/**
* @begin Draw tree and labels in SVG
*
* @param width Width (pixels) to draw tree + labels in
* @param height
* @param label_space Width (pixels) of space to draw leaf labels in
* @param font_height Height of font to use to draw labels
* @param default_labels Name of group of labels to show by default
*
*/
function tree2svg($obj, $width = 400, $height = 400, $label_space = 150, $font_height = 10, $force_height = false, $default_labels = 'taxa')
{
//----------------------------------------------------------------------------------------------
$t = new Tree();
$t->Parse($obj->tree->newick);
$t->BuildWeights($t->GetRoot());
$tree_width = $width - $label_space;
if (!$force_height) {
// adjust height to accomodate tree
$height = $t->GetNumLeaves() * ($font_height + $font_height / 3);
$inset = $font_height;
} else {
$inset = 0;
}
// Drawing properties
$attr = array();
$attr['inset'] = $inset;
$attr['width'] = $tree_width;
$attr['height'] = $height;
$attr['font_height'] = $font_height;
$attr['line_width'] = 1;
// Don't draw labels (we do this afterwards)
$attr['draw_leaf_labels'] = false;
$attr['draw_internal_labels'] = false;
$td = NULL;
if ($t->HasBranchLengths()) {
$td = new PhylogramTreeDrawer($t, $attr);
} else {
$td = new RectangleTreeDrawer($t, $attr);
}
$td->CalcCoordinates();
if (!$force_height) {
$port = new SVGPort('', $width, $td->max_height + $attr['font_height']);
} else {
$port = new SVGPort('', $width, $height + 2);
}
$port->StartGroup('tree');
$td->Draw($port);
$port->EndGroup();
// labels
if ($label_space > 0) {
$ni = new NodeIterator($t->getRoot());
// raw labels (OTUs)
$port->StartGroup('otu', 'otu' == $default_labels || !isset($obj->translations));
$q = $ni->Begin();
while ($q != NULL) {
if ($q->IsLeaf()) {
$p0 = $q->GetAttribute('xy');
$p0['x'] += $font_height / 3;
$text = $q->Getlabel();
$text = str_replace("_", " ", $text);
$action = 'onclick="node_info(\'' . htmlentities($text) . '\');"';
$port->DrawText($p0, $text, $action);
}
$q = $ni->Next();
}
$port->EndGroup();
if ($obj->translations) {
// Tree has a one or more translation tables
foreach ($obj->translations as $k => $v) {
// Draw labels as a separate group
$port->StartGroup($k, $k == $default_labels ? true : false);
$q = $ni->Begin();
while ($q != NULL) {
if ($q->IsLeaf()) {
$p0 = $q->GetAttribute('xy');
$p0['x'] += $font_height / 3;
$label = $q->Getlabel();
if (is_array($v)) {
if (isset($v[$label])) {
$label = $v[$label];
} else {
// No translation for this OTU
$label = '[' . $label . ']';
}
} else {
if (isset($v->{$label})) {
$label = $v->{$label};
} else {
// No translation for this OTU
$label = '[' . $label . ']';
}
}
$action = 'onclick="node_info(\'' . $q->Getlabel() . '\');"';
$port->DrawText($p0, $label, $action);
}
$q = $ni->Next();
}
$port->EndGroup();
}
}
}
$svg = $port->GetOutput();
return $svg;
}
function Draw($port)
{
parent::Draw($port);
if ($this->draw_scale_bar) {
$this->DrawScaleBar($port);
}
}