![\"Expand\"](\"/images/Expand.gif\")
";
- var contract_html = " ![\"Contract\"](\"/images/Contract.gif\")
";
-
- $('#title2, #title3, #title4').prepend(expand_html).addClass('1');
-
- $('#title1, #title5').prepend(contract_html).addClass('0');
-
- for(i=1;i<=5;i++){
- $('#title'+i).click(function(){
- if ($(this).hasClass('0')) {
- $(this).find('span').replaceWith(expand_html);
- $(this).removeClass('0');
- $(this).addClass('1');
- }
- else {
- $(this).find('span').replaceWith(contract_html);
- $(this).removeClass('1');
- $(this).addClass('0');
- }
- });
- }
-
- // Exclude cases by attributes
-
- $('div.attribute_values:first').css('display', 'inline'); //Display the dropdown menu with the first attribute's distinct values
-
- $('select[name=exclude_menu]').change(function(){
- $('div.attribute_values').css('display', 'none'); //clear all other menus when a new attribute is selected
- attribute = $(this).val();
- //attribute = $('select[name=exclude_menu]').val();
- menu = $('div.attribute_values').find('[name=\''+attribute+'\']');
- menu.parent().css('display', 'inline');
- });
-
- primary_row_count = $('#primary').find('tr').length - 1;
- other_row_count = $('#other').find('tr').length - 1;
-
- if (primary_row_count >= other_row_count) {
- row_count = primary_row_count;
- }
- else {
- row_count = other_row_count;
- }
-
- $('div.attribute_values').children('select').change(function(){
- exclude_value = $(this).val();
- });
-});
-
-$(window).load(function(){
-
- //ZS: These are needed in a few places; looping through rows by index is faster than doing a "find" search
- numPrimaryRows = $('#sortable1').find('tr').length;
- numOtherRows = $('#sortable2').find('tr').length;
-
-
-///////////////////////////////
-//Basic Statistics
-///////////////////////////////
-
- /////////////////////////////////////////////////////////////////
- // Hide unselected Basic Statistics tabs (when just BXD strains
- // are selected, hide the results for all strains/non-BXD)
- /////////////////////////////////////////////////////////////////
-
- $('#stats_tabs1').hide();
- $('#stats_tabs2').hide();
-
- $('#sectionbody2').find('select[name=stats_mdp]').change(function(){
- selected = $('#sectionbody2').find('select[name=stats_mdp] option:selected').val();
- for (i=0;i<=2;i++){
- $('#stats_tabs'+i).hide();
- }
- $('#stats_tabs'+selected).show();
- });
-
- ////////////////////////////////////////////////////////////////////////
- // Select the same tab across each sample group (when a Box Plot is
- // selected for BXD, switching to Non-BXD will also display a Box Plot)
- ////////////.///////////////////////////////////////////////////////////
-
- var $tabs1 = $('#stats_tabs0').tabs();
- var $tabs2 = $('#stats_tabs1').tabs();
- var $tabs3 = $('#stats_tabs2').tabs();
-
- $tabs1.tabs({
- show: function(event, ui) {
- var selected = $tabs1.tabs('option','selected');
- $tabs2.tabs('select',selected);
- $tabs3.tabs('select',selected);
- }
- });
- $tabs2.tabs({
- show: function(event, ui) {
- var selected = $tabs2.tabs('option','selected');
- $tabs1.tabs('select',selected);
- $tabs3.tabs('select',selected);
- }
- });
- $tabs3.tabs({
- show: function(event, ui) {
- var selected = $tabs3.tabs('option','selected');
- $tabs1.tabs('select',selected);
- $tabs2.tabs('select',selected);
- }
- });
-
-
-///////////////////////////////
-//Calculate Correlations
-///////////////////////////////
-
- $('#sectionbody3').find('input[name="sample_corr"]').click(function() {
- dbValue = $('select[name=database1] option:selected').val();
- $('input[name=database]').val(dbValue);
- criteriaValue = $('select[name=criteria1] option:selected').val();
- $('input[name=criteria]').val(criteriaValue);
- MDPValue = $('select[name=MDPChoice1] option:selected').val();
- $('input[name=MDPChoice]').val(MDPValue);
-
- methodValue = $('input[name=sample_method]:checked').val();
-
- //This simple method can be used now that 'method' is defaulted to None instead of ''
- if (methodValue == "1"){
- $('input[name=method]').val('1');
- }
- else{
- $('input[name=method]').val('2');
- }
-
- dataEditingFunc(this.form,'correlation');
- });
-
- $('#sectionbody3').find('input[name="lit_corr"]').click(function() {
- dbValue = $('select[name=database2] option:selected').val();
- $('input[name=database]').val(dbValue);
- criteriaValue = $('select[name=criteria2] option:selected').val();
- $('input[name=criteria]').val(criteriaValue);
- MDPValue = $('select[name=MDPChoice2] option:selected').val();
- $('input[name=MDPChoice]').val(MDPValue);
-
- $('input[name=method]').val('3');
-
- dataEditingFunc(this.form,'correlation');
- });
-
- $('#sectionbody3').find('input[name="tiss_corr"]').click(function() {
- dbValue = $('select[name=database3] option:selected').val();
- $('input[name=database]').val(dbValue);
- criteriaValue = $('select[name=criteria3] option:selected').val();
- $('input[name=criteria]').val(criteriaValue);
- MDPValue = $('select[name=MDPChoice3] option:selected').val();
- $('input[name=MDPChoice]').val(MDPValue);
-
- methodValue = $('input[name=tissue_method]:checked').val();
-
- if (methodValue == "4"){
- $('input[name=method]').val('4');
- }
- else{
- $('input[name=method]').val('5');
- }
- dataEditingFunc(this.form,'correlation');
- });
-
-///////////////////////////////
-//Mapping Tools
-///////////////////////////////
-
- $('#sectionbody4').find('input[name=interval]').click(function() {
- chrValue = $('select[name=chromosomes1] option:selected').val();
- $('input[name=chromosomes]').val(chrValue);
- scaleValue = $('select[name=scale1] option:selected').val();
- $('input[name=scale]').val(scaleValue);
- $('input[name=controlLocus]').val('');
-
- //Changed the way permValue, bootValue, and parentsValue are acquired; before it was $(____).is(':checked');
- permValue = $('input[name=permCheck1]:checked').val();
- $('input[name=permCheck]').val(permValue);
-
- bootValue = $('input[name=bootCheck1]:checked').val();
- $('input[name=bootCheck]').val(bootValue);
-
- if ($('input[name=parentsf14regression1]:checked').length > 0){
- $('input[name=parentsf14regression]').val('on');
- } else {
- $('input[name=parentsf14regression]').val('off');
- }
-
- varValue = $('input[name=applyVarianceSE1]:checked').val();
- $('input[name=applyVarianceSE]').val(varValue);
-
- dataEditingFunc(this.form,'intervalMap');
- });
-
- var tiptext = "e.g., rs12345";
- controlLocus = $('#sectionbody4').find('input[name=controlLocus]');
-
- if(controlLocus.val() == '' || controlLocus == tiptext) {
- controlLocus.addClass('searchtip').val(tiptext);
- }
-
- controlLocus.focus(function(e) {
- if(controlLocus.val() == tiptext) {
- controlLocus.val('');
- }
- controlLocus.removeClass('searchtip');
- });
-
- controlLocus.blur(function(e) {
- if(controlLocus.val() == '') {
- controlLocus.addClass('searchtip').val(tiptext);
- } else if(controlLocus.val() == tiptext) {
- controlLocus.addClass('searchtip');
- } else {
- controlLocus.removeClass('searchtip');
- }
- });
-
- $('#sectionbody4').find('input[name=composite]').click(function() {
- chrValue = $('select[name=chromosomes2] option:selected').val();
- $('input[name=chromosomes]').val(chrValue);
- scaleValue = $('select[name=scale2] option:selected').val();
- $('input[name=scale]').val(scaleValue);
- controlValue = controlLocus.val();
- if (controlValue != tiptext){
- controlLocus.val(controlValue);
- }
- else{
- controlLocus.val('');
- }
-
- //Changed the way permValue, bootValue, and parentsValue are acquired; before it was $(____).is(':checked');
- permValue = $('input[name=permCheck2]:checked').val();
- $('input[name=permCheck]').val(permValue);
-
- bootValue = $('input[name=bootCheck2]:checked').val();
- $('input[name=bootCheck]').val(bootValue);
-
- if ($('input[name=parentsf14regression3]:checked').length > 0){
- $('input[name=parentsf14regression]').val('on');
- } else {
- $('input[name=parentsf14regression]').val('off');
- }
-
- dataEditingFunc(this.form,'intervalMap');
-
- });
-
- $('#sectionbody4').find('input[name=marker]').click(function() {
- //Changed the way parentsValue is acquired; before it was $(____).is(':checked');
- if ($('input[name=parentsf14regression2]:checked').length > 0){
- $('input[name=parentsf14regression]').val('on');
- } else {
- $('input[name=parentsf14regression]').val('off');
- }
-
- varValue = $('input[name=applyVarianceSE2]:checked').val();
- $('input[name=applyVarianceSE]').val(varValue);
-
- dataEditingFunc(this.form,'markerRegression');
- });
-
-///////////////////////////////
-//Review and Edit Data
-///////////////////////////////
-
- $('input[name=excludeGroup]').click(function(){
- for (i = 1;i <= Math.max(primary_row_count,other_row_count)-1; i++){
- valueExists = 0;
- $('#Primary_'+i+',#Other_'+i).children().each(function(){
- if ($(this).text() == exclude_value) {
- $('#Primary_'+i+',#Other_'+i).addClass('blocked').find('input[type=text]').val('x');
- valueExists = 1;
- return false;
- }
- });
- }
- });
-
- $('.update').click(function(){
- windowName = 'formTarget' + (new Date().getTime());
- newWindow = open("",windowName,"menubar=1,toolbar=1,location=1,resizable=1,status=1,scrollbars=0,directories=1,width=900");
- document.dataInput.target = windowName;
- document.dataInput.submitID.value = "basicStatistics";
-
- primaryData = getTraitData()[0];
- otherData = getTraitData()[1];
- allData = getTraitData()[2];
-
- if (otherData[0].length > 0) {
- if ($('select[name="stats_mdp"] option:selected').val() == 0) {
- document.dataInput.strainNames.value = allData[0].toString();
- document.dataInput.strainVals.value = allData[1].toString();
- document.dataInput.strainVars.value = allData[2].toString();
- }
- else if ($('select[name="stats_mdp"] option:selected').val() == 1) {
- document.dataInput.strainNames.value = primaryData[0].toString();
- document.dataInput.strainVals.value = primaryData[1].toString();
- document.dataInput.strainVars.value = primaryData[2].toString();
- }
- else {
- document.dataInput.strainNames.value = otherData[0].toString();
- document.dataInput.strainVals.value = otherData[1].toString();
- document.dataInput.strainVars.value = otherData[2].toString();
- }
- }
- else {
- document.dataInput.strainNames.value = allData[0].toString();
- document.dataInput.strainVals.value = allData[1].toString();
- document.dataInput.strainVars.value = allData[2].toString();
- }
-
- document.dataInput.submit();
- });
-
- $('input[name="export"]').click(function(){
- windowName = 'formTarget' + (new Date().getTime());
- newWindow = open("",windowName,"menubar=1,toolbar=1,location=1,resizable=1,status=1,scrollbars=0,directories=1,width=900");
- document.dataInput.target = windowName;
- document.dataInput.submitID.value = "exportData";
-
- primaryData = getTraitData()[0];
- otherData = getTraitData()[1];
-
- document.dataInput.strainNames.value = primaryData[0].toString();
- document.dataInput.strainVals.value = primaryData[1].toString();
- document.dataInput.strainVars.value = primaryData[2].toString();
-
- document.dataInput.otherStrainNames.value = otherData[0].toString();
- document.dataInput.otherStrainVals.value = otherData[1].toString();
- document.dataInput.otherStrainVars.value = otherData[2].toString();
-
- attribute_names = new Array();
- $('#primary,#other').find('th.attribute_name').each(function(){
- attribute_names.push($(this).val().toString());
- });
-
- primary_attribute_values = ""; //This string will be structured as a dictionary with a set of values for each attribute; it will be parsed in the ExportPage class
- other_attribute_values = "";
-
- attr_counter = 1; // Counter for each different attribute
- row_counter = 1; // Counter for each value for each attribute
- while (attr_counter <= attribute_names.length){
- attribute_name = $('#primary,#other').find('th.attribute_name:eq('+ (attr_counter-1).toString() + ')').text();
- primary_row_count = $('#primary').find('tr').length - 1;
- other_row_count = $('#other').find('tr').length - 1;
-
- primary_attribute_values += attribute_name + " : ";
- other_attribute_values += attribute_name + " : ";
-
- primary_value_string = ""; //This string of values (in the format 'a,b,c', etc) will be appended to the primary_attribute_values string
- for (row_counter = 1;row_counter <= numPrimaryRows; row_counter++){
- value = $('#primary_attribute'+attr_counter.toString()+'_sample'+row_counter.toString()).text();
- if (row_counter == primary_row_count) {
- primary_value_string += (value + " / ");
- }
- else{
- primary_value_string += (value + ",");
- }
- }
-
- primary_attribute_values += primary_value_string;
-
- other_value_string = ""; //This string of values (in the format 'a,b,c', etc) will be appended to the other_attribute_values string
- for (row_counter = 1;row_counter <= numOtherRows; row_counter++){
- value = $('#other_attribute'+attr_counter.toString()+'_sample'+row_counter.toString()).text();
- if (row_counter == other_row_count) {
- other_value_string += (value + " / ");
- }
- else{
- other_value_string += (value + ",");
- }
- }
- other_attribute_values += other_value_string;
- attr_counter += 1
- }
-
- document.dataInput.extra_attributes.value = primary_attribute_values;
- document.dataInput.other_extra_attributes.value = other_attribute_values;
-
- document.dataInput.submit();
- });
-
- var thisTable = $('#sortable1,#sortable2'); //ZS: variable representing each table, because it's used often
-
- thisTable.find('input[name="selectCheck"]').click(function(){
- if($(this).is(':checked')){
- $(this).parent("").parent("").children("td").css("background-color", "yellow");
- }
- else{
- if(!($(this).parent().parent().hasClass('outlier'))){
- $(this).parent().parent().children("td").css("background-color", "white");
- }
- }
- });
-
- $('input[name=resetButton]').click(function(){
-
