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. Formatted as text.
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"
,
$column) {
if (
($firstMeasurement == true) ||
(
($columnName != "Feature") &&
($columnName != "Reporter") &&
($columnName != "Gene")
)
) {
$output .= "\t" . $MeasurementName . $columnName ;
}
}
$firstMeasurement = false;
}
$firstMeasurement = true;
// second row the column names:
$output .= "\nFeatureIDs";
foreach ($MeasurementNamesArray as $MeasurementName)
{
foreach ($input[$MeasurementName] as $columnName => $column) {
if (
($firstMeasurement == true) ||
(
($columnName != "Feature") &&
($columnName != "Reporter") &&
($columnName != "Gene")
)
) {
$output .= "\t" . $columnName ;
}
}
$firstMeasurement = false;
}
// now list the expression values...
// similar loop as before, except that it's wrapped in a featureid loop as well
foreach ($FeatureIDs as $FeatureID)
{
$firstMeasurement = true;
$output .= "\n" . $FeatureID;
foreach ($MeasurementNamesArray as $MeasurementName)
{
foreach ($input[$MeasurementName] as $columnName => $column)
{
if (
($firstMeasurement == true) ||
(
($columnName != "Feature") &&
($columnName != "Reporter") &&
($columnName != "Gene")
)
) {
$output .= "\t" . $column[$FeatureID];
}
}
$firstMeasurement = false;
}
}
]]>
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