Will take a list of Gene names, a list of Measurement names and a list of Column Types and produce a table. All values are coloured in relation to the a reference. In the list of Measurement names, the first Measurement listed is taken to be the reference.
php run.php -file=../../sequences/geneHunterPHP.xml -display=last -profile="The mouse microarray experiment" -GeneNames="Affy:Mouse430_2:1415670_at,Affy:Mouse430_2:1415671_at,Affy:Mouse430_2:1415672_at,Affy:Mouse430_2:1415673_at" -ColumnType="RMA Normalised" -MeasurementIDs="0,1"
,
createElement("result");
$rootDom = $domNew->appendChild($root);
// make a table
$table = $domNew->createElement("table");
$tableDom = $rootDom->appendChild($table);
$tableDom->setAttribute("border", "1");
$tr = $domNew->createElement("tr");
$trDom = $tableDom->appendChild($tr);
// if the user has supplied a list of specific measurements,
// make a list of measurement names from user input,
if ($MeasurementNames != "*" ) {
$MeasurementNamesArray = explode(",", $MeasurementNames );
} else
// or if the user requested *,
// make the array from the keys of the $input array
{
$MeasurementNamesArray = array_keys($input);
}
// create table headings from this array
foreach ($MeasurementNamesArray as $MeasurementName )
{
$th = $domNew->createElement("th");
$thDom = $trDom->appendChild($th);
$text = $domNew->createTextNode($MeasurementName);
$text = $thDom->appendChild($text);
}
$tr1 = $domNew->createElement("tr");
$tr1Dom = $tableDom->appendChild($tr1);
// generate columns for each measurement
foreach ($MeasurementNamesArray as $MeasurementName)
{
$td = $domNew->createElement("td");
$tdDom = $tr1Dom->appendChild($td);
// some measurement names may not actually have data...
if (isset($input[$MeasurementName]) )
{
$cols = $input[$MeasurementName];
$colNames = array_keys($cols);
// create a sub table
$table2 = $domNew->createElement("table");
$table2Dom = $tdDom->appendChild($table2);
$table2Dom->setAttribute("border", "1");
$tr = $domNew->createElement("tr");
$trDom = $table2Dom->appendChild($tr);
// assign headings to each column in the sub table
foreach ($colNames as $colName)
{
$th = $domNew->createElement("th");
$thDom = $trDom->appendChild($th);
/* note createTextNode is better than createElement
* for inserting text as it escapes it
*/
$text = $domNew->createTextNode($colName);
$text = $thDom->appendChild($text);
}
$featureIDs = array_keys($cols["Feature"]);
// fill the columns
foreach ($featureIDs as $featureID) {
$tr = $domNew->createElement("tr");
$trDom = $table2Dom->appendChild($tr);
foreach ($colNames as $colName)
{
$td = $domNew->createElement("td");
$tdDom = $trDom->appendChild($td);
// colour the cells by comparing expression values with original
if (is_numeric($cols[$colName][$featureID]) )
{
if ($firstTime == true)
{
$colour = "blue";
} elseif ( $cols[$colName][$featureID] > $originalValues[$colName][$featureID] )
{
$colour = "red";
} elseif ( $cols[$colName][$featureID] < $originalValues[$colName][$featureID] ) {
$colour = "green";
} else
{
$colour = "black";
}
$tdDom->setAttribute("style", "color:white;background-color:$colour;");
}
$text = $domNew->createTextNode($cols[$colName][$featureID]);
$text = $tdDom->appendChild($text);
if ($firstTime == true)
{
$originalValues[$colName][$featureID] = $cols[$colName][$featureID];
}
}
}
if ($firstTime == true)
{
$firstTime = false;
}
}
}
$output = $domNew;
]]>
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