- //ZS: Reset "hide no value" and "hide outliers"
- $('#showHideOptions').find('input[name=showHideNoValue]').val(' Hide No Value ');
- $('#showHideOptions').find('input[name=showHideOutliers]').val(' Hide Outliers ');
- noValShown = 1;
- outliersShown = 1;
-
- for (i=1;i<=numPrimaryRows-1;i++){
- var thisRow = $('#Primary_'+i);
- if (thisRow.is('.invisible')){
- thisRow.removeClass('invisible');
- }
- if (thisRow.is('.blocked')){
- thisRow.removeClass('blocked');
- }
- if (thisRow.is(':not(.outlier)')){
- thisRow.css("background-color", "white");
- }
-
- var thisValueField = thisRow.find('.valueField');
-
- var originalValue = thisValueField[0].defaultValue;
- var thisClassNames = thisRow.find('input:eq(1)').attr('class').split(/\s+/);
- var valueClass = thisClassNames[thisClassNames.length-1];
- thisRow.find('input:eq(1)').removeClass(valueClass).addClass(originalValue).val(originalValue);
-
- if (thisValueField.length > 1){
- var originalValue = thisValueField[1].defaultValue;
- var thisClassNames = thisRow.find('input:eq(2)').attr('class').split(/\s+/);
- var valueClass = thisClassNames[thisClassNames.length-1];
- thisRow.find('input:eq(2)').removeClass(valueClass).addClass(originalValue).val(originalValue);
- }
- }
- for (i=1;i<=numOtherRows-1;i++){
- var thisRow = $('#Other_'+i);
- if (thisRow.is('.invisible')){
- thisRow.removeClass('invisible')
- }
- if (thisRow.is('.blocked')){
- thisRow.removeClass('blocked');
- }
- if (thisRow.is(':not(.outlier)')){
- thisRow.css("background-color", "white");
- }
-
- var thisValueField = thisRow.find('.valueField');
-
- var originalValue = thisValueField[0].defaultValue;
- var thisClassNames = thisRow.find('input:eq(1)').attr('class').split(/\s+/);
- var valueClass = thisClassNames[thisClassNames.length-1];
- thisRow.find('input:eq(1)').removeClass(valueClass).addClass(originalValue).val(originalValue);
-
- if (thisValueField.length > 1){
- var originalValue = thisValueField[1].defaultValue;
- var thisClassNames = thisRow.find('input:eq(2)').attr('class').split(/\s+/);
- var valueClass = thisClassNames[thisClassNames.length-1];
- thisRow.find('input:eq(2)').removeClass(valueClass).addClass(originalValue).val(originalValue);
- }
- }
- });
-
- var tiptext2 = "e.g., 4, 6-30, 43";
- var blockField = $('#showHideOptions').find('input[name=removeField]'); //ZS: Field where user inputs the index of the samples he/she wants to block; created variable because it's used often
-
- if(blockField.val() == '' || blockField.val() == tiptext2) {
- blockField.addClass('searchtip');
- blockField.val(tiptext2);
- }
-
- blockField.focus(function(e) {
- if(blockField.val() == tiptext2) {
- blockField.val('');
- }
- blockField.removeClass('searchtip');
- });
-
- blockField.blur(function(e) {
- if(blockField.val() == '') {
- blockField.addClass('searchtip');
- blockField.val(tiptext2);
- } else if(blockField.val() == tiptext2) {
- blockField.addClass('searchtip');
- } else {
- blockField.removeClass('searchtip');
- }
- });
-
- var noValShown = new Boolean(1);
- var outliersShown = new Boolean(1);
-
- $('#showHideOptions').bind('click', function(e){
- var target = e.target;
- $target = $(target);
-
- if (target.name === 'blockSamples'){
- if (blockField.val() == tiptext2){
- blockField.val('')
- }
- blockedText = blockField.val();
- blockedTextSplit = new Array();
- blockedItems = new Array();
-
- blockedTextSplit = blockedText.split(/\,/);
-
- for (i=0;i<=blockedTextSplit.length-1;i++) {
- var item = blockedTextSplit[i];
- if(item.indexOf('-') != -1){
- subArray = new Array();
- subArray = item.split('-');
- num1 = parseInt(subArray[0]);
- num2 = parseInt(subArray[1]);
- for (j=num1;j<=num2;j=j+1){
- blockedItems.push(j);
- }
- }
- else if(!(isNaN(item))) {
- blockedItems.push(item);
- }
- }
-
- for (i=0;i<=blockedItems.length-1;i++) {
- item = blockedItems[i];
- if ($('select[name=block_method]').val() == '0') {
- var thisRow = $('#Other_'+item);
- }
- else {
- var thisRow = $('#Primary_'+item);
- }
-
- if (thisRow.is('.novalue')) {
- continue;
- }
- else {
- thisRow.addClass('blocked').find('input.valueField').val('x');
- }
-
- //First look at value cell
- var thisCell = thisRow.find('input:eq(1)');
- var thisClassNames = thisCell.attr('class').split(/\s+/);
- var valueClass = thisClassNames[thisClassNames.length-1];
- var header = thisRow.parents('table.tablesorter').find('th.header:contains("Value"):eq(0)');
- if (header.hasClass('headerSortUp')){
- thisCell.removeClass(valueClass).addClass('-9999');
- } else if (header.hasClass('headerSortDown')){
- thisCell.removeClass(valueClass).addClass('9999');
- } else {
- thisCell.removeClass(valueClass).addClass('-9999');
- }
-
- //Check if there is an SE column
- if (thisRow.find('input.valueField').length > 1) {
- var thisCell = thisRow.find('input:eq(2)');
- var thisClassNames = thisCell.attr('class').split(/\s+/);
- var valueClass = thisClassNames[thisClassNames.length-1];
- var header = thisRow.parents('table.tablesorter').find('th.header:contains("SE"):eq(0)');
- if (header.hasClass('headerSortUp')){
- thisCell.removeClass(valueClass).addClass('-9999');
- } else if (header.hasClass('headerSortDown')){
- thisCell.removeClass(valueClass).addClass('9999');
- } else {
- thisCell.removeClass(valueClass).addClass('-9999');
- }
- }
- }
- }
-
- else if (target.name === 'showHideNoValue'){
- if (noValShown) {
- $('#showHideOptions').find('input[name=showHideNoValue]').val(' Show No Value ');
- for (i=1;i<=Math.max(numPrimaryRows,numOtherRows)-1;i++) {
- if (i<=numPrimaryRows-1) {
- var thisRow = $('#Primary_'+i);
- if (thisRow.is('.novalue:visible') || thisRow.is('.blocked:visible')){
- jQuery(thisRow).addClass('invisible');
- }
- }
- if (i<=numOtherRows-1){
- var thisOtherRow = $('#Other_'+i);
- if (thisOtherRow.is('.novalue:visible') || thisOtherRow.is('.blocked:visible')){
- if (thisOtherRow.is(':visible')){
- jQuery(thisOtherRow).addClass('invisible');
- }
- }
- }
- }
- noValShown = 0;
- }
- else {
- $('#showHideOptions').find('input[name=showHideNoValue]').val(' Hide No Value ');
- for (i=1;i<=Math.max(numPrimaryRows,numOtherRows)-1;i++) {
- if (i<=numPrimaryRows-1) {
- var thisRow = $('#Primary_'+i);
- if (thisRow.is('.novalue') || thisRow.is('.blocked')){
- jQuery(thisRow).removeClass('invisible');
- if (!(outliersShown)) {
- if (thisRow.is('.outlier:visible')){
- jQuery(thisRow).addClass('invisible');
- }
- }
- }
- }
- if (i<=numOtherRows-1){
- var thisOtherRow = $('#Other_'+i);
- if (thisOtherRow.is('.novalue') || thisOtherRow.is('.blocked')){
- jQuery(thisOtherRow).removeClass('invisible');
- if (!(outliersShown)) {
- if (thisOtherRow.is('.outlier:visible')){
- jQuery(thisOtherRow).addClass('invisible');
- }
- }
- }
- }
- }
- noValShown = 1;
- }
- }
-
- else if (target.name === 'showHideOutliers'){
- if (outliersShown){
- $('#showHideOptions').find('input[name=showHideOutliers]').val(' Show Outliers ');
- for (i=1;i<=Math.max(numPrimaryRows,numOtherRows)-1;i++) {
- if (i<=numPrimaryRows-1) {
- thisRow = $('#Primary_'+i);
- if (thisRow.is('.outlier:visible') && (!(thisRow.is('.invisible')))) {
- thisRow.addClass('invisible')
- }
- }
- if (i<=numOtherRows-1) {
- thisOtherRow = $('#Other_'+i);
- if (thisOtherRow.is('.outlier:visible') && (!(thisOtherRow.is('.invisible')))) {
- thisOtherRow.addClass('invisible')
- }
- }
- }
- outliersShown = 0;
- }
- else {
- $('#showHideOptions').find('input[name=showHideOutliers]').val(' Hide Outliers ');
- for (i=1;i<=Math.max(numPrimaryRows,numOtherRows)-1;i++) {
- if (i<=numPrimaryRows-1) {
- thisRow = $('#Primary_'+i);
- if (thisRow.is('.outlier') && (!(thisRow.is(':visible')))) {
- if (!(noValShown)) {
- if (thisRow.is('.blocked')){
- continue;
- }
- }
- jQuery(thisRow).removeClass('invisible')
- }
- }
- if (i<=numOtherRows-1) {
- thisOtherRow = $('#Other_'+i);
- if (thisOtherRow.is('.outlier') && (!(thisOtherRow.is(':visible')))) {
- if (!(noValShown)) {
- if (thisOtherRow.is('.blocked')){
- continue;
- }
- }
- jQuery(thisOtherRow).removeClass('invisible')
- }
- }
- }
- outliersShown = 1;
- }
- }
- return false;
- });
-});
-
-function getTraitData(){
- primary_row_count = $('#sortable1').find('tr').length - 1;
- other_row_count = $('#sortable2').find('tr').length - 1;
-
- primaryStrainNames = new Array();
- primaryVals = new Array();
- primaryVars = new Array();
-
- allStrainNames = new Array();
- allVals = new Array();
- allVars = new Array();
-
- for (i = 1;i <= primary_row_count; i++){
- thisRow = $('#Primary_'+i);
- strainName = thisRow.find('span:first').text();
- primaryStrainNames.push(strainName);
- allStrainNames.push(strainName);
- strainVal = thisRow.find('input:eq(1)').val();
- primaryVals.push(strainVal);
- allVals.push(strainVal);
- strainVar = ''; // Just to initialize it in case there is no var
- strainVar = thisRow.find('input:eq(2)').val();
- primaryVars.push(strainVar);
- allVars.push(strainVar);
- }
-
- otherStrainNames = new Array();
- otherVals = new Array();
- otherVars = new Array();
-
- for (j = 1;j <= other_row_count; j++){
- thisRow = $('#Other_'+j)
- strainName = thisRow.find('span:first').text();
- otherStrainNames.push(strainName);
- strainVal = thisRow.find('input:eq(1)').val();
- otherVals.push(strainVal);
- strainVar = ''; // Just to initialize it in case there is no var
- strainVar = thisRow.find('input:eq(2)').val();
- otherVars.push(strainVar);
-
- if (jQuery.inArray(strainName, allStrainNames) == -1) {
- allStrainNames.push(strainName);
- allVals.push(strainVal);
- allVars.push(strainVar);
- }
- }
-
- primaryData = [primaryStrainNames, primaryVals, primaryVars];
- otherData = [otherStrainNames, otherVals, otherVars];
- allData = [allStrainNames, allVals, allVars];
-
- return [primaryData, otherData, allData];
-}
+ var thisTable = $('#sortable1,#sortable2');
+ thisTable.bind("update propertychange keyup input paste", function (e) {
-/*
-used by networkGraphPageBody.py
-*/
+ var target = e.target;
+ $target = $(target);
-//Default to plain text + symbol for the "Export Graph File" button
-$('input[name=exportGraphFile]').live('click', function() { window.open($('input[name=exportFilename]').val() + "_plain_symbol.txt") });
+ if (target.nodeName.toLowerCase() == 'input') {
+ thisClassNames = $target.attr('class').split(/\s+/);
+ valueClass = thisClassNames[thisClassNames.length - 1];
+ newValue = $target.val();
+ thisParent = $target.parent('td');
+ thisParentId = thisParent.attr('id');
+
+ $target.removeClass(valueClass);
+
+ if (newValue == 'x') {
+ thisParent.parent('tr').addClass('blocked');
+ } else {
+ $('#' + thisParentId).children('input.valueField:eq(0)').addClass(newValue);
+ }
+ }
+ });
+
+ ////////////////////////////////////
+ // Initially close tabs
+ ////////////////////////////////////
+ thisForm = $('form[name="dataInput"]');
+
+ $('#sectionbody2').hide();
+ $('#sectionbody3').hide();
+ $('#sectionbody4').hide();
+
+ $('#title1').click(function () {
+ $('#sectionbody1').toggle();
+ return false;
+ });
+ $('#title2').click(function () {
+ $('#sectionbody2').toggle();
+ return false;
+ });
+ $('#title3').click(function () {
+ $('#sectionbody3').toggle();
+ return false;
+ });
+ $('#title4').click(function () {
+ $('#sectionbody4').toggle();
+ return false;
+ });
+ $('#title5').click(function () {
+ $('#sectionbody5').toggle();
+ return false;
+ });
-function changeFormat(graphName){
- var graphFormat = $('#exportFormat').val();
- var traitType = $('#traitType').val();
- $('input[name=exportGraphFile]').die('click');
- if (graphFormat=="xgmml"){
- if (traitType=="symbol"){
- var graphFile = graphName+ "_xgmml_symbol.txt";
- $('input[name=exportGraphFile]').live('click', function() { window.open(graphFile) });
+ //////////////////////////////////////////////////////////////
+ // Switch out + and - icon when you click each section header
+ //////////////////////////////////////////////////////////////
+ var expand_html = " ";
+ var contract_html = " ";
+
+ $('#title2, #title3, #title4').prepend(expand_html).addClass('1');
+
+ $('#title1, #title5').prepend(contract_html).addClass('0');
+
+ for (i = 1; i <= 5; i++) {
+ $('#title' + i).click(function () {
+ if ($(this).hasClass('0')) {
+ $(this).find('span').replaceWith(expand_html);
+ $(this).removeClass('0');
+ $(this).addClass('1');
+ } else {
+ $(this).find('span').replaceWith(contract_html);
+ $(this).removeClass('1');
+ $(this).addClass('0');
+ }
+ });
+ }
+
+ // Exclude cases by attributes
+ $('div.attribute_values:first').css('display', 'inline'); //Display the dropdown menu with the first attribute's distinct values
+ $('select[name=exclude_menu]').change(function () {
+ $('div.attribute_values').css('display', 'none'); //clear all other menus when a new attribute is selected
+ attribute = $(this).val();
+ //attribute = $('select[name=exclude_menu]').val();
+ menu = $('div.attribute_values').find('[name=\'' + attribute + '\']');
+ menu.parent().css('display', 'inline');
+ });
+
+ primary_row_count = $('#primary').find('tr').length - 1;
+ other_row_count = $('#other').find('tr').length - 1;
+
+ if (primary_row_count >= other_row_count) {
+ row_count = primary_row_count;
+ } else {
+ row_count = other_row_count;
+ }
+
+ $('div.attribute_values').children('select').change(function () {
+ exclude_value = $(this).val();
+ });
+});
+
+$(window).load(function () {
+
+ //ZS: These are needed in a few places; looping through rows by index is faster than doing a "find" search
+ numPrimaryRows = $('#sortable1').find('tr').length;
+ numOtherRows = $('#sortable2').find('tr').length;
+
+
+ ///////////////////////////////
+ //Basic Statistics
+ ///////////////////////////////
+ /////////////////////////////////////////////////////////////////
+ // Hide unselected Basic Statistics tabs (when just BXD strains
+ // are selected, hide the results for all strains/non-BXD)
