if (!file_exists("tmp_images/module_trait_relationship_map.{$filetype}")) {
continue;
}
echo '<input type="checkbox" name="c1" onclick="showMe(\'div1\', this)">';
echo "<b>Check this box to see Module Trait Relationship diagram. Identify the modules that are highest in their association with clinical phenotypes. The selection perfom by the drop-down menus showing respective module colours and phenotypes.</b>\n";
echo '<div id="div1"style="display:none"';
echo "<a><img width='100%' src='tmp_images/module_trait_relationship_map.{$filetype}' ISMAP/></a>";
echo "</div>\n";
break;
}
echo "<hr />\n";
// perform database search
if (!empty($modcolour) and !empty($clinical)) {
require_once "func_public_qtl.php";
require_once "func_conversion_58.php";
$public_qtls = get_public_qtls($linkLocali, "name");
print_r($public_qtls);
echo "<p><a href=\"networks/presentModule.php?modcolour={$modcolour}\">" . "<b>Click to open gene network for module with Cytoscape</i>)</b>" . "</a>" . "</p>\n";
$query = "SELECT module_trait_moduleMembership.trait_id as trait_id" . ",trait.gene_name as gene_name" . ",trait.chromosome as chromosome" . ",round((trait.start+trait.stop)/2)/1000000 as pos" . ",trait.mean as mean" . ",trait.sd as sd" . ",trait.name as name" . ",module_trait_pheno_geneSignificance.GS_" . $cli . ",module_trait_moduleMembership.MM_" . $modcolour . ",qtl.Chromosome as qtl_Chromosome" . ",qtl.cMorgan_Peak as qtl_cMorgan_Peak" . ",qtl.covariates as qtl_covariates" . ",qtl.LOD as qtl_lod" . " FROM module_trait_moduleMembership " . " LEFT JOIN module_trait_pheno_geneSignificance USING(trait_id) " . " LEFT JOIN trait USING(trait_id) " . " LEFT JOIN qtl on module_trait_moduleMembership.trait_id=qtl.Trait " . " WHERE module_trait_moduleMembership.moduleColor='{$modcolour}' " . "";
if (!empty($mm)) {
$query .= "AND module_trait_moduleMembership.MM_" . $modcolour . " >= " . $mm;
}
if (!empty($gs)) {
$query .= "AND module_trait_pheno_geneSignificance.GS_" . $cli . " >= " . $gs;
}
if (!empty($LODmin)) {
$query .= "AND qtl.LOD >= " . $LODmin . " ";
}
if (empty($order)) {
$order .= "trait.chromosome ASC, trait_id, qtl.LOD DESC";
}
function select_from_public_qtls($dbh, $checkboxes = FALSE)
{
if (empty($dbh)) {
die("func_public_qtl.php: select_from_public_qtls was passed empty dbh.\n");
}
$qtlsByC = get_public_qtls($dbh, "chromosome");
#echo "---------<p>qtlsByC:"; print_r($qtlsByC); echo "</p> ---------";
echo "<table>";
$orderOfChromosomes = list_chromosomes();
foreach ($orderOfChromosomes as $c) {
if (empty($qtlsByC["{$c}"])) {
continue;
}
$qtls = $qtlsByC["{$c}"];
# echo "<p>qtls:"; print_r($qtls); echo "</p>";
foreach ($qtls as $q) {
echo "<tr><td>";
if ($checkboxes) {
echo "<input name=\"cqtl[]\" type=\"checkbox\" value=\"" . $q["name"] . "\" />";
}
echo "<small>";
$mbpFrom = intval($q["start_bps"]) / 1000000;
$mbpTo = intval($q["stop_bps"]) / 1000000;
echo '<a onClick="fillChrFromTo(' . $q["chr"] . ",{$mbpFrom},{$mbpTo})\">" . $q["name"] . "</a>";
echo "</small></td>";
echo "<td align=right><small><a onClick=\"fillChr(" . $q["chr"] . ")\">" . $q["chr"] . "</a></small></td>";
echo "<td align=right><small><a onClick=\"fillFrom(" . $mbpFrom . ")\">" . $q["start_bps"] . "</a></small></td>";
echo "<td align=right><small><a onClick=\"fillTo(" . $mbpTo . ")\">" . $q["stop_bps"] . "</a></small></td>";
echo "</tr>\n";
}
}
echo "</table>";
}
