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spetreemap.php
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spetreemap.php
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<?php
// BIDDSAT - BIoDiversity DataSet Assessment Tool
// Copyright (C) 2012 Javier Otegui
// This file is part of BIDDSAT.
// BIDDSAT is free software: you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation, either version 3 of the License, or
// (at your option) any later version.
// BIDDSAT is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
// GNU General Public License for more details.
// You should have received a copy of the GNU General Public License
// along with BIDDSAT. If not, see <http://www.gnu.org/licenses/>.
// Contact: javier.otegui@gmail.com
include 'header.php';
$filename=$path.'Taxonomy.txt';
$datalink = checkFile($filename, $db, $prov, $dataset);
$file=file($filename);
$data=array();
$kingdoms=array();
$phyla=array();
$classes=array();
$orders=array();
$families=array();
$tempkingdoms=array();
$colorsadded=0;
foreach($file as $line) {
$temparray=explode("\t", $line);
$color='';
if($temparray[0]=='NULL') {
$temparray[0]='Null kingdom';
} else {
$temparray[0]=$temparray[0].' kingdom';
}
if($temparray[1]=='NULL') {
$temparray[1]='Null phylum';
} else {
$temparray[1]=$temparray[1].' phylum';
}
if($temparray[2]=='NULL') {
$temparray[2]='Null class';
} else {
$temparray[2]=$temparray[2].' class';
}
if($temparray[3]=='NULL') {
$temparray[3]='Null order';
} else {
$temparray[3]=$temparray[3].' order';
}
if($temparray[4]=='NULL') {
$temparray[4]='Null family';
} else {
$temparray[4]=$temparray[4].' family';
}
for($i=0; $i<count($tempkingdoms); $i++) {
if ($temparray[0]==$tempkingdoms[$i][0]) {
$color=$tempkingdoms[$i][1];
break;
}
}
if ($color=='') {
$colorsadded++;
array_push($tempkingdoms, array($temparray[0], $colorsadded));
}
array_push($data, $temparray);
array_push($kingdoms, array($temparray[0], 'Taxonomy', $temparray[5], 0));
array_push($phyla, array($temparray[1].' - '.$temparray[0], $temparray[0], $temparray[5], 0));
array_push($classes, array($temparray[2].' - '.$temparray[1].' - '.$temparray[0], $temparray[1].' - '.$temparray[0], $temparray[5], 0));
array_push($orders, array($temparray[3].' - '.$temparray[2].' - '.$temparray[1].' - '.$temparray[0], $temparray[2].' - '.$temparray[1].' - '.$temparray[0], $temparray[5], 0));
array_push($families, array($temparray[4].' - '.$temparray[3].' - '.$temparray[2].' - '.$temparray[1].' - '.$temparray[0], $temparray[3].' - '.$temparray[2].' - '.$temparray[1].' - '.$temparray[0], $temparray[5], $colorsadded));
}
unset($temparray);
array_shift($data);
array_shift($kingdoms);
array_shift($phyla);
array_shift($classes);
array_shift($orders);
array_shift($families);
$length=count($data);
function array_collapse($array) {
$temparray=array();
for ($temp=0; $temp<count($array); $temp++) {
$success=0;
$foundkey=0;
$temp0=$array[$temp][0];
$temp1=$array[$temp][1];
$temp2=$array[$temp][2];
for ($i=0; $i<count($temparray); $i++) {
if ($temparray[$i][0]==$temp0 and $temparray[$i][1]==$temp1) {
$success=1;
$foundkey=$i;
}
}
if($success==0) {
array_push($temparray, $array[$temp]);
} else {
$temparray[$foundkey][2]=$temparray[$foundkey][2]+$temp2;
}
}
return $temparray;
}
$final_kingdoms=array_collapse($kingdoms);
$final_phyla=array_collapse($phyla);
$final_classes=array_collapse($classes);
$final_orders=array_collapse($orders);
$final_families=array_collapse($families);
$levels=array_merge($final_kingdoms, $final_phyla, $final_classes, $final_orders, $final_families);
?>
<html>
<head>
<script type='text/javascript' src='https://www.google.com/jsapi'></script>
<script type='text/javascript'>
google.load("visualization", "1", {packages:["treemap"]});
google.setOnLoadCallback(drawChart);
function drawChart() {
var data = new google.visualization.DataTable();
data.addColumn('string', 'Taxon');
data.addColumn('string', 'Parent');
data.addColumn('number', 'Number of Species');
data.addColumn('number', 'Kingdom');
data.addRows([
["Taxonomy", null, 0, 0],
<?php
for($i=0; $i<count($levels); $i++) {
echo ' ["'.$levels[$i][0].'", "'.$levels[$i][1].'", '.$levels[$i][2].', '.$levels[$i][3].'],'."\n";
}
?>
]);
var tree = new google.visualization.TreeMap(document.getElementById('visualization'));
tree.draw(data, {
maxDepth: 5,
headerHeight: 15,
fontColor: 'black',
showScale: false,
// default color: 99FFCC
maxColor: '#0000FF',
midColor: '#00FF00',
minColor: '#FF0000',
maxDepth: 3
});
}
</script>
</head>
<body>
<h3>Species Tree Map of the taxonomy of publisher <?php echo $prov; if($dataset<>'all') { echo ', data resource '.$dataset; } ?>.</h3>
Taxonomically hierarchical tree map from kingdom to family. The size of the squares is proportional to the number of different species.<br>
Left click a level to zoom in. Right click to zoom out one level. Put mouse over a cell to see complete name.<br><br>
<div id="visualization" style="width: 1200px; height: 800px;"></div>
<?php echo $datalink."   ".$endbutton; ?>
</body>
</html>