+ /////////////////////////////////////////////////////////////////
+ $('#stats_tabs1').hide();
+ $('#stats_tabs2').hide();
+
+ $('#sectionbody2').find('select[name=stats_mdp]').change(function () {
+ selected = $('#sectionbody2').find('select[name=stats_mdp] option:selected').val();
+ for (i = 0; i <= 2; i++) {
+ $('#stats_tabs' + i).hide();
+ }
+ $('#stats_tabs' + selected).show();
+ });
+
+ ////////////////////////////////////////////////////////////////////////
+ // Select the same tab across each sample group (when a Box Plot is
+ // selected for BXD, switching to Non-BXD will also display a Box Plot)
+ ////////////.///////////////////////////////////////////////////////////
+ var $tabs1 = $('#stats_tabs0').tabs();
+ var $tabs2 = $('#stats_tabs1').tabs();
+ var $tabs3 = $('#stats_tabs2').tabs();
+
+ $tabs1.tabs({
+ show: function (event, ui) {
+ var selected = $tabs1.tabs('option', 'selected');
+ $tabs2.tabs('select', selected);
+ $tabs3.tabs('select', selected);
+ }
+ });
+ $tabs2.tabs({
+ show: function (event, ui) {
+ var selected = $tabs2.tabs('option', 'selected');
+ $tabs1.tabs('select', selected);
+ $tabs3.tabs('select', selected);
+ }
+ });
+ $tabs3.tabs({
+ show: function (event, ui) {
+ var selected = $tabs3.tabs('option', 'selected');
+ $tabs1.tabs('select', selected);
+ $tabs2.tabs('select', selected);
+ }
+ });
+
+
+ ///////////////////////////////
+ //Calculate Correlations
+ ///////////////////////////////
+ $('#sectionbody3').find('input[name="sample_corr"]').click(function () {
+ dbValue = $('select[name=database1] option:selected').val();
+ $('input[name=database]').val(dbValue);
+ criteriaValue = $('select[name=criteria1] option:selected').val();
+ $('input[name=criteria]').val(criteriaValue);
+ MDPValue = $('select[name=MDPChoice1] option:selected').val();
+ $('input[name=MDPChoice]').val(MDPValue);
+
+ methodValue = $('input[name=sample_method]:checked').val();
+
+ //This simple method can be used now that 'method' is defaulted to None instead of ''
+ if (methodValue == "1") {
+ $('input[name=method]').val('1');
+ } else {
+ $('input[name=method]').val('2');
+ }
+
+ dataEditingFunc(this.form, 'correlation');
+ });
+
+ $('#sectionbody3').find('input[name="lit_corr"]').click(function () {
+ dbValue = $('select[name=database2] option:selected').val();
+ $('input[name=database]').val(dbValue);
+ criteriaValue = $('select[name=criteria2] option:selected').val();
+ $('input[name=criteria]').val(criteriaValue);
+ MDPValue = $('select[name=MDPChoice2] option:selected').val();
+ $('input[name=MDPChoice]').val(MDPValue);
+
+ $('input[name=method]').val('3');
+
+ dataEditingFunc(this.form, 'correlation');
+ });
+
+ $('#sectionbody3').find('input[name="tiss_corr"]').click(function () {
+ dbValue = $('select[name=database3] option:selected').val();
+ $('input[name=database]').val(dbValue);
+ criteriaValue = $('select[name=criteria3] option:selected').val();
+ $('input[name=criteria]').val(criteriaValue);
+ MDPValue = $('select[name=MDPChoice3] option:selected').val();
+ $('input[name=MDPChoice]').val(MDPValue);
+
+ methodValue = $('input[name=tissue_method]:checked').val();
+
+ if (methodValue == "4") {
+ $('input[name=method]').val('4');
+ } else {
+ $('input[name=method]').val('5');
+ }
+ dataEditingFunc(this.form, 'correlation');
+ });
+
+ ///////////////////////////////
+ //Mapping Tools
+ ///////////////////////////////
+ $('#sectionbody4').find('input[name=interval]').click(function () {
+ chrValue = $('select[name=chromosomes1] option:selected').val();
+ $('input[name=chromosomes]').val(chrValue);
+ scaleValue = $('select[name=scale1] option:selected').val();
+ $('input[name=scale]').val(scaleValue);
+ $('input[name=controlLocus]').val('');
+
+ //Changed the way permValue, bootValue, and parentsValue are acquired; before it was $(____).is(':checked');
+ permValue = $('input[name=permCheck1]:checked').val();
+ $('input[name=permCheck]').val(permValue);
+
+ bootValue = $('input[name=bootCheck1]:checked').val();
+ $('input[name=bootCheck]').val(bootValue);
+
+ if ($('input[name=parentsf14regression1]:checked').length > 0) {
+ $('input[name=parentsf14regression]').val('on');
+ } else {
+ $('input[name=parentsf14regression]').val('off');
+ }
+
+ varValue = $('input[name=applyVarianceSE1]:checked').val();
+ $('input[name=applyVarianceSE]').val(varValue);
+
+ dataEditingFunc(this.form, 'intervalMap');
+ });
+
+ var tiptext = "e.g., rs12345";
+ controlLocus = $('#sectionbody4').find('input[name=controlLocus]');
+
+ if (controlLocus.val() == '' || controlLocus == tiptext) {
+ controlLocus.addClass('searchtip').val(tiptext);
+ }
+
+ controlLocus.focus(function (e) {
+ if (controlLocus.val() == tiptext) {
+ controlLocus.val('');
+ }
+ controlLocus.removeClass('searchtip');
+ });
+
+ controlLocus.blur(function (e) {
+ if (controlLocus.val() == '') {
+ controlLocus.addClass('searchtip').val(tiptext);
+ } else if (controlLocus.val() == tiptext) {
+ controlLocus.addClass('searchtip');
+ } else {
+ controlLocus.removeClass('searchtip');
+ }
+ });
+
+ $('#sectionbody4').find('input[name=composite]').click(function () {
+ chrValue = $('select[name=chromosomes2] option:selected').val();
+ $('input[name=chromosomes]').val(chrValue);
+ scaleValue = $('select[name=scale2] option:selected').val();
+ $('input[name=scale]').val(scaleValue);
+ controlValue = controlLocus.val();
+ if (controlValue != tiptext) {
+ controlLocus.val(controlValue);
+ } else {
+ controlLocus.val('');
+ }
+
+ //Changed the way permValue, bootValue, and parentsValue are acquired; before it was $(____).is(':checked');
+ permValue = $('input[name=permCheck2]:checked').val();
+ $('input[name=permCheck]').val(permValue);
+
+ bootValue = $('input[name=bootCheck2]:checked').val();
+ $('input[name=bootCheck]').val(bootValue);
+
+ if ($('input[name=parentsf14regression3]:checked').length > 0) {
+ $('input[name=parentsf14regression]').val('on');
+ } else {
+ $('input[name=parentsf14regression]').val('off');
+ }
+
+ dataEditingFunc(this.form, 'intervalMap');
+
+ });
+
+ $('#sectionbody4').find('input[name=marker]').click(function () {
+ //Changed the way parentsValue is acquired; before it was $(____).is(':checked');
+ if ($('input[name=parentsf14regression2]:checked').length > 0) {
+ $('input[name=parentsf14regression]').val('on');
+ } else {
+ $('input[name=parentsf14regression]').val('off');
+ }
+
+ varValue = $('input[name=applyVarianceSE2]:checked').val();
+ $('input[name=applyVarianceSE]').val(varValue);
+
+ dataEditingFunc(this.form, 'markerRegression');
+ });
+
+ ///////////////////////////////
+ //Review and Edit Data
+ ///////////////////////////////
+ $('input[name=excludeGroup]').click(function () {
+ for (i = 1; i <= Math.max(primary_row_count, other_row_count) - 1; i++) {
+ valueExists = 0;
+ $('#Primary_' + i + ',#Other_' + i).children().each(function () {
+ if ($(this).text() == exclude_value) {
+ $('#Primary_' + i + ',#Other_' + i).addClass('blocked').find('input[type=text]').val('x');
+ valueExists = 1;
+ return false;
}
- else if (traitType=="name"){
- var graphFile = graphName+ "_xgmml_name.txt";
- $('input[name=exportGraphFile]').live('click', function() { window.open(graphFile) });
+ });
+ }
+ });
+
+ $('.update').click(function () {
+ windowName = 'formTarget' + (new Date().getTime());
+ var windowHeight; // windowHeight and windowWidth are used to place the window in the center of the screen
+ var windowWidth;
+ windowHeight = (window.screen.height/2) - (350 + 10)
+ windowWidth = (window.screen.width/2) - (450 + 50)
+ newWindow = open("",windowName,"menubar=1,toolbar=1,resizable=1,left=" + windowWidth + ",top=" + windowHeight + ",screenX=" + windowWidth + ",screenY=" + windowHeight + ",status=1,scrollbars=0,directories=1");
+
+ document.dataInput.target = windowName;
+ document.dataInput.submitID.value = "basicStatistics";
+
+ primaryData = getTraitData()[0];
+ otherData = getTraitData()[1];
+ allData = getTraitData()[2];
+
+ if (otherData[0].length > 0) {
+ if ($('select[name="stats_mdp"] option:selected').val() == 0) {
+ document.dataInput.strainNames.value = allData[0].toString();
+ document.dataInput.strainVals.value = allData[1].toString();
+ document.dataInput.strainVars.value = allData[2].toString();
+ } else if ($('select[name="stats_mdp"] option:selected').val() == 1) {
+ document.dataInput.strainNames.value = primaryData[0].toString();
+ document.dataInput.strainVals.value = primaryData[1].toString();
+ document.dataInput.strainVars.value = primaryData[2].toString();
+ } else {
+ document.dataInput.strainNames.value = otherData[0].toString();
+ document.dataInput.strainVals.value = otherData[1].toString();
+ document.dataInput.strainVars.value = otherData[2].toString();
+ }
+ } else {
+ document.dataInput.strainNames.value = allData[0].toString();
+ document.dataInput.strainVals.value = allData[1].toString();
+ document.dataInput.strainVars.value = allData[2].toString();
+ }
+
+ document.dataInput.submit();
+ });
+
+ $('input[name="export"]').click(function () {
+ windowName = 'formTarget' + (new Date().getTime());
+ newWindow = open("", windowName, "menubar=1,toolbar=1,location=1,resizable=1,status=1,scrollbars=0,directories=1,width=900");
+ document.dataInput.target = windowName;
+ document.dataInput.submitID.value = "exportData";
+
+ primaryData = getTraitData()[0];
+ otherData = getTraitData()[1];
+
+ document.dataInput.strainNames.value = primaryData[0].toString();
+ document.dataInput.strainVals.value = primaryData[1].toString();
+ document.dataInput.strainVars.value = primaryData[2].toString();
+
+ document.dataInput.otherStrainNames.value = otherData[0].toString();
+ document.dataInput.otherStrainVals.value = otherData[1].toString();
+ document.dataInput.otherStrainVars.value = otherData[2].toString();
+
+ attribute_names = new Array();
+ $('#primary,#other').find('th.attribute_name').each(function () {
+ attribute_names.push($(this).val().toString());
+ });
+
+ primary_attribute_values = ""; //This string will be structured as a dictionary with a set of values for each attribute; it will be parsed in the ExportPage class
+ other_attribute_values = "";
+
+ attr_counter = 1; // Counter for each different attribute
+ row_counter = 1; // Counter for each value for each attribute
+ while (attr_counter <= attribute_names.length) {
+ attribute_name = $('#primary,#other').find('th.attribute_name:eq(' + (attr_counter - 1).toString() + ')').text();
+ primary_row_count = $('#primary').find('tr').length - 1;
+ other_row_count = $('#other').find('tr').length - 1;
+
+ primary_attribute_values += attribute_name + " : ";
+ other_attribute_values += attribute_name + " : ";
+
+ primary_value_string = ""; //This string of values (in the format 'a,b,c', etc) will be appended to the primary_attribute_values string
+ for (row_counter = 1; row_counter <= numPrimaryRows; row_counter++) {
+ value = $('#primary_attribute' + attr_counter.toString() + '_sample' + row_counter.toString()).text();
+ if (row_counter == primary_row_count) {
+ primary_value_string += (value + " / ");
+ } else {
+ primary_value_string += (value + ",");
}
+ }
+
+ primary_attribute_values += primary_value_string;
+
+ other_value_string = ""; //This string of values (in the format 'a,b,c', etc) will be appended to the other_attribute_values string
+ for (row_counter = 1; row_counter <= numOtherRows; row_counter++) {
+ value = $('#other_attribute' + attr_counter.toString() + '_sample' + row_counter.toString()).text();
+ if (row_counter == other_row_count) {
+ other_value_string += (value + " / ");
+ } else {
+ other_value_string += (value + ",");
+ }
+ }
+ other_attribute_values += other_value_string;
+ attr_counter += 1
+ }
+
+ document.dataInput.extra_attributes.value = primary_attribute_values;
+ document.dataInput.other_extra_attributes.value = other_attribute_values;
+
+ document.dataInput.submit();
+ });
+
+ var thisTable = $('#sortable1,#sortable2'); //ZS: variable representing each table, because it's used often
+ thisTable.find('input[name="selectCheck"]').click(function () {
+ if ($(this).is(':checked')) {
+ $(this).parent("").parent("").children("td").css("background-color", "yellow");
+ } else {
+ if (!($(this).parent().parent().hasClass('outlier'))) {
+ $(this).parent().parent().children("td").css("background-color", "white");
+ }
}
+ });
- else if (graphFormat=="plain"){
- if (traitType=="symbol"){
- var graphFile = graphName+ "_plain_symbol.txt";
- $('input[name=exportGraphFile]').live('click', function() { window.open(graphFile) });
+ $('input[name=resetButton]').click(function () {
+
+ //ZS: Reset "hide no value" and "hide outliers"
+ $('#showHideOptions').find('input[name=showHideNoValue]').val(' Hide No Value ');
+ $('#showHideOptions').find('input[name=showHideOutliers]').val(' Hide Outliers ');
+ noValShown = 1;
+ outliersShown = 1;
+
+ for (i = 1; i <= numPrimaryRows - 1; i++) {
+ var thisRow = $('#Primary_' + i);
+ if (thisRow.is('.invisible')) {
+ thisRow.removeClass('invisible');
+ }
+ if (thisRow.is('.blocked')) {
+ thisRow.removeClass('blocked');
+ }
+ if (thisRow.is(':not(.outlier)')) {
+ thisRow.css("background-color", "white");
+ }
+
+ var thisValueField = thisRow.find('.valueField');
+
+ var originalValue = thisValueField[0].defaultValue;
+ var thisClassNames = thisRow.find('input:eq(1)').attr('class').split(/\s+/);
+ var valueClass = thisClassNames[thisClassNames.length - 1];
+ thisRow.find('input:eq(1)').removeClass(valueClass).addClass(originalValue).val(originalValue);
+
+ if (thisValueField.length > 1) {
+ var originalValue = thisValueField[1].defaultValue;
+ var thisClassNames = thisRow.find('input:eq(2)').attr('class').split(/\s+/);
+ var valueClass = thisClassNames[thisClassNames.length - 1];
+ thisRow.find('input:eq(2)').removeClass(valueClass).addClass(originalValue).val(originalValue);
