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Dk gene table #173

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Dk gene table #173

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8707262
add gene table and a gene table link on the homepage
preetisi Feb 28, 2019
2743001
Merge branch 'master' of https://github.com/broadinstitute/dig-diabet…
preetisi Feb 28, 2019
4c582ef
filter only exeq techology phenotypes
preetisi Mar 1, 2019
89f91da
front page phenotype list changed
dkjang Mar 1, 2019
a13db65
gene association search UI implemented
dkjang Mar 1, 2019
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2 changes: 1 addition & 1 deletion grails-app/conf/Config.groovy
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Expand Up @@ -619,7 +619,7 @@ portal.data.versionDesignator = [ new PortalVersionBean("t2d", // label for
"",
'5010306206573083521',
1, // do we have parent level associations to show
0, // Do we have gene level associations to show?
1, // Do we have gene level associations to show?
1, // add a link to the GRS module into the headers. Note that the GRS module is available whether or not the link is in place
1, // no longer used?
0, // if true then entering a gene takes you to a region page around that chain
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1 change: 1 addition & 0 deletions grails-app/controllers/org/broadinstitute/mpg/HomeController.groovy
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Expand Up @@ -94,6 +94,7 @@ class HomeController {
for (org.broadinstitute.mpg.diabetes.metadata.PhenotypeBean phenotype in phenotypeList.sort{it.sortOrder}) {
JSONObject phenoRecord = new JSONObject()
phenoRecord['systemId'] = phenotype.parent.systemId
phenoRecord['technology'] = phenotype.parent.parent.technology
phenoRecord['translatedSystemId'] = g.message(code: "metadata." + phenotype.parent.systemId, default: phenotype.parent.systemId)
phenoRecord['name'] = phenotype.name
phenoRecord['translatedPhenotype'] = g.message(code: "metadata." + phenotype.name, default: phenotype.name)
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11 changes: 10 additions & 1 deletion grails-app/services/org/broadinstitute/mpg/RestServerService.groovy
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Expand Up @@ -2054,13 +2054,22 @@ time required=${(afterCall.time - beforeCall.time) / 1000} seconds
GetDataQueryHolder getDataQueryHolder = GetDataQueryHolder.createGetDataQueryHolder(filters, searchBuilderService, metaDataService,MetaDataService.METADATA_GENE)

// for now let's make the assumption that we always want to look at case and control counts for this phenotype. We can manufacture those if we cut some corners
List <String> piecesOfThePropertyName = propertyName.split("_")
// List <String> piecesOfThePropertyName = propertyName.split("_")

//HACK EXPERIMENT - checking if given property for Exeq shows data or not.

List <String> piecesOfThePropertyName = []
piecesOfThePropertyName.add("MINA")
piecesOfThePropertyName.add("NS_STRICT")

String propertyNameForCaseCount = "ACA_PH_"+piecesOfThePropertyName[1]
String propertyNameForControlCount = "ACU_PH_"+piecesOfThePropertyName[1]
String propertyNameForOddsRatio = "OR_"+piecesOfThePropertyName[1]
String propertyNameForMINARatio = "MINA_"+piecesOfThePropertyName[1]
addColumnsForPProperties(resultColumnsToDisplay, phenotypeName, dataSetName, propertyName)
addColumnsForPProperties(resultColumnsToDisplay, phenotypeName, dataSetName, propertyNameForOddsRatio)
addColumnsForPProperties(resultColumnsToDisplay, phenotypeName, dataSetName, propertyNameForCaseCount)
addColumnsForPProperties(resultColumnsToDisplay, phenotypeName, dataSetName, propertyNameForMINARatio)
addColumnsForPProperties(resultColumnsToDisplay, phenotypeName, dataSetName, propertyNameForControlCount)

getDataQueryHolder.addProperties(resultColumnsToDisplay)
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35 changes: 24 additions & 11 deletions grails-app/views/home/portalHome.gsp
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Expand Up @@ -186,27 +186,40 @@
</a>
</div>
<div class="traits-filter-wrapper">
<h2 style="font-size:20px; font-weight:300;"><g:message code="trait.search.header" default="View full GWAS results for a phenotype" /></h2>

