// Show different graphs about this gene; variant type (DNA, RNA & Protein level), ...
$sID = rawurldecode($_PE[1]);
define('PAGE_TITLE', 'Graphs & statistics on gene ' . $sID);
$_T->printHeader();
$_T->printTitle();
// Load authorization, collaborators and up see statistics about all variants, not just the public ones.
lovd_isAuthorized('gene', $sID);
// Check if there are variants at all.
$nVariants = $_DB->query('SELECT COUNT(*) FROM ' . TABLE_VARIANTS . ' AS vog INNER JOIN ' . TABLE_VARIANTS_ON_TRANSCRIPTS . ' AS vot USING (id) INNER JOIN ' . TABLE_TRANSCRIPTS . ' AS t ON (vot.transcriptid = t.id) WHERE t.geneid = ?' . ($_AUTH['level'] >= LEVEL_COLLABORATOR ? '' : ' AND statusid >= ' . STATUS_MARKED), array($sID))->fetchColumn();
if (!$nVariants) {
lovd_showInfoTable('There are currently no ' . ($_AUTH['level'] >= LEVEL_COLLABORATOR ? '' : 'public ') . 'variants in this gene.', 'stop');
$_T->printFooter();
exit;
}
require ROOT_PATH . 'class/graphs.php';
$_G = new LOVD_Graphs();
lovd_includeJS('lib/flot/jquery.flot.min.js');
lovd_includeJS('lib/flot/jquery.flot.pie.min.js');
print ' <!--[if lte IE 8]><SCRIPT type="text/javascript" src="lib/flot/excanvas.min.js"></SCRIPT><![endif]-->' . "\n\n";
// FIXME; Implement:
// Check what's left here.
// - Variant types (RNA).
// - Locations of variants (exon and intron numbers)?
// - Variants in this gene reported in individuals with which diseases?
// * Too bad we don't know if these variants cause this disease. Search for pathogenicity only? YES
// We need to create the DIV containers, the Graph object will fill it in.
// To save ourselves a lot of code, we'll build the DIV containers as templates.
$aGraphs = array('Variant type (DNA level, all ' . ($_AUTH['level'] >= LEVEL_COLLABORATOR ? '' : 'public ') . 'variants)' => array('variantsTypeDNA_all' => 'All ' . ($_AUTH['level'] >= LEVEL_COLLABORATOR ? '' : 'public ') . 'variants', 'variantsTypeDNA_unique' => 'Unique ' . ($_AUTH['level'] >= LEVEL_COLLABORATOR ? '' : 'public ') . 'variants'), 'Variant type (DNA level, all ' . ($_AUTH['level'] >= LEVEL_COLLABORATOR ? '' : 'public ') . 'pathogenic variants)' => array('variantsTypeDNA_all_pathogenic' => 'All ' . ($_AUTH['level'] >= LEVEL_COLLABORATOR ? '' : 'public ') . 'pathogenic variants', 'variantsTypeDNA_unique_pathogenic' => 'Unique ' . ($_AUTH['level'] >= LEVEL_COLLABORATOR ? '' : 'public ') . 'pathogenic variants'), 'Variant type (Protein level, all ' . ($_AUTH['level'] >= LEVEL_COLLABORATOR ? '' : 'public ') . 'variants) (note: numbers are sums for all transcripts of this gene)' => array('variantsTypeProtein_all' => 'All ' . ($_AUTH['level'] >= LEVEL_COLLABORATOR ? '' : 'public ') . 'variants', 'variantsTypeProtein_unique' => 'Unique ' . ($_AUTH['level'] >= LEVEL_COLLABORATOR ? '' : 'public ') . 'variants'), 'Variant type (Protein level, all ' . ($_AUTH['level'] >= LEVEL_COLLABORATOR ? '' : 'public ') . 'pathogenic variants) (note: numbers are sums for all transcripts of this gene)' => array('variantsTypeProtein_all_pathogenic' => 'All ' . ($_AUTH['level'] >= LEVEL_COLLABORATOR ? '' : 'public ') . 'pathogenic variants', 'variantsTypeProtein_unique_pathogenic' => 'Unique ' . ($_AUTH['level'] >= LEVEL_COLLABORATOR ? '' : 'public ') . 'pathogenic variants'), 'Variant location (DNA level, all ' . ($_AUTH['level'] >= LEVEL_COLLABORATOR ? '' : 'public ') . 'variants) (note: numbers are sums for all transcripts of this gene)' => array('variantsLocations_all' => 'All ' . ($_AUTH['level'] >= LEVEL_COLLABORATOR ? '' : 'public ') . 'variants', 'variantsLocations_unique' => 'Unique ' . ($_AUTH['level'] >= LEVEL_COLLABORATOR ? '' : 'public ') . 'variants'), 'Variant type (DNA level, all ' . ($_AUTH['level'] >= LEVEL_COLLABORATOR ? '' : 'public ') . 'pathogenic variants) (note: numbers are sums for all transcripts of this gene)' => array('variantsLocations_all_pathogenic' => 'All ' . ($_AUTH['level'] >= LEVEL_COLLABORATOR ? '' : 'public ') . 'pathogenic variants', 'variantsLocations_unique_pathogenic' => 'Unique ' . ($_AUTH['level'] >= LEVEL_COLLABORATOR ? '' : 'public ') . 'pathogenic variants'));
foreach ($aGraphs as $sCategory => $aCategory) {
print ' <H5>' . $sCategory . '</H5>' . "\n" . ' <TABLE border="0" cellpadding="2" cellspacing="0" width="900" style="height : 320px;">' . "\n" . ' <TR valign="top">';
foreach ($aCategory as $sGraphID => $sTitle) {
* You should have received a copy of the GNU General Public License
* along with LOVD. If not, see <http://www.gnu.org/licenses/>.