+ }
+ }
+ for (i = 1; i <= numOtherRows - 1; i++) {
+ var thisRow = $('#Other_' + i);
+ if (thisRow.is('.invisible')) {
+ thisRow.removeClass('invisible')
+ }
+ if (thisRow.is('.blocked')) {
+ thisRow.removeClass('blocked');
+ }
+ if (thisRow.is(':not(.outlier)')) {
+ thisRow.css("background-color", "white");
+ }
+
+ var thisValueField = thisRow.find('.valueField');
+
+ var originalValue = thisValueField[0].defaultValue;
+ var thisClassNames = thisRow.find('input:eq(1)').attr('class').split(/\s+/);
+ var valueClass = thisClassNames[thisClassNames.length - 1];
+ thisRow.find('input:eq(1)').removeClass(valueClass).addClass(originalValue).val(originalValue);
+
+ if (thisValueField.length > 1) {
+ var originalValue = thisValueField[1].defaultValue;
+ var thisClassNames = thisRow.find('input:eq(2)').attr('class').split(/\s+/);
+ var valueClass = thisClassNames[thisClassNames.length - 1];
+ thisRow.find('input:eq(2)').removeClass(valueClass).addClass(originalValue).val(originalValue);
+ }
+ }
+ });
+
+ var tiptext2 = "e.g., 4, 6-30, 43";
+ var blockField = $('#showHideOptions').find('input[name=removeField]'); //ZS: Field where user inputs the index of the samples he/she wants to block; created variable because it's used often
+ if (blockField.val() == '' || blockField.val() == tiptext2) {
+ blockField.addClass('searchtip');
+ blockField.val(tiptext2);
+ }
+
+ blockField.focus(function (e) {
+ if (blockField.val() == tiptext2) {
+ blockField.val('');
+ }
+ blockField.removeClass('searchtip');
+ });
+
+ blockField.blur(function (e) {
+ if (blockField.val() == '') {
+ blockField.addClass('searchtip');
+ blockField.val(tiptext2);
+ } else if (blockField.val() == tiptext2) {
+ blockField.addClass('searchtip');
+ } else {
+ blockField.removeClass('searchtip');
+ }
+ });
+
+ var noValShown = new Boolean(1);
+ var outliersShown = new Boolean(1);
+
+ $('#showHideOptions').bind('click', function (e) {
+ var target = e.target;
+ $target = $(target);
+
+ if (target.name === 'blockSamples') {
+ if (blockField.val() == tiptext2) {
+ blockField.val('')
+ }
+ blockedText = blockField.val();
+ blockedTextSplit = new Array();
+ blockedItems = new Array();
+
+ blockedTextSplit = blockedText.split(/\,/);
+
+ for (i = 0; i <= blockedTextSplit.length - 1; i++) {
+ var item = blockedTextSplit[i];
+ if (item.indexOf('-') != -1) {
+ subArray = new Array();
+ subArray = item.split('-');
+ num1 = parseInt(subArray[0]);
+ num2 = parseInt(subArray[1]);
+ for (j = num1; j <= num2; j = j + 1) {
+ blockedItems.push(j);
+ }
+ } else if (!(isNaN(item))) {
+ blockedItems.push(item);
+ }
+ }
+
+ for (i = 0; i <= blockedItems.length - 1; i++) {
+ item = blockedItems[i];
+ if ($('select[name=block_method]').val() == '0') {
+ var thisRow = $('#Other_' + item);
+ } else {
+ var thisRow = $('#Primary_' + item);
+ }
+
+ if (thisRow.is('.novalue')) {
+ continue;
+ } else {
+ thisRow.addClass('blocked').find('input.valueField').val('x');
+ }
+
+ //First look at value cell
+ var thisCell = thisRow.find('input:eq(1)');
+ var thisClassNames = thisCell.attr('class').split(/\s+/);
+ var valueClass = thisClassNames[thisClassNames.length - 1];
+ var header = thisRow.parents('table.tablesorter').find('th.header:contains("Value"):eq(0)');
+ if (header.hasClass('headerSortUp')) {
+ thisCell.removeClass(valueClass).addClass('-9999');
+ } else if (header.hasClass('headerSortDown')) {
+ thisCell.removeClass(valueClass).addClass('9999');
+ } else {
+ thisCell.removeClass(valueClass).addClass('-9999');
+ }
+
+ //Check if there is an SE column
+ if (thisRow.find('input.valueField').length > 1) {
+ var thisCell = thisRow.find('input:eq(2)');
+ var thisClassNames = thisCell.attr('class').split(/\s+/);
+ var valueClass = thisClassNames[thisClassNames.length - 1];
+ var header = thisRow.parents('table.tablesorter').find('th.header:contains("SE"):eq(0)');
+ if (header.hasClass('headerSortUp')) {
+ thisCell.removeClass(valueClass).addClass('-9999');
+ } else if (header.hasClass('headerSortDown')) {
+ thisCell.removeClass(valueClass).addClass('9999');
+ } else {
+ thisCell.removeClass(valueClass).addClass('-9999');
+ }
+ }
+ }
+ } else if (target.name === 'showHideNoValue') {
+ if (noValShown) {
+ $('#showHideOptions').find('input[name=showHideNoValue]').val(' Show No Value ');
+ for (i = 1; i <= Math.max(numPrimaryRows, numOtherRows) - 1; i++) {
+ if (i <= numPrimaryRows - 1) {
+ var thisRow = $('#Primary_' + i);
+ if (thisRow.is('.novalue:visible') || thisRow.is('.blocked:visible')) {
+ jQuery(thisRow).addClass('invisible');
+ }
+ }
+ if (i <= numOtherRows - 1) {
+ var thisOtherRow = $('#Other_' + i);
+ if (thisOtherRow.is('.novalue:visible') || thisOtherRow.is('.blocked:visible')) {
+ if (thisOtherRow.is(':visible')) {
+ jQuery(thisOtherRow).addClass('invisible');
+ }
+ }
+ }
+ }
+ noValShown = 0;
+ } else {
+ $('#showHideOptions').find('input[name=showHideNoValue]').val(' Hide No Value ');
+ for (i = 1; i <= Math.max(numPrimaryRows, numOtherRows) - 1; i++) {
+ if (i <= numPrimaryRows - 1) {
+ var thisRow = $('#Primary_' + i);
+ if (thisRow.is('.novalue') || thisRow.is('.blocked')) {
+ jQuery(thisRow).removeClass('invisible');
+ if (!(outliersShown)) {
+ if (thisRow.is('.outlier:visible')) {
+ jQuery(thisRow).addClass('invisible');
+ }
+ }
+ }
+ }
+ if (i <= numOtherRows - 1) {
+ var thisOtherRow = $('#Other_' + i);
+ if (thisOtherRow.is('.novalue') || thisOtherRow.is('.blocked')) {
+ jQuery(thisOtherRow).removeClass('invisible');
+ if (!(outliersShown)) {
+ if (thisOtherRow.is('.outlier:visible')) {
+ jQuery(thisOtherRow).addClass('invisible');
+ }
+ }
+ }
+ }
}
- else if (traitType=="name"){
- var graphFile = graphName+ "_plain_name.txt";
- $('input[name=exportGraphFile]').live('click', function() { window.open(graphFile) });
+ noValShown = 1;
+ }
+ } else if (target.name === 'showHideOutliers') {
+ if (outliersShown) {
+ $('#showHideOptions').find('input[name=showHideOutliers]').val(' Show Outliers ');
+ for (i = 1; i <= Math.max(numPrimaryRows, numOtherRows) - 1; i++) {
+ if (i <= numPrimaryRows - 1) {
+ thisRow = $('#Primary_' + i);
+ if (thisRow.is('.outlier:visible') && (!(thisRow.is('.invisible')))) {
+ thisRow.addClass('invisible')
+ }
+ }
+ if (i <= numOtherRows - 1) {
+ thisOtherRow = $('#Other_' + i);
+ if (thisOtherRow.is('.outlier:visible') && (!(thisOtherRow.is('.invisible')))) {
+ thisOtherRow.addClass('invisible')
+ }
+ }
+ }
+ outliersShown = 0;
+ } else {
+ $('#showHideOptions').find('input[name=showHideOutliers]').val(' Hide Outliers ');
+ for (i = 1; i <= Math.max(numPrimaryRows, numOtherRows) - 1; i++) {
+ if (i <= numPrimaryRows - 1) {
+ thisRow = $('#Primary_' + i);
+ if (thisRow.is('.outlier') && (!(thisRow.is(':visible')))) {
+ if (!(noValShown)) {
+ if (thisRow.is('.blocked')) {
+ continue;
+ }
+ }
+ jQuery(thisRow).removeClass('invisible')
+ }
+ }
+ if (i <= numOtherRows - 1) {
+ thisOtherRow = $('#Other_' + i);
+ if (thisOtherRow.is('.outlier') && (!(thisOtherRow.is(':visible')))) {
+ if (!(noValShown)) {
+ if (thisOtherRow.is('.blocked')) {
+ continue;
+ }
+ }
+ jQuery(thisOtherRow).removeClass('invisible')
+ }
+ }
}
+ outliersShown = 1;
+ }
+ }
+ return false;
+ });
+});
+
+function getTraitData() {
+ primary_row_count = $('#sortable1').find('tr').length - 1;
+ other_row_count = $('#sortable2').find('tr').length - 1;
+
+ primaryStrainNames = new Array();
+ primaryVals = new Array();
+ primaryVars = new Array();
+
+ allStrainNames = new Array();
+ allVals = new Array();
+ allVars = new Array();
+
+ for (i = 1; i <= primary_row_count; i++) {
+ thisRow = $('#Primary_' + i);
+ strainName = thisRow.find('span:first').text();
+ primaryStrainNames.push(strainName);
+ allStrainNames.push(strainName);
+ strainVal = thisRow.find('input:eq(1)').val();
+ primaryVals.push(strainVal);
+ allVals.push(strainVal);
+ strainVar = ''; // Just to initialize it in case there is no var
+ strainVar = thisRow.find('input:eq(2)').val();
+ primaryVars.push(strainVar);
+ allVars.push(strainVar);
+ }
+
+ otherStrainNames = new Array();
+ otherVals = new Array();
+ otherVars = new Array();
+
+ for (j = 1; j <= other_row_count; j++) {
+ thisRow = $('#Other_' + j)
+ strainName = thisRow.find('span:first').text();
+ otherStrainNames.push(strainName);
+ strainVal = thisRow.find('input:eq(1)').val();
+ otherVals.push(strainVal);
+ strainVar = ''; // Just to initialize it in case there is no var
+ strainVar = thisRow.find('input:eq(2)').val();
+ otherVars.push(strainVar);
+
+ if (jQuery.inArray(strainName, allStrainNames) == -1) {
+ allStrainNames.push(strainName);
+ allVals.push(strainVal);
+ allVars.push(strainVar);
}
+ }
+
+ primaryData = [primaryStrainNames, primaryVals, primaryVars];
+ otherData = [otherStrainNames, otherVals, otherVars];
+ allData = [allStrainNames, allVals, allVars];
+
+ return [primaryData, otherData, allData];
}
+/*
+used by networkGraphPageBody.py
+*/
+
+//Default to plain text + symbol for the "Export Graph File" button
+$('input[name=exportGraphFile]').live('click', function () {
+ window.open($('input[name=exportFilename]').val() + "_plain_symbol.txt")
+});
+
+function changeFormat(graphName) {
+ var graphFormat = $('#exportFormat').val();
+ var traitType = $('#traitType').val();
+
+ $('input[name=exportGraphFile]').die('click');
+
+ if (graphFormat == "xgmml") {
+ if (traitType == "symbol") {
+ var graphFile = graphName + "_xgmml_symbol.txt";
+ $('input[name=exportGraphFile]').live('click', function () {
+ window.open(graphFile)
+ });
+ } else if (traitType == "name") {
+ var graphFile = graphName + "_xgmml_name.txt";
+ $('input[name=exportGraphFile]').live('click', function () {
+ window.open(graphFile)
+ });
+ }
+ } else if (graphFormat == "plain") {
+ if (traitType == "symbol") {
+ var graphFile = graphName + "_plain_symbol.txt";
+ $('input[name=exportGraphFile]').live('click', function () {
+ window.open(graphFile)
+ });
+ } else if (traitType == "name") {
+ var graphFile = graphName + "_plain_name.txt";
+ $('input[name=exportGraphFile]').live('click', function () {
+ window.open(graphFile)
+ });
+ }
+ }
+}
\ No newline at end of file
diff --git a/web/webqtl/correlation/CorrelationPage.py b/web/webqtl/correlation/CorrelationPage.py
index 8ce669cb..1fd16021 100755
--- a/web/webqtl/correlation/CorrelationPage.py
+++ b/web/webqtl/correlation/CorrelationPage.py
@@ -23,6 +23,9 @@
# Created by GeneNetwork Core Team 2010/08/10
#
# Last updated by NL 2011/02/11
+# Last updated by Christian Fernandez 2012/04/07
+# Refactored correlation calculation into smaller functions in preparation of
+# separating html from existing code
import string
from math import *
@@ -47,447 +50,324 @@ from dbFunction import webqtlDatabaseFunction
import utility.webqtlUtil #this is for parallel computing only.
from correlation import correlationFunction
+import logging
+logging.basicConfig(filename="/tmp/gn_log", level=logging.INFO)
+_log = logging.getLogger("correlation")
-class CorrelationPage(templatePage):
+METHOD_SAMPLE_PEARSON = "1"
+METHOD_SAMPLE_RANK = "2"
+METHOD_LIT = "3"
+METHOD_TISSUE_PEARSON = "4"
+METHOD_TISSUE_RANK = "5"
- corrMinInformative = 4
+TISSUE_METHODS = [METHOD_TISSUE_PEARSON, METHOD_TISSUE_RANK]
- def __init__(self, fd):
+TISSUE_MOUSE_DB = 1
- #XZ, 01/14/2009: This method is for parallel computing only.
- #XZ: It is supposed to be called when "Genetic Correlation, Pearson's r" (method 1)
- #XZ: or "Genetic Correlation, Spearman's rho" (method 2) is selected
- def compute_corr( input_nnCorr, input_trait, input_list, computing_method):
+class AuthException(Exception): pass
- allcorrelations = []
- for line in input_list:
- tokens = line.split('","')
- tokens[-1] = tokens[-1][:-2] #remove the last "
- tokens[0] = tokens[0][1:] #remove the first "
+class Trait(object):
+ def __init__(self, name, raw_values = None, lit_corr = None, tissue_corr = None, p_tissue = None):
+ self.name = name
+ self.raw_values = raw_values
+ self.lit_corr = lit_corr
+ self.tissue_corr = tissue_corr
+ self.p_tissue = p_tissue
+ self.correlation = 0
+ self.p_value = 0
- traitdataName = tokens[0]
- database_trait = tokens[1:]
+ @staticmethod
+ def from_csv(line, data_start = 1):
+ name = line[0]
+ numbers = line[data_start:]
+ # _log.info(numbers)
+ numbers = [ float(number) for number in numbers ]
- if computing_method == "1": #XZ: Pearson's r
- corr,nOverlap = utility.webqtlUtil.calCorrelationText(input_trait, database_trait, input_nnCorr)
- else: #XZ: Spearman's rho
- corr,nOverlap = utility.webqtlUtil.calCorrelationRankText(input_trait, database_trait, input_nnCorr)
- traitinfo = [traitdataName,corr,nOverlap]
- allcorrelations.append(traitinfo)
+ return Trait(name, raw_values = numbers)
- return allcorrelations
+ def calculate_correlation(self, values, method):
+ """Calculate the correlation value and p value according to the method specified"""
+ #ZS: This takes the list of values of the trait our selected trait is being correlated against and removes the values of the samples our trait has no value for
+ #There's probably a better way of dealing with this, but I'll have to ask Christian
+ updated_raw_values = []
+ updated_values = []
+ for i in range(len(values)):
+ if values[i] != "None":
+ updated_raw_values.append(self.raw_values[i])
+ updated_values.append(values[i])
- templatePage.__init__(self, fd)
+ self.raw_values = updated_raw_values
+ values = updated_values
- if not self.openMysql():
- return
-
- if not fd.genotype:
- fd.readGenotype()
+ if method == METHOD_SAMPLE_PEARSON or method == METHOD_LIT or method == METHOD_TISSUE_PEARSON:
+ corr,nOverlap = webqtlUtil.calCorrelation(self.raw_values, values, len(values))
+ else:
+ corr,nOverlap = webqtlUtil.calCorrelationRank(self.raw_values, values, len(values))
- #XZ, 09/18/2008: get the information such as value, variance of the input strain names from the form.
