<div class="panel-body" style="border:0px solid green; ">
<div id="svgCanvas" class="row-fluid" style="border:0px solid red; ">
Loading tree... <img src="loading.gif" />
</div>
</div>
</div>
<br/>
<!-- Panel: Summary -->
<div id="results-summary" class="panel panel-default">
<div class="panel-heading"><span class="glyphicon glyphicon-certificate"></span> Summary</div>
<div style="height:350px; overflow:auto;">
<table class="table" id="results-QA-table" style="display:none;"></table>
</div>
<table class="table">
<tr>
<td style="width:75%; vertical-align:middle">
With selected cells, plot:
<a aria-controls="results-QA-table" class="DTTT_button DTTT_button_text" onclick="javascript:analyze_subset('cnvprofiles')"><span>CNV profiles</span></a>