*
*************/
define('ROOT_PATH', './');
require ROOT_PATH . 'inc-init.php';
if ($_AUTH) {
// If authorized, check for updates.
require ROOT_PATH . 'inc-upgrade.php';
}
define('PAGE_TITLE', 'Current system status');
$_T->printHeader();
$_T->printTitle();
print ' <I>Current time: ' . date('r') . '</I><BR><BR>' . "\n\n";
require ROOT_PATH . 'class/graphs.php';
$_G = new LOVD_Graphs();
lovd_includeJS('lib/flot/jquery.flot.min.js');
lovd_includeJS('lib/flot/jquery.flot.pie.min.js');
print ' <!--[if lte IE 8]><SCRIPT type="text/javascript" src="lib/flot/excanvas.min.js"></SCRIPT><![endif]-->' . "\n\n";
// Statistics about genes:
$nGenes = $_DB->query('SELECT COUNT(*) FROM ' . TABLE_GENES)->fetchColumn();
// Genes, how many variants found? || Genes, how many diseases linked?
print ' <H5>Genes (' . $nGenes . ')</H5>' . "\n" . ' <TABLE border="0" cellpadding="2" cellspacing="0" width="900" style="height : 300px; border-bottom : 3px double #CCC;">' . "\n" . ' <TR valign="top">' . "\n" . ' <TD width="50%">' . "\n" . ' <B>' . ($_AUTH['level'] >= LEVEL_COLLABORATOR ? 'V' : 'Public v') . 'ariants per gene</B><BR>' . "\n" . ' <DIV id="genesNumberOfVariants" style="width : 325px; height : 250px;"><IMG src="gfx/lovd_loading.gif" alt="Loading..."></DIV><DIV id="genesNumberOfVariants_hover"> </DIV></TD>' . "\n" . ' <TD width="50%">' . "\n" . ' <B>Linked diseases per gene</B><BR>' . "\n" . ' <DIV id="genesLinkedDiseases" style="width : 325px; height : 250px;"><IMG src="gfx/lovd_loading.gif" alt="Loading..."></DIV><DIV id="genesLinkedDiseases_hover"> </DIV></TD></TR></TABLE><BR>' . "\n\n";
// Variant types (DNA level), whole database.
print ' <H5>Variant type (DNA level)</H5>' . "\n" . ' <TABLE border="0" cellpadding="2" cellspacing="0" width="900" style="height : 320px;">' . "\n" . ' <TR valign="top">' . "\n" . ' <TD width="50%">' . "\n" . ' <B>All ' . ($_AUTH['level'] >= LEVEL_COLLABORATOR ? '' : 'public ') . ' variants</B><BR>' . "\n" . ' <DIV id="variantsTypeDNA_all" style="width : 325px; height : 250px;"><IMG src="gfx/lovd_loading.gif" alt="Loading..."></DIV><DIV id="variantsTypeDNA_all_hover"> </DIV></TD>' . "\n" . ' <TD width="50%">' . "\n" . ' <B>Unique ' . ($_AUTH['level'] >= LEVEL_COLLABORATOR ? '' : 'public ') . 'variants</B><BR>' . "\n" . ' <DIV id="variantsTypeDNA_unique" style="width : 325px; height : 250px;"><IMG src="gfx/lovd_loading.gif" alt="Loading..."></DIV><DIV id="variantsTypeDNA_unique_hover"> </DIV></TD></TR></TABLE>' . "\n\n";
$_T->printFooter(false);
$_G->genesNumberOfVariants('genesNumberOfVariants', '*', $_AUTH['level'] >= LEVEL_COLLABORATOR);
$_G->genesLinkedDiseases('genesLinkedDiseases', '*');
$_G->variantsTypeDNA('variantsTypeDNA_all', '*', $_AUTH['level'] >= LEVEL_COLLABORATOR, false);
$_G->variantsTypeDNA('variantsTypeDNA_unique', '*', $_AUTH['level'] >= LEVEL_COLLABORATOR, true);
// Number of genes, number of variants in total, number of unique variants, number of diseases, etc? Not in graphs...