- if fd.allstrainlist:
- mdpchoice = fd.formdata.getvalue('MDPChoice')
- #XZ, in HTML source code, it is "BXD Only" or "BXH only", and so on
- if mdpchoice == "1":
- strainlist = fd.f1list + fd.strainlist
- #XZ, in HTML source code, it is "MDP Only"
- elif mdpchoice == "2":
- strainlist = []
- strainlist2 = fd.f1list + fd.strainlist
- for strain in fd.allstrainlist:
- if strain not in strainlist2:
- strainlist.append(strain)
- #So called MDP Panel
- if strainlist:
- strainlist = fd.f1list+fd.parlist+strainlist
- #XZ, in HTML source code, it is "All Cases"
+ self.correlation = corr
+ self.overlap = nOverlap
+
+ if self.overlap < 3:
+ self.p_value = 1.0
+ else:
+ #ZS - This is probably the wrong way to deal with this. Correlation values of 1.0 definitely exist (the trait correlated against itself), so zero division needs to br prevented.
+ if abs(self.correlation) >= 1.0:
+ self.p_value = 0.0
else:
- strainlist = fd.allstrainlist
- #XZ, 09/18/2008: put the trait data into dictionary fd.allTraitData
- fd.readData(fd.allstrainlist)
- else:
- mdpchoice = None
- strainlist = fd.strainlist
- #XZ, 09/18/2008: put the trait data into dictionary fd.allTraitData
- fd.readData()
+ ZValue = 0.5*log((1.0+self.correlation)/(1.0-self.correlation))
+ ZValue = ZValue*sqrt(self.overlap-3)
+ self.p_value = 2.0*(1.0 - reaper.normp(abs(ZValue)))
- #XZ, 3/16/2010: variable RISet must be pass by the form
- RISet = fd.RISet
- #XZ, 12/12/2008: get species infomation
- species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=RISet)
+
- #XZ, 09/18/2008: get all information about the user selected database.
- self.target_db_name = fd.formdata.getvalue('database')
+#XZ, 01/14/2009: This method is for parallel computing only.
+#XZ: It is supposed to be called when "Genetic Correlation, Pearson's r" (method 1)
+#XZ: or "Genetic Correlation, Spearman's rho" (method 2) is selected
+def compute_corr( input_nnCorr, input_trait, input_list, computing_method):
+
+ allcorrelations = []
+
+ for line in input_list:
+ tokens = line.split('","')
+ tokens[-1] = tokens[-1][:-2] #remove the last "
+ tokens[0] = tokens[0][1:] #remove the first "
+
+ traitdataName = tokens[0]
+ database_trait = tokens[1:]
+
+ if computing_method == "1": #XZ: Pearson's r
+ corr,nOverlap = utility.webqtlUtil.calCorrelationText(input_trait, database_trait, input_nnCorr)
+ else: #XZ: Spearman's rho
+ corr,nOverlap = utility.webqtlUtil.calCorrelationRankText(input_trait, database_trait, input_nnCorr)
+ traitinfo = [traitdataName,corr,nOverlap]
+ allcorrelations.append(traitinfo)
+
+ return allcorrelations
+
+def get_correlation_method_key(form_data):
+ #XZ, 09/28/2008: if user select "1", then display 1, 3 and 4.
+ #XZ, 09/28/2008: if user select "2", then display 2, 3 and 5.
+ #XZ, 09/28/2008: if user select "3", then display 1, 3 and 4.
+ #XZ, 09/28/2008: if user select "4", then display 1, 3 and 4.
+ #XZ, 09/28/2008: if user select "5", then display 2, 3 and 5.
+
+ method = form_data.formdata.getvalue("method")
+ if method not in ["1", "2", "3" ,"4", "5"]:
+ return "1"
+
+ return method
+
+
+def get_custom_trait(form_data, cursor):
+ """Pulls the custom trait, if it exists, out of the form data"""
+ trait_name = form_data.formdata.getvalue('fullname')
+
+ if trait_name:
+ trait = webqtlTrait(fullname=trait_name, cursor=cursor)
+ trait.retrieveInfo()
+ return trait
+ else:
+ return None
+
+
+#XZ, 09/18/2008: get the information such as value, variance of the input strain names from the form.
+def get_sample_data(form_data):
+ if form_data.allstrainlist:
+ mdpchoice = form_data.formdata.getvalue('MDPChoice')
+ #XZ, in HTML source code, it is "BXD Only" or "BXH only", and so on
+ if mdpchoice == "1":
+ strainlist = form_data.f1list + form_data.strainlist
+ #XZ, in HTML source code, it is "MDP Only"
+ elif mdpchoice == "2":
+ strainlist = []
+ strainlist2 = form_data.f1list + form_data.strainlist
+ for strain in form_data.allstrainlist:
+ if strain not in strainlist2:
+ strainlist.append(strain)
+ #So called MDP Panel
+ if strainlist:
+ strainlist = form_data.f1list+form_data.parlist+strainlist
+ #XZ, in HTML source code, it is "All Cases"
+ else:
+ strainlist = form_data.allstrainlist
+ #XZ, 09/18/2008: put the trait data into dictionary form_data.allTraitData
+ form_data.readData(form_data.allstrainlist)
+ else:
+ mdpchoice = None
+ strainlist = form_data.strainlist
+ #XZ, 09/18/2008: put the trait data into dictionary form_data.allTraitData
+ form_data.readData()
+
+ return strainlist
+
+
+def get_mdp_choice(form_data):
+ if form_data.allstrainlist:
+ return form_data.formdata.getvalue("MDPChoice")
+ else:
+ return None
+
+
+def get_species(fd, cursor):
+ #XZ, 3/16/2010: variable RISet must be pass by the form
+ RISet = fd.RISet
+ #XZ, 12/12/2008: get species infomation
+ species = webqtlDatabaseFunction.retrieveSpecies(cursor=cursor, RISet=RISet)
+ return species
+
+
+def sortTraitCorrelations(traits, method="1"):
+ if method in TISSUE_METHODS:
+ traits.sort(key=lambda trait: trait.tissue_corr != None and abs(trait.tissue_corr), reverse=True)
+ elif method == METHOD_LIT:
+ traits.sort(key=lambda trait: trait.lit_corr != None and abs(trait.lit_corr), reverse=True)
+ else:
+ traits.sort(key=lambda trait: trait.correlation != None and abs(trait.correlation), reverse=True)
+
+ return traits
+
+
+def auth_user_for_db(db, cursor, target_db_name, privilege, username):
+ """Authorize a user for access to a database if that database is
+ confidential. A db (identified by a record in ProbeSetFreeze) contains a
+ list of authorized users who may access it, as well as its confidentiality
+ level.
+
+ If the current user's privilege level is greater than 'user', ie: root or
+ admin, then they are automatically authed, otherwise, check the
+ AuthorizedUsers field for the presence of their name."""
+
+ if db.type == 'ProbeSet':
+ cursor.execute('SELECT Id, Name, FullName, confidentiality, AuthorisedUsers FROM ProbeSetFreeze WHERE Name = "%s"' % target_db_name)
+ indId, indName, indFullName, confidential, AuthorisedUsers = cursor.fetchall()[0]
+
+ if confidential:
+ authorized = 0
+
+ #for the dataset that confidentiality is 1
+ #1. 'admin' and 'root' can see all of the dataset
+ #2. 'user' can see the dataset that AuthorisedUsers contains his id(stored in the Id field of User table)
+ if webqtlConfig.USERDICT[privilege] > webqtlConfig.USERDICT['user']:
+ authorized = 1
+ else:
+ if username in AuthorisedUsers.split(","):
+ authorized = 1
+
+ if not authorized:
+ raise AuthException("The %s database you selected is not open to the public at this time, please go back and select other database." % indFullName)
- try:
- self.db = webqtlDataset(self.target_db_name, self.cursor)
- except:
- heading = "Correlation Table"
- detail = ["The database you just requested has not been established yet."]
- self.error(heading=heading,detail=detail)
- return
- #XZ, 09/18/2008: check if user has the authority to get access to the database.
- if self.db.type == 'ProbeSet':
- self.cursor.execute('SELECT Id, Name, FullName, confidentiality, AuthorisedUsers FROM ProbeSetFreeze WHERE Name = "%s"' % self.target_db_name)
- indId, indName, indFullName, confidential, AuthorisedUsers = self.cursor.fetchall()[0]
+class CorrelationPage(templatePage):
- if confidential == 1:
- access_to_confidential_dataset = 0
+ corrMinInformative = 4
- #for the dataset that confidentiality is 1
- #1. 'admin' and 'root' can see all of the dataset
- #2. 'user' can see the dataset that AuthorisedUsers contains his id(stored in the Id field of User table)
- if webqtlConfig.USERDICT[self.privilege] > webqtlConfig.USERDICT['user']:
- access_to_confidential_dataset = 1
- else:
- AuthorisedUsersList=AuthorisedUsers.split(',')
- if AuthorisedUsersList.__contains__(self.userName):
- access_to_confidential_dataset = 1
+ PAGE_HEADING = "Correlation Table"
+ CORRELATION_METHODS = {"1" : "Genetic Correlation (Pearson's r)",
+ "2" : "Genetic Correlation (Spearman's rho)",
+ "3" : "SGO Literature Correlation",
+ "4" : "Tissue Correlation (Pearson's r)",
+ "5" : "Tissue Correlation (Spearman's rho)"}
- if not access_to_confidential_dataset:
- #Error, Confidential Database
- heading = "Correlation Table"
- detail = ["The %s database you selected is not open to the public at this time, please go back and select other database." % indFullName]
- self.error(heading=heading,detail=detail,error="Confidential Database")
- return
+ RANK_ORDERS = {"1": 0, "2": 1, "3": 0, "4": 0, "5": 1}
- #XZ, 09/18/2008: filter out the strains that have no value.
- _strains, _vals, _vars, N = fd.informativeStrains(strainlist)
- N = len(_strains)
+ def error(self, message, error="Error", heading = None):
+ heading = heading or self.PAGE_HEADING
+ return templatePage.error(heading = heading, detail = [message], error=error)
- if N < self.corrMinInformative:
- heading = "Correlation Table"
- detail = ['Fewer than %d strain data were entered for %s data set. No calculation of correlation has been attempted.' % (self.corrMinInformative, RISet)]
- self.error(heading=heading,detail=detail)
+ def __init__(self, fd):
+
+ # Call the superclass constructor
+ templatePage.__init__(self, fd)
+
+ # Connect to the database
+ if not self.openMysql():
return
- #XZ, 09/28/2008: if user select "1", then display 1, 3 and 4.
- #XZ, 09/28/2008: if user select "2", then display 2, 3 and 5.
- #XZ, 09/28/2008: if user select "3", then display 1, 3 and 4.
- #XZ, 09/28/2008: if user select "4", then display 1, 3 and 4.
- #XZ, 09/28/2008: if user select "5", then display 2, 3 and 5.
- methodDict = {"1":"Genetic Correlation (Pearson's r)","2":"Genetic Correlation (Spearman's rho)","3":"SGO Literature Correlation","4":"Tissue Correlation (Pearson's r)", "5":"Tissue Correlation (Spearman's rho)"}
- self.method = fd.formdata.getvalue('method')
- if self.method not in ("1","2","3","4","5"):
- self.method = "1"
+ # Read the genotype from a file
+ if not fd.genotype:
+ fd.readGenotype()
- self.returnNumber = int(fd.formdata.getvalue('criteria'))
+ sample_list = get_sample_data(fd)
+ mdp_choice = get_mdp_choice(fd) # No idea what this is yet
+ self.species = get_species(fd, self.cursor)
- myTrait = fd.formdata.getvalue('fullname')
- if myTrait:
- myTrait = webqtlTrait(fullname=myTrait, cursor=self.cursor)
- myTrait.retrieveInfo()
+ #XZ, 09/18/2008: get all information about the user selected database.
+ target_db_name = fd.formdata.getvalue('database')
+ self.target_db_name = target_db_name
- # We will not get Literature Correlations if there is no GeneId because there is nothing to look against
try:
- input_trait_GeneId = int(fd.formdata.getvalue('GeneId'))
+ self.db = webqtlDataset(target_db_name, self.cursor)
except:
- input_trait_GeneId = None
+ detail = ["The database you just requested has not been established yet."]
+ self.error(detail)
+ return
- # We will not get Tissue Correlations if there is no gene symbol because there is nothing to look against
+ # Auth if needed
try:
- input_trait_symbol = myTrait.symbol
- except:
- input_trait_symbol = None
-
-
- #XZ, 12/12/2008: if the species is rat or human, translate the geneid to mouse geneid
- input_trait_mouse_geneid = self.translateToMouseGeneID(species, input_trait_GeneId)
-
-
- #XZ: As of Nov/13/2010, this dataset is 'UTHSC Illumina V6.2 RankInv B6 D2 average CNS GI average (May 08)'
- TissueProbeSetFreezeId = 1
-
- #XZ, 09/22/2008: If we need search by GeneId,
- #XZ, 09/22/2008: we have to check if this GeneId is in the literature or tissue correlation table.
- #XZ, 10/15/2008: We also to check if the selected database is probeset type.
- if self.method == "3" or self.method == "4" or self.method == "5":
- if self.db.type != "ProbeSet":
- self.error(heading="Wrong correlation type",detail="It is not possible to compute the %s between your trait and data in this %s database. Please try again after selecting another type of correlation." % (methodDict[self.method],self.db.name),error="Correlation Type Error")
- return
-
- """
- if not input_trait_GeneId:
- self.error(heading="No Associated GeneId",detail="This trait has no associated GeneId, so we are not able to show any literature or tissue related information.",error="No GeneId Error")
- return
- """
-
- #XZ: We have checked geneid did exist
-
- if self.method == "3":
- if not input_trait_GeneId or not self.checkForLitInfo(input_trait_mouse_geneid):
- self.error(heading="No Literature Info",detail="This gene does not have any associated Literature Information.",error="Literature Correlation Error")
- return
-
- if self.method == "4" or self.method == "5":
- if not input_trait_symbol:
- self.error(heading="No Tissue Correlation Information",detail="This gene does not have any associated Tissue Correlation Information.",error="Tissue Correlation Error")
- return
-
- if not self.checkSymbolForTissueCorr(TissueProbeSetFreezeId, myTrait.symbol):
- self.error(heading="No Tissue Correlation Information",detail="This gene does not have any associated Tissue Correlation Information.",error="Tissue Correlation Error")
- return
-
-############################################################################################################################################
-
- allcorrelations = []
- nnCorr = len(_vals)
-
- #XZ: Use the fast method only for probeset dataset, and this dataset must have been created.
