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>"; }