- #XZ: Otherwise, use original method
-
- useFastMethod = False
-
- if self.db.type == "ProbeSet":
-
- DatabaseFileName = self.getFileName( target_db_name=self.target_db_name )
- DirectoryList = os.listdir(webqtlConfig.TEXTDIR) ### List of existing text files. Used to check if a text file already exists
-
- if DatabaseFileName in DirectoryList:
- useFastMethod = True
-
- if useFastMethod:
- if 1:
- #try:
- useLit = False
- if self.method == "3":
- litCorrs = self.fetchLitCorrelations(species=species, GeneId=input_trait_GeneId, db=self.db, returnNumber=self.returnNumber)
- useLit = True
-
- useTissueCorr = False
- if self.method == "4" or self.method == "5":
- tissueCorrs = self.fetchTissueCorrelations(db=self.db, primaryTraitSymbol=input_trait_symbol, TissueProbeSetFreezeId=TissueProbeSetFreezeId, method=self.method, returnNumber = self.returnNumber)
- useTissueCorr = True
-
- datasetFile = open(webqtlConfig.TEXTDIR+DatabaseFileName,'r')
-
- #XZ, 01/08/2009: read the first line
- line = datasetFile.readline()
- dataset_strains = webqtlUtil.readLineCSV(line)[1:]
-
- #XZ, 01/08/2009: This step is critical. It is necessary for this new method.
- #XZ: The original function fetchAllDatabaseData uses all strains stored in variable _strains to
- #XZ: retrieve the values of each strain from database in real time.
- #XZ: The new method uses all strains stored in variable dataset_strains to create a new variable
- #XZ: _newvals. _newvals has the same length as dataset_strains. The items in _newvals is in
- #XZ: the same order of items in dataset_strains. The value of each item in _newvals is either
- #XZ: the value of correspinding strain in _vals or 'None'.
- _newvals = []
- for item in dataset_strains:
- if item in _strains:
- _newvals.append(_vals[_strains.index(item)])
- else:
- _newvals.append('None')
-
- nnCorr = len(_newvals)
-
- #XZ, 01/14/2009: If literature corr or tissue corr is selected,
- #XZ: there is no need to use parallel computing.
- if useLit or useTissueCorr:
- for line in datasetFile:
- traitdata=webqtlUtil.readLineCSV(line)
- traitdataName = traitdata[0]
- traitvals = traitdata[1:]
-
- if useLit:
- if not litCorrs.has_key( traitdataName ):
- continue
-
- if useTissueCorr:
- if not tissueCorrs.has_key( traitdataName ):
- continue
-
- if self.method == "3" or self.method == "4":
- corr,nOverlap = webqtlUtil.calCorrelationText(traitvals,_newvals,nnCorr)
- else:
- corr,nOverlap = webqtlUtil.calCorrelationRankText(traitvals,_newvals,nnCorr)
-
- traitinfo = [traitdataName,corr,nOverlap]
-
- if useLit:
- traitinfo.append(litCorrs[traitdataName])
-
- if useTissueCorr:
- tempCorr, tempPValue = tissueCorrs[traitdataName]
- traitinfo.append(tempCorr)
- traitinfo.append(tempPValue)
-
- allcorrelations.append(traitinfo)
- #XZ, 01/14/2009: If genetic corr is selected, use parallel computing
- else:
- input_line_list = datasetFile.readlines()
- all_line_number = len(input_line_list)
-
- step = 1000
- job_number = math.ceil( float(all_line_number)/step )
-
- job_input_lists = []
-
- for job_index in range( int(job_number) ):
- starti = job_index*step
- endi = min((job_index+1)*step, all_line_number)
-
- one_job_input_list = []
-
- for i in range( starti, endi ):
- one_job_input_list.append( input_line_list[i] )
-
- job_input_lists.append( one_job_input_list )
-
- ppservers = ()
- # Creates jobserver with automatically detected number of workers
- job_server = pp.Server(ppservers=ppservers)
-
- jobs = []
- results = []
-
- for one_job_input_list in job_input_lists: #pay attention to modules from outside
- jobs.append( job_server.submit(func=compute_corr, args=(nnCorr, _newvals, one_job_input_list, self.method), depfuncs=(), modules=("utility.webqtlUtil",)) )
-
- for one_job in jobs:
- one_result = one_job()
- results.append( one_result )
-
- for one_result in results:
- for one_traitinfo in one_result:
- allcorrelations.append( one_traitinfo )
-
- datasetFile.close()
- totalTraits = len(allcorrelations)
- #except:
- # useFastMethod = False
- # self.error(heading="No computation method",detail="Something is wrong within the try except block in CorrelationPage python module.",error="Computation Error")
- # return
-
- #XZ, 01/08/2009: use the original method to retrieve from database and compute.
- if not useFastMethod:
-
- traitdatabase, dataStartPos = self.fetchAllDatabaseData(species=species, GeneId=input_trait_GeneId, GeneSymbol=input_trait_symbol, strains=_strains, db=self.db, method=self.method, returnNumber=self.returnNumber, tissueProbeSetFreezeId=TissueProbeSetFreezeId)
-
- totalTraits = len(traitdatabase) #XZ, 09/18/2008: total trait number
-
- for traitdata in traitdatabase:
- traitdataName = traitdata[0]
- traitvals = traitdata[dataStartPos:]
- if self.method == "1" or self.method == "3" or self.method == "4":
- corr,nOverlap = webqtlUtil.calCorrelation(traitvals,_vals,nnCorr)
- else:
- corr,nOverlap = webqtlUtil.calCorrelationRank(traitvals,_vals,nnCorr)
-
- traitinfo = [traitdataName,corr,nOverlap]
-
- #XZ, 09/28/2008: if user select '3', then fetchAllDatabaseData would give us LitCorr in the [1] position
- #XZ, 09/28/2008: if user select '4' or '5', then fetchAllDatabaseData would give us Tissue Corr in the [1] position
- #XZ, 09/28/2008: and Tissue Corr P Value in the [2] position
- if input_trait_GeneId and self.db.type == "ProbeSet":
- if self.method == "3":
- traitinfo.append( traitdata[1] )
- if self.method == "4" or self.method == "5":
- traitinfo.append( traitdata[1] )
- traitinfo.append( traitdata[2] )
-
- allcorrelations.append(traitinfo)
+ auth_user_for_db(self.db, self.cursor, target_db_name, self.privilege, self.userName)
+ except AuthException, e:
+ detail = [e.message]
+ return self.error(detail)
+ #XZ, 09/18/2008: filter out the strains that have no value.
+ self.sample_names, vals, vars, N = fd.informativeStrains(sample_list)
-#############################################################
+ #CF - If less than a minimum number of strains/cases in common, don't calculate anything
+ if len(self.sample_names) < self.corrMinInformative:
+ detail = ['Fewer than %d strain data were entered for %s data set. No calculation of correlation has been attempted.' % (self.corrMinInformative, fd.RISet)]
+ self.error(heading=PAGE_HEADING,detail=detail)
- if self.method == "3" and input_trait_GeneId:
- allcorrelations.sort(webqtlUtil.cmpLitCorr)
- #XZ, 3/31/2010: Theoretically, we should create one function 'comTissueCorr'
- #to compare each trait by their tissue corr p values.
- #But because the tissue corr p values are generated by permutation test,
- #the top ones always have p value 0. So comparing p values actually does nothing.
- #In addition, for the tissue data in our database, the N is always the same.
- #So it's safe to compare with tissue corr statistic value.
- #That's the same as literature corr.
- elif self.method in ["4","5"] and input_trait_GeneId:
- allcorrelations.sort(webqtlUtil.cmpLitCorr)
- else:
- allcorrelations.sort(webqtlUtil.cmpCorr)
+ self.method = get_correlation_method_key(fd)
+ correlation_method = self.CORRELATION_METHODS[self.method]
+ rankOrder = self.RANK_ORDERS[self.method]
- #XZ, 09/20/2008: we only need the top ones.
- self.returnNumber = min(self.returnNumber,len(allcorrelations))
- allcorrelations = allcorrelations[:self.returnNumber]
+ # CF - Number of results returned
+ self.returnNumber = int(fd.formdata.getvalue('criteria'))
- addLiteratureCorr = False
- addTissueCorr = False
+ self.record_count = 0
- traitList = []
- for item in allcorrelations:
- thisTrait = webqtlTrait(db=self.db, name=item[0], cursor=self.cursor)
- thisTrait.retrieveInfo( QTL='Yes' )
+ myTrait = get_custom_trait(fd, self.cursor)
- nOverlap = item[2]
- corr = item[1]
- #XZ: calculate corrPValue
- if nOverlap < 3:
- corrPValue = 1.0
- else:
- if abs(corr) >= 1.0:
- corrPValue = 0.0
- else:
- ZValue = 0.5*log((1.0+corr)/(1.0-corr))
- ZValue = ZValue*sqrt(nOverlap-3)
- corrPValue = 2.0*(1.0 - reaper.normp(abs(ZValue)))
-
- thisTrait.Name = item[0]
- thisTrait.corr = corr
- thisTrait.nOverlap = nOverlap
- thisTrait.corrPValue = corrPValue
- # NL, 07/19/2010
- # js function changed, add a new parameter rankOrder for js function 'showTissueCorrPlot'
- rankOrder = 0;
- if self.method in ["2","5"]:
- rankOrder = 1;
- thisTrait.rankOrder =rankOrder
-
- #XZ, 26/09/2008: Method is 4 or 5. Have fetched tissue corr, but no literature correlation yet.
- if len(item) == 5:
- thisTrait.tissueCorr = item[3]
- thisTrait.tissuePValue = item[4]
- addLiteratureCorr = True
+ # We will not get Literature Correlations if there is no GeneId because there is nothing to look against
+ self.gene_id = int(fd.formdata.getvalue('GeneId') or 0)
- #XZ, 26/09/2008: Method is 3, Have fetched literature corr, but no tissue corr yet.
- elif len(item) == 4:
- thisTrait.LCorr = item[3]
- thisTrait.mouse_geneid = self.translateToMouseGeneID(species, thisTrait.geneid)
- addTissueCorr = True
+ # We will not get Tissue Correlations if there is no gene symbol because there is nothing to look against
+ self.trait_symbol = myTrait.symbol
+
- #XZ, 26/09/2008: Method is 1 or 2. Have NOT fetched literature corr and tissue corr yet.
- # Phenotype data will not have geneid, and neither will some probes
- # we need to handle this because we will get an attribute error
- else:
- if input_trait_mouse_geneid and self.db.type=="ProbeSet":
- addLiteratureCorr = True
- if input_trait_symbol and self.db.type=="ProbeSet":
- addTissueCorr = True
+ #XZ, 12/12/2008: if the species is rat or human, translate the geneid to mouse geneid
+ self.input_trait_mouse_gene_id = self.translateToMouseGeneID(self.species, self.gene_id)
- traitList.append(thisTrait)
+ #XZ: As of Nov/13/2010, this dataset is 'UTHSC Illumina V6.2 RankInv B6 D2 average CNS GI average (May 08)'
+ self.tissue_probeset_freeze_id = 1
- if addLiteratureCorr:
- traitList = self.getLiteratureCorrelationByList(input_trait_mouse_geneid, species, traitList)
- if addTissueCorr:
- traitList = self.getTissueCorrelationByList( primaryTraitSymbol=input_trait_symbol, traitList=traitList,TissueProbeSetFreezeId =TissueProbeSetFreezeId, method=self.method)
+ traitList = self.correlate(vals)
+
+ _log.info("Done doing correlation calculation")
-########################################################
+############################################################################################################################################
TD_LR = HT.TD(height=200,width="100%",bgColor='#eeeeee')
mainfmName = webqtlUtil.genRandStr("fm_")
form = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name= mainfmName, submit=HT.Input(type='hidden'))
- hddn = {'FormID':'showDatabase', 'ProbeSetID':'_','database':self.target_db_name, 'databaseFull':self.db.fullname, 'CellID':'_', 'RISet':RISet, 'identification':fd.identification}
+ hddn = {'FormID': 'showDatabase',
+ 'ProbeSetID': '_',
+ 'database': self.target_db_name,
+ 'databaseFull': self.db.fullname,
+ 'CellID': '_',
+ 'RISet': fd.RISet,
+ 'identification': fd.identification}
if myTrait:
hddn['fullname']=fd.formdata.getvalue('fullname')
- if mdpchoice:
- hddn['MDPChoice']=mdpchoice
+ if mdp_choice:
+ hddn['MDPChoice']=mdp_choice
#XZ, 09/18/2008: pass the trait data to next page by hidden parameters.
@@ -510,13 +390,13 @@ class CorrelationPage(templatePage):
#XZ, 3/11/2010: add one parameter to record if the method is rank order.
form.append(HT.Input(name="rankOrder", value="%s" % rankOrder, type='hidden'))
- form.append(HT.Input(name="TissueProbeSetFreezeId", value="%s" % TissueProbeSetFreezeId, type='hidden'))
+ form.append(HT.Input(name="TissueProbeSetFreezeId", value="%s" % self.tissue_probeset_freeze_id, type='hidden'))
####################################
# generate the info on top of page #
####################################
- info = self.getTopInfo(myTrait=myTrait, method=self.method, db=self.db, target_db_name=self.target_db_name, returnNumber=self.returnNumber, methodDict=methodDict, totalTraits=totalTraits, identification=fd.identification )
+ info = self.getTopInfo(myTrait=myTrait, method=self.method, db=self.db, target_db_name=self.target_db_name, returnNumber=self.returnNumber, methodDict=self.CORRELATION_METHODS, totalTraits=traitList, identification=fd.identification )
##############
# Excel file #
@@ -536,7 +416,7 @@ class CorrelationPage(templatePage):
#####################################################################
-
+ #Select All, Deselect All, Invert Selection, Add to Collection
mintmap = HT.Href(url="#redirect", onClick="databaseFunc(document.getElementsByName('%s')[0], 'showIntMap');" % mainfmName)
mintmap_img = HT.Image("/images/multiple_interval_mapping1_final.jpg", name='mintmap', alt="Multiple Interval Mapping", title="Multiple Interval Mapping", style="border:none;")
mintmap.append(mintmap_img)
@@ -555,10 +435,10 @@ class CorrelationPage(templatePage):
partialCorr = HT.Href(url="#redirect", onClick="databaseFunc(document.getElementsByName('%s')[0], 'partialCorrInput');" % mainfmName)
partialCorr_img = HT.Image("/images/partial_correlation_final.jpg", name='partialCorr', alt="Partial Correlation", title="Partial Correlation", style="border:none;")
partialCorr.append(partialCorr_img)
- addselect = HT.Href(url="#redirect", onClick="addRmvSelection('%s', document.getElementsByName('%s')[0], 'addToSelection');" % (RISet, mainfmName))
+ addselect = HT.Href(url="#redirect", onClick="addRmvSelection('%s', document.getElementsByName('%s')[0], 'addToSelection');" % (fd.RISet, mainfmName))
addselect_img = HT.Image("/images/add_collection1_final.jpg", name="addselect", alt="Add To Collection", title="Add To Collection", style="border:none;")
addselect.append(addselect_img)
- selectall = HT.Href(url="#redirect", onClick="checkAll(document.getElementsByName('%s')[0]);" % mainfmName)
+ selectall = HT.Href(url="#redirect", onClick="checkAll(document.getElementsByName('%s')[0]);" % mainfmName)
selectall_img = HT.Image("/images/select_all2_final.jpg", name="selectall", alt="Select All", title="Select All", style="border:none;")
selectall.append(selectall_img)
selectinvert = HT.Href(url="#redirect", onClick = "checkInvert(document.getElementsByName('%s')[0]);" % mainfmName)
@@ -575,20 +455,90 @@ class CorrelationPage(templatePage):
selectandor.append(('OR','or'))
selectandor.selected.append('AND')
- pageTable = HT.TableLite(cellSpacing=0,cellPadding=0,width="100%", border=0, align="Left")
- containerTable = HT.TableLite(cellSpacing=0,cellPadding=0,width="90%",border=0, align="Left")
+ #External analysis tools
+ GCATButton = HT.Href(url="#redirect", onClick="databaseFunc(document.getElementsByName('%s')[0], 'GCAT');" % mainfmName)
+ GCATButton_img = HT.Image("/images/GCAT_logo_final.jpg", name="GCAT", alt="GCAT", title="GCAT", style="border:none")
+ GCATButton.append(GCATButton_img)
+
+ ODE = HT.Href(url="#redirect", onClick="databaseFunc(document.getElementsByName('%s')[0], 'ODE');" % mainfmName)
+ ODE_img = HT.Image("/images/ODE_logo_final.jpg", name="ode", alt="ODE", title="ODE", style="border:none")
+ ODE.append(ODE_img)
+
+ '''
+ #XZ, 07/07/2010: I comment out this block of code.
+ WebGestaltScript = HT.Script(language="Javascript")
+ WebGestaltScript.append("""
+setTimeout('openWebGestalt()', 2000);
+function openWebGestalt(){
+var thisForm = document['WebGestalt'];
+makeWebGestaltTree(thisForm, '%s', %d, 'edag_only.php');
+}
+ """ % (mainfmName, len(traitList)))
+ '''
+
+ self.cursor.execute('SELECT GeneChip.GO_tree_value FROM GeneChip, ProbeFreeze, ProbeSetFreeze WHERE GeneChip.Id = ProbeFreeze.ChipId and ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and ProbeSetFreeze.Name = "%s"' % self.db.name)
+ result = self.cursor.fetchone()
+
+ if result:
+ GO_tree_value = result[0]
+
+ if GO_tree_value:
+
+ WebGestalt = HT.Href(url="#redirect", onClick="databaseFunc(document.getElementsByName('%s')[0], 'GOTree');" % mainfmName)
+ WebGestalt_img = HT.Image("/images/webgestalt_icon_final.jpg", name="webgestalt", alt="Gene Set Analysis Toolkit", title="Gene Set Analysis Toolkit", style="border:none")
+ WebGestalt.append(WebGestalt_img)
+
+ hddnWebGestalt = {
+ 'id_list':'',
+ 'correlation':'',
+ 'id_value':'',
+ 'llid_list':'',
+ 'id_type':GO_tree_value,
+ 'idtype':'',
+ 'species':'',
+ 'list':'',
+ 'client':''}
+
+ hddnWebGestalt['ref_type'] = hddnWebGestalt['id_type']
+ hddnWebGestalt['cat_type'] = 'GO'
+ hddnWebGestalt['significancelevel'] = 'Top10'
+
+ if self.species == 'rat':
+ hddnWebGestalt['org'] = 'Rattus norvegicus'
+ elif self.species == 'human':
+ hddnWebGestalt['org'] = 'Homo sapiens'
+ elif self.species == 'mouse':
+ hddnWebGestalt['org'] = 'Mus musculus'
+ else:
+ hddnWebGestalt['org'] = ''
+
+ for key in hddnWebGestalt.keys():
+ form.append(HT.Input(name=key, value=hddnWebGestalt[key], type='hidden'))
+
- optionsTable = HT.TableLite(cellSpacing=2, cellPadding=0,width="320", height="80", border=0, align="Left")
- optionsTable.append(HT.TR(HT.TD(selectall), HT.TD(reset), HT.TD(selectinvert), HT.TD(addselect), align="left"))
- optionsTable.append(HT.TR(HT.TD(" "*1,"Select"), HT.TD("Deselect"), HT.TD(" "*1,"Invert"), HT.TD(" "*3,"Add")))
+ #Create tables with options, etc
+
+ pageTable = HT.TableLite(cellSpacing=0,cellPadding=0,width="100%", border=0, align="Left")
+
+ containerTable = HT.TableLite(cellSpacing=0,cellPadding=0,width="90%",border=0, align="Left")
+
+
+ if not GO_tree_value:
+ optionsTable = HT.TableLite(cellSpacing=2, cellPadding=0,width="480", height="80", border=0, align="Left")
+ optionsTable.append(HT.TR(HT.TD(selectall), HT.TD(reset), HT.TD(selectinvert), HT.TD(addselect), HT.TD(GCATButton), HT.TD(ODE), align="left"))
+ optionsTable.append(HT.TR(HT.TD(" "*1,"Select"), HT.TD("Deselect"), HT.TD(" "*1,"Invert"), HT.TD(" "*3,"Add"), HT.TD("Gene Set"), HT.TD(" "*2,"GCAT")))
+ else:
+ optionsTable = HT.TableLite(cellSpacing=2, cellPadding=0,width="560", height="80", border=0, align="Left")
+ optionsTable.append(HT.TR(HT.TD(selectall), HT.TD(reset), HT.TD(selectinvert), HT.TD(addselect), HT.TD(GCATButton), HT.TD(ODE), HT.TD(WebGestalt), align="left"))
+ optionsTable.append(HT.TR(HT.TD(" "*1,"Select"), HT.TD("Deselect"), HT.TD(" "*1,"Invert"), HT.TD(" "*3,"Add"), HT.TD("Gene Set"), HT.TD(" "*2,"GCAT"), HT.TD(" "*3, "ODE")))
containerTable.append(HT.TR(HT.TD(optionsTable)))
functionTable = HT.TableLite(cellSpacing=2,cellPadding=0,width="480",height="80", border=0, align="Left")
functionRow = HT.TR(HT.TD(networkGraph, width="16.7%"), HT.TD(cormatrix, width="16.7%"), HT.TD(partialCorr, width="16.7%"), HT.TD(mcorr, width="16.7%"), HT.TD(mintmap, width="16.7%"), HT.TD(heatmap), align="left")
labelRow = HT.TR(HT.TD(" "*1,HT.Text("Graph")), HT.TD(" "*1,HT.Text("Matrix")), HT.TD(" "*1,HT.Text("Partial")), HT.TD(HT.Text("Compare")), HT.TD(HT.Text("QTL Map")), HT.TD(HT.Text(text="Heat Map")))
functionTable.append(functionRow, labelRow)
- containerTable.append(HT.TR(HT.TD(functionTable), HT.BR()))
+ containerTable.append(HT.TR(HT.TD(functionTable), HT.BR()))
#more_options = HT.Image("/images/more_options1_final.jpg", name='more_options', alt="Expand Options", title="Expand Options", style="border:none;", Class="toggleShowHide")
@@ -597,12 +547,14 @@ class CorrelationPage(templatePage):
moreOptions = HT.Input(type='button',name='options',value='More Options', onClick="",Class="toggle")
fewerOptions = HT.Input(type='button',name='options',value='Fewer Options', onClick="",Class="toggle")
+ """
if (fd.formdata.getvalue('showHideOptions') == 'less'):
- containerTable.append(HT.TR(HT.TD(" "), height="10"), HT.TR(HT.TD(HT.Div(fewerOptions, Class="toggleShowHide"))))
- containerTable.append(HT.TR(HT.TD(" ")))
+ containerTable.append(HT.TR(HT.TD(" "), height="10"), HT.TR(HT.TD(HT.Div(fewerOptions, Class="toggleShowHide"))))
+ containerTable.append(HT.TR(HT.TD(" ")))
else:
- containerTable.append(HT.TR(HT.TD(" "), height="10"), HT.TR(HT.TD(HT.Div(moreOptions, Class="toggleShowHide"))))
- containerTable.append(HT.TR(HT.TD(" ")))
+ containerTable.append(HT.TR(HT.TD(" "), height="10"), HT.TR(HT.TD(HT.Div(moreOptions, Class="toggleShowHide"))))
+ containerTable.append(HT.TR(HT.TD(" ")))
+ """
containerTable.append(HT.TR(HT.TD(HT.Span(selecttraits,' with r > ',selectgt, ' ',selectandor, ' r < ',selectlt,Class="bd1 cbddf fs11")), style="display:none;", Class="extra_options"))
@@ -615,9 +567,9 @@ class CorrelationPage(templatePage):
if self.db.type=="Geno":
- containerTable.append(HT.TR(HT.TD(xlsUrl, height=40)))
+ containerTable.append(HT.TR(HT.TD(xlsUrl, height=60)))
- pageTable.append(HT.TR(HT.TD(containerTable)))
+ pageTable.append(HT.TR(HT.TD(containerTable)))
tblobj['header'], worksheet = self.getTableHeaderForGeno( method=self.method, worksheet=worksheet, newrow=newrow, headingStyle=headingStyle)
newrow += 1
@@ -636,9 +588,9 @@ class CorrelationPage(templatePage):
div = HT.Div(webqtlUtil.genTableObj(tblobj=tblobj, file=filename, sortby=sortby, tableID = "sortable", addIndex = "1"), corrScript, Id="sortable")
- pageTable.append(HT.TR(HT.TD(div)))
+ pageTable.append(HT.TR(HT.TD(div)))
- form.append(HT.Input(name='ShowStrains',type='hidden', value =1),
+ form.append(HT.Input(name='ShowStrains',type='hidden', value =1),
HT.Input(name='ShowLine',type='hidden', value =1),
HT.P(), HT.P(), pageTable)
TD_LR.append(corrHeading, info, form, HT.P())
@@ -649,9 +601,9 @@ class CorrelationPage(templatePage):
elif self.db.type=="Publish":
- containerTable.append(HT.TR(HT.TD(xlsUrl, height=40)))
+ containerTable.append(HT.TR(HT.TD(xlsUrl, height=40)))
- pageTable.append(HT.TR(HT.TD(containerTable)))
+ pageTable.append(HT.TR(HT.TD(containerTable)))
tblobj['header'], worksheet = self.getTableHeaderForPublish(method=self.method, worksheet=worksheet, newrow=newrow, headingStyle=headingStyle)
newrow += 1
@@ -661,7 +613,7 @@ class CorrelationPage(templatePage):
corrScript = HT.Script(language="Javascript")
corrScript.append("var corrArray = new Array();")
- tblobj['body'], worksheet, corrScript = self.getTableBodyForPublish(traitList=traitList, formName=mainfmName, worksheet=worksheet, newrow=newrow, corrScript=corrScript, species=species)
+ tblobj['body'], worksheet, corrScript = self.getTableBodyForPublish(traitList=traitList, formName=mainfmName, worksheet=worksheet, newrow=newrow, corrScript=corrScript, species=self.species)
workbook.close()
@@ -671,7 +623,7 @@ class CorrelationPage(templatePage):
# NL, 07/27/2010. genTableObj function has been moved from templatePage.py to webqtlUtil.py;
div = HT.Div(webqtlUtil.genTableObj(tblobj=tblobj, file=filename, sortby=sortby, tableID = "sortable", addIndex = "1"), corrScript, Id="sortable")
- pageTable.append(HT.TR(HT.TD(div)))
+ pageTable.append(HT.TR(HT.TD(div)))
form.append(
HT.Input(name='ShowStrains',type='hidden', value =1),
@@ -685,7 +637,6 @@ class CorrelationPage(templatePage):
elif self.db.type=="ProbeSet":
-
tblobj['header'], worksheet = self.getTableHeaderForProbeSet(method=self.method, worksheet=worksheet, newrow=newrow, headingStyle=headingStyle)
newrow += 1
@@ -694,7 +645,7 @@ class CorrelationPage(templatePage):
corrScript = HT.Script(language="Javascript")
corrScript.append("var corrArray = new Array();")
- tblobj['body'], worksheet, corrScript = self.getTableBodyForProbeSet(traitList=traitList, primaryTrait=myTrait, formName=mainfmName, worksheet=worksheet, newrow=newrow, corrScript=corrScript, species=species)
+ tblobj['body'], worksheet, corrScript = self.getTableBodyForProbeSet(traitList=traitList, primaryTrait=myTrait, formName=mainfmName, worksheet=worksheet, newrow=newrow, corrScript=corrScript, species=self.species)
workbook.close()
objfile = open('%s.obj' % (webqtlConfig.TMPDIR+filename), 'wb')
@@ -741,95 +692,21 @@ class CorrelationPage(templatePage):
#updated by NL. Delete function generateJavaScript, move js files to dhtml.js, webqtl.js and jqueryFunction.js
#variables: filename, strainIds and vals are required by getquerystring function
- strainIds=self.getStrainIds(species=species, strains=_strains)
+ strainIds=self.getStrainIds(species=self.species, strains=self.sample_names)
var1 = HT.Input(name="filename", value=filename, type='hidden')
var2 = HT.Input(name="strainIds", value=strainIds, type='hidden')
- var3 = HT.Input(name="vals", value=_vals, type='hidden')
+ var3 = HT.Input(name="vals", value=vals, type='hidden')
customizerButton = HT.Input(type="button", Class="button", value="Add Correlation", onClick = "xmlhttpPost('%smain.py?FormID=AJAX_table', 'sortable', (getquerystring(this.form)))" % webqtlConfig.CGIDIR)
containerTable.append(HT.TR(HT.TD(HT.Span(var1,var2,var3,customizerButton, "with", dbCustomizer, Class="bd1 cbddf fs11"), HT.BR(), HT.BR()), style="display:none;", Class="extra_options"))
- #outside analysis part
- GCATButton = HT.Href(url="#redirect", onClick="databaseFunc(document.getElementsByName('%s')[0], 'GCAT');" % mainfmName)
- GCATButton_img = HT.Image("/images/GCAT_logo_final.jpg", name="GCAT", alt="GCAT", title="GCAT", style="border:none")
- GCATButton.append(GCATButton_img)
-
- ODE = HT.Href(url="#redirect", onClick="databaseFunc(document.getElementsByName('%s')[0], 'ODE');" % mainfmName)
- ODE_img = HT.Image("/images/ODE_logo_final.jpg", name="ode", alt="ODE", title="ODE", style="border:none")
- ODE.append(ODE_img)
+ containerTable.append(HT.TR(HT.TD(xlsUrl, HT.BR(), HT.BR())))
- '''
- #XZ, 07/07/2010: I comment out this block of code.
- WebGestaltScript = HT.Script(language="Javascript")
- WebGestaltScript.append("""
-setTimeout('openWebGestalt()', 2000);
-function openWebGestalt(){
- var thisForm = document['WebGestalt'];
- makeWebGestaltTree(thisForm, '%s', %d, 'edag_only.php');
-}
- """ % (mainfmName, len(traitList)))
- '''
-
- self.cursor.execute('SELECT GeneChip.GO_tree_value FROM GeneChip, ProbeFreeze, ProbeSetFreeze WHERE GeneChip.Id = ProbeFreeze.ChipId and ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and ProbeSetFreeze.Name = "%s"' % self.db.name)
- result = self.cursor.fetchone()
+ pageTable.append(HT.TR(HT.TD(containerTable)))
- if result:
- GO_tree_value = result[0]
+ pageTable.append(HT.TR(HT.TD(div)))
- if GO_tree_value:
-
- WebGestalt = HT.Href(url="#redirect", onClick="databaseFunc(document.getElementsByName('%s')[0], 'GOTree');" % mainfmName)
- WebGestalt_img = HT.Image("/images/webgestalt_icon_final.jpg", name="webgestalt", alt="Gene Set Analysis Toolkit", title="Gene Set Analysis Toolkit", style="border:none")
- WebGestalt.append(WebGestalt_img)
-
- hddnWebGestalt = {
- 'id_list':'',
- 'correlation':'',
- 'id_value':'',
- 'llid_list':'',
- 'id_type':GO_tree_value,
- 'idtype':'',
- 'species':'',
- 'list':'',
- 'client':''}
-
- hddnWebGestalt['ref_type'] = hddnWebGestalt['id_type']
- hddnWebGestalt['cat_type'] = 'GO'
- hddnWebGestalt['significancelevel'] = 'Top10'
-
- if species == 'rat':
- hddnWebGestalt['org'] = 'Rattus norvegicus'
- elif species == 'human':
- hddnWebGestalt['org'] = 'Homo sapiens'
- elif species == 'mouse':
- hddnWebGestalt['org'] = 'Mus musculus'
- else:
- hddnWebGestalt['org'] = ''
-
- for key in hddnWebGestalt.keys():
- form.append(HT.Input(name=key, value=hddnWebGestalt[key], type='hidden'))
-
-
- LinkOutTable = HT.TableLite(cellSpacing=2,cellPadding=0,width="320",height="80", border=0, align="Left")
-
- if not GO_tree_value:
- LinkOutRow = HT.TR(HT.TD(GCATButton, width="50%"), HT.TD(ODE, width="50%"), align="left")
- LinkOutLabels = HT.TR(HT.TD(" ", HT.Text("GCAT"), width="50%"), HT.TD(" ",HT.Text("ODE"), width="50%"), align="left")
- else:
- LinkOutRow = HT.TR(HT.TD(WebGestalt, width="25%"), HT.TD(GCATButton, width="25%"), HT.TD(ODE, width="25%"), align="left")
- LinkOutLabels = HT.TR(HT.TD(HT.Text("Gene Set")), HT.TD(" "*2, HT.Text("GCAT")), HT.TD(" "*3, HT.Text("ODE")), style="display:none;", Class="extra_options")
-
- LinkOutTable.append(LinkOutRow,LinkOutLabels)
-
- containerTable.append(HT.TR(HT.TD(LinkOutTable), Class="extra_options", style="display:none;"))
-
- containerTable.append(HT.TR(HT.TD(xlsUrl, HT.BR(), HT.BR())))
-
- pageTable.append(HT.TR(HT.TD(containerTable)))
-
- pageTable.append(HT.TR(HT.TD(div)))
-
- if species == 'human':
+ if self.species == 'human':
heatmap = ""
form.append(HT.Input(name='ShowStrains',type='hidden', value =1),
@@ -1009,7 +886,7 @@ Resorting this table Your list of "+j+" transcripts is being exported to the Gene Ontology Tree Machine for analysis. This window will soon be replaced with the main GOTM results."; } else - { + { var waithtml1 ="
Your should select at least one transcript to export to the Gene Ontology Tree Machine for analysis."; } html += waithtml1; @@ -152,7 +152,11 @@ function showDatabase3(formName, Database,ProbeSetID,CellID){ document[formName].database.value = Database; document[formName].ProbeSetID.value = ProbeSetID; document[formName].CellID.value = CellID; - document[formName].submit(); + console.log("formName:", formName) + console.log("document[formName]:", document[formName]) + console.log("submit turned off for debugging") + console.log("showDatabase3 is deprecated for the flask version of this site") + //document[formName].submit(); } @@ -188,10 +192,10 @@ function showTrait(fmName){ var thisForm = getForm(fmName); if (thisForm == null || showTrait.arguments.length < 2) return; - + windowName = genNewWin(); thisForm.target = windowName; - + thisForm.FormID.value = "showDatabase"; thisForm.ProbeSetID.value = showTrait.arguments[1]; if (showTrait.arguments.length > 2) @@ -205,10 +209,10 @@ function showCateGraph(fmName){ var thisForm = getForm(fmName); if (thisForm == null || showCateGraph.arguments.length < 2) return; - + windowName = genNewWin(); thisForm.target = windowName; - + thisForm.FormID.value = "showCategoryGraph"; thisForm.interval1.value = showCateGraph.arguments[1]; thisForm.interval2.value = showCateGraph.arguments[2]; @@ -219,22 +223,22 @@ function showCorrPlot(fmName){ var thisForm = getForm(fmName); if (thisForm == null || showCorrPlot.arguments.length < 2) return; - + windowName = genNewWin(); thisForm.target = windowName; - + thisForm.FormID.value = "showCorrelationPlot"; thisForm.ProbeSetID.value = showCorrPlot.arguments[1]; if (showCorrPlot.arguments.length > 2) thisForm.CellID.value = showCorrPlot.arguments[2]; else thisForm.CellID.value = ""; - + thisForm.X_geneSymbol.value = null; thisForm.Y_geneSymbol.value = null; thisForm.submit(); - + } @@ -242,12 +246,12 @@ function showCorrPlotThird(fmName){ var thisForm = getForm(fmName); if (thisForm == null || showCorrPlotThird.arguments.length < 3) return; - + windowName = genNewWin(); thisForm.target = windowName; - + var olddb = thisForm.database.value; - + thisForm.FormID.value = "showCorrelationPlot"; thisForm.database.value = showCorrPlotThird.arguments[1]; thisForm.ProbeSetID.value = showCorrPlotThird.arguments[2]; @@ -284,15 +288,15 @@ function ODE(thisForm, script){ var windowName = 'formTarget' + (new Date().getTime()); var newWindow = open("", windowName, "width=900,menubar=0,toolbar=1,resizable=1,status=1,scrollbars=1"); var html = ""; - if (j == 0){ + if (j == 0){ j = length; trait_list2 = trait_list_all; correlation2 = correlation_all; llid_list2 = llid_list_all; } - + var waithtml1 ="
Your list of "+j+" transcripts is being exported to the ODE for analysis. This window will soon be replaced with the results."; - + html += waithtml1; newWindow.document.write(html); newWindow.document.close(); @@ -302,14 +306,14 @@ function ODE(thisForm, script){ thisForm.correlation.value = correlation2.join(','); thisForm.id_value.value = thisForm.correlation.value; thisForm.llid_list.value = llid_list2.join(','); - + // ODE - + thisForm.idtype.value = thisForm.id_type.value; thisForm.species.value = thisForm.org.value; thisForm.list.value = thisForm.id_list.value; thisForm.client.value = "genenetwork"; - + thisForm.target = windowName; var oldaction = thisForm.action; thisForm.action = script; @@ -318,13 +322,13 @@ function ODE(thisForm, script){ } } */ -// 02/12/2009 +// 02/12/2009 // Lei Yan /*scripts in the Dataediting form*/ function dataEditingFunc(thisForm,submitIdValue){ - + windowName = 'formTarget' + (new Date().getTime()); if (thisForm.FormID.value!='secondRegression'){ @@ -336,7 +340,7 @@ function dataEditingFunc(thisForm,submitIdValue){ } else if (submitIdValue == "addRecord"){ - windowName = thisForm.RISet.value; + windowName = thisForm.RISet.value; var name = thisForm.identification.value; if (name != ""){ } @@ -352,7 +356,7 @@ function dataEditingFunc(thisForm,submitIdValue){ newWindow = open("",windowName,"menubar=1,toolbar=1,location=1,resizable=1,status=1,scrollbars=1,directories=1,width=900"); thisForm.target = windowName; - newWindow.focus(); + newWindow.focus(); thisForm.submitID.value = submitIdValue; thisForm.submit(); } @@ -394,7 +398,7 @@ function addRmvSelection(windowName, thisForm, addORrmv){ thisForm.target = windowName; thisForm.FormID.value = addORrmv; thisForm.submit(); - newWindow.focus(); + newWindow.focus(); } function batchSelection(thisForm){ @@ -424,7 +428,7 @@ function showTop10(formName, submitIdValue){ if ((submitIdValue == "markerRegression")||(submitIdValue == "compositeRegression")){ thisForm.topten.value = "topten"; } - + thisForm.submitID.value = submitIdValue; thisForm.submit(); } @@ -441,12 +445,12 @@ function showIndividualChromosome(formName, submitIdValue, ii){ } if (match == 0) return; - + windowName = 'formTarget' + (new Date().getTime()); newWindow = open("",windowName,"menubar=1,toolbar=1,location=1,resizable=1,status=1,scrollbars=1,directories=1,width=900"); newWindow.focus(); thisForm.target = windowName; - + if (submitIdValue == "showIntMap"){ thisForm.chromosomes.value = ii; } @@ -529,10 +533,10 @@ function dataWindow(form){ } -function xchange() { +function xchange() { var select = document.crossChoice.RISet; var value = select.options[select.selectedIndex].value; - + if (value !="BDAI") return; document.crossChoice.variance.checked = false; } @@ -580,97 +584,97 @@ function crossinfo2(){ function checkWidth(){ var width = document.getElementsByName('plotSize')[0].value - + if (width < 600) { alert("Plot size is too small - setting size to 600") document.getElementsByName('plotSize')[0].value = 600 - } + } } function changeLineColor(){ var lineColor = document.getElementsByName('lineColorSel')[0].value - + document.getElementsByName('lineColor')[0].value = lineColor } function changeLineSize(){ var lineSize = document.getElementsByName('lineSizeSel')[0].value - + document.getElementsByName('lineSize')[0].value = lineSize } function changeIdColor(){ var idColor = document.getElementsByName('idColorSel')[0].value - + document.getElementsByName('idColor')[0].value = idColor } function changeIdFont(){ var idFont = document.getElementsByName('idFontSel')[0].value - + document.getElementsByName('idFont')[0].value = idFont } function changeIdSize(){ var idSize = document.getElementsByName('idSizeSel')[0].value - + document.getElementsByName('idSize')[0].value = idSize } function changeSymbolColor(){ var symbolColor = document.getElementsByName('colorSel')[0].value - + document.getElementsByName('symbolColor')[0].value = symbolColor } function changeSymbol(){ var symbol = document.getElementsByName('symbolSel')[0].value - + document.getElementsByName('symbol')[0].value = symbol } function changeFilled(){ var filled = document.getElementsByName('fillSel')[0].value - + document.getElementsByName('filled')[0].value = filled } function changeSize(){ var symbolSize = document.getElementsByName('sizeSel')[0].value - + document.getElementsByName('symbolSize')[0].value = symbolSize } -function checkAll(thisForm){ +function checkAll(thisForm){ var length = thisForm.searchResult.length; for(var i = 0; i < length; i++) { thisForm.searchResult[i].checked = true; highlight(thisForm.searchResult[i]); } -} +} -function checkNone(thisForm){ +function checkNone(thisForm){ var length = thisForm.searchResult.length; for(var i = 0; i < length; i++) { thisForm.searchResult[i].checked = false; highlight(thisForm.searchResult[i]); } -} +} -function checkInvert(thisForm){ +function checkInvert(thisForm){ var length = thisForm.searchResult.length; for(var i = 0; i < length; i++) { thisForm.searchResult[i].checked = !(thisForm.searchResult[i].checked); highlight(thisForm.searchResult[i]); } -} +} /*Not used anymore*/ -function checkTraits2(thisForm){ +function checkTraits2(thisForm){ var length = thisForm.searchResult.length; var category = thisForm.selectmenu.value; for(var i = 0; i < length; i++) @@ -720,18 +724,18 @@ function checkTraits2(thisForm){ else {} } -} +} function checkNumeric(field,limit,resetvalue,compares,fdname) { - pattern = /^-?[0-9]*\.?[0-9]*$/; + pattern = /^-?[0-9]*\.?[0-9]*$/; if(pattern.test(field.value)==false) { alert("Not numeric in " + fdname); field.value = resetvalue; } - else + else { if (compares == 'gthan') { if(field.value > limit) @@ -748,7 +752,7 @@ function checkNumeric(field,limit,resetvalue,compares,fdname) } } -function checkTraits(thisForm){ +function checkTraits(thisForm){ var length = thisForm.searchResult.length; var andor = thisForm.selectandor.value; var gthan = parseFloat(thisForm.selectgt.value); @@ -780,7 +784,7 @@ function checkTraits(thisForm){ } -function checkPM(thisForm){ +function checkPM(thisForm){ var length = thisForm.searchResult.length; for(var i = 0; i < length; i++) { @@ -792,8 +796,8 @@ function checkPM(thisForm){ {thisForm.searchResult[i].checked = false;} highlight(thisForm.searchResult[i]); } -} -function checkMM(thisForm){ +} +function checkMM(thisForm){ var length = thisForm.searchResult.length; for(var i = 0; i < length; i++) { @@ -804,14 +808,14 @@ function checkMM(thisForm){ {thisForm.searchResult[i].checked = false;} highlight(thisForm.searchResult[i]); } -} +} -function directPermuAlert(thisForm){ - if (thisForm.directPermuCheckbox.checked){ - alert("Interaction permutation will take long time to compute.\n Check this box only when necessary."); +function directPermuAlert(thisForm){ + if (thisForm.directPermuCheckbox.checked){ + alert("Interaction permutation will take long time to compute.\n Check this box only when necessary."); } -} +} function cliqueDatabase(pid){ var windowName = 'clique'; @@ -869,7 +873,7 @@ function snpbrowser_function_refresh() { for (var i=1; i
| + + | +
| - - | -
Special thanks to CYP1A2 and AHR.
GeneNetwork is supported by:
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-ctext += ' '
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-ctext += ' '
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-ctext += '  '
-ctext += ' '
-ctext += ' | '
-ctext += ' '
-ctext += '  '
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-ctext += '
| ' -ctext += ' | ' -ctext += '' -ctext += ' | ' -ctext += '' -ctext += ' | ' -ctext += '' -ctext += ' | ' -ctext += '' -ctext += ' | ' -ctext += '' -ctext += ' | ' -ctext += '' -ctext += ' | ' -ctext += '' -ctext += ' | ' -ctext += ' | ' -ctext += '' -ctext += ' ' -ctext += ' | ' -ctext += '
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| ' +ctext += ' | ' +ctext += '' +ctext += ' | ' +ctext += '' +ctext += ' | ' +ctext += '' +ctext += ' | ' +ctext += '' +ctext += ' | ' +ctext += '' +ctext += ' | ' +ctext += '' +ctext += ' | ' +ctext += '' +ctext += ' | ' +ctext += ' | ' +ctext += '' +ctext += ' ' +ctext += ' | ' +ctext += '
|
- Select and - Search - - - -______________________________________________________ - -Quick HELP - Examples and User's Guide You can also use advanced - commands. Copy these simple examples- into the Get Any or Combined search fields: - -
+
+ GeneNetwork+Open source bioinformatics for systems genetics
+
+ |
-
+
-
- Websites Affiliated with - GeneNetwork +
+
+
+
+ Select and search+
+
- Getting started+____________________________ +
How to Use - GeneNetwork +-+ Mirror and Development - Sites +
User Guide+Read the + + user guide.-
+
- Advanced commands+GeneNetwork supports a variety of advanced searches. -History and - Archive - --- |
-
To try them out copy these examples into the search field:
+ ++ Take the 30 minute + GeneNetwork tour that includes screen shots and + typical steps in the analysis. +
+ ++ For information about + resources and methods, select the Info buttons next to the Group + and Database fields above. +
+ +The conditions + and contact + pages have information on the status of data sets + and advice on their use and citation.
+ +The + + time machine + has earlier versions that correspond to specific publication dates. +
+ +Try the + development site to explore experimental data and features.
+Open source bioinformatics for systems genetics
- Brought to you by the University of Tennessee
GeneNetwork supports a variety of advanced searches.
- -To try them out copy these examples into the search field:
- -- Take the 30 minute - GeneNetwork tour that includes screen shots and - typical steps in the analysis. -
- -- For information about - resources and methods, select the Info buttons next to the Group - and Database fields above. -
- -The conditions - and contact - pages have information on the status of data sets - and advice on their use and citation.
- -The - - time machine - has earlier versions that correspond to specific publication dates. -
- -Try the - development site to explore experimental data and features.
-