<g:if test="${portalVersionBean.variantAssociationsExists} && ${portalVersionBean.geneLevelDataExists}">

<div class="radio-inline">
<label><input type="radio" name="radio-gene-association" class="radio" onchange="mpgSoftware.homePage.switchVisibility(['variant-association-ui-wrapper'],['gene-association-ui-wrapper']);" checked> View variant association</label>
</div>
<div class="radio-inline">
<label><input type="radio" name="radio-gene-association" class="radio" onchange="mpgSoftware.homePage.switchVisibility(['gene-association-ui-wrapper'], ['variant-association-ui-wrapper']);" > View gene association</label>
</div>

</g:if>

<g:if test="${portalVersionBean.variantAssociationsExists}">
<h2 style="font-size:20px; font-weight:300;"><g:message code="trait.search.header" default="View full GWAS results for a phenotype" /></h2>
<div class="form-inline" style="padding-top: 10px;">
<div class="traits-filter-ui">
<div class="form-inline variant-association-ui-wrapper">
<!--<div class="traits-filter-ui" style="display:none;">
<span style="display:block; margin: -20px 0 8px 0; font-size:13px;">(ex: bmi, glycemic; '=phenotype' for exact match)</span>
<input id="traits-filter" onfocus="mpgSoftware.traitsFilter.filterOnFocus()" oninput="mpgSoftware.traitsFilter.filterTraitsTable('#traits-list-table')" placeholder="Filter phenotypes" type="text" class="form-control input-sm" style="clear: left; float:left; width: 89%; height: 35px; background-color:#fff; border:none; border-bottom-left-radius: 5px; border-top-left-radius: 5px; border-bottom-right-radius: 0px; border-top-right-radius: 0px; margin:0 0 5px 0; font-size: 16px;">
<div style="float: right; font-size: 20px; padding: 5px 0 1px 0; color: #666; background-color: #fff; width: 10%; height: 35px; border-bottom-right-radius: 5px; border-top-right-radius: 5px; text-align: center; margin-right: 1%" onclick="mpgSoftware.traitsFilter.clearTraitsSearch()" onmouseover="mpgSoftware.traitsFilter.setBtnOver(this)" onmouseout="mpgSoftware.traitsFilter.setBtnOut(this)" ><span class="glyphicon glyphicon-refresh" aria-hidden="true"></span></div>
</div>
<div class="traits-select-ui" style="display:none;">
<select name="" id="trait-input" class="form-control input-sm" style="width: 83%; height: 35px; background-color:#fff; border:none; border-radius: 0; border-top-left-radius: 3px; border-bottom-left-radius: 3px; margin:0; font-size: 16px;">
</div>-->
<div class="traits-select-ui variant-association-ui" style="">
<select name="" id="trait-input" class="form-control input-sm selectpicker" data-live-search="true" style="width: 83%; height: 35px; background-color:#fff; border:none; border-radius: 0; border-top-left-radius: 3px; border-bottom-left-radius: 3px; margin:0; font-size: 16px;">
</select>
<button id="traitSearchLaunch" class="btn btn-primary btn-sm" type="button" style="width:15%; height: 35px; background-color:#fff; color: #000; border:none; border-radius: 5px; margin:0; background-image:url(${resource(dir: 'images', file: 'button_arrow.svg')}); background-repeat: no-repeat; background-position: center right;"><g:message code="mainpage.button.imperative"/>&nbsp;&nbsp;&nbsp;</button>
</div>
</div>
</g:if>
<g:if test="${portalVersionBean.geneLevelDataExists}">
<h2 style="font-size:20px; font-weight:300;"><g:message code="gene.search.header" default="View full GWAS results for a phenotype" /></h2>
<div class="form-inline" style="padding-top: 10px;">
<select name="" id="gene-trait-input" class="form-control input-sm" style="width: 83%; height: 35px; background-color:#fff; border:none; border-radius: 0; border-top-left-radius: 3px; border-bottom-left-radius: 3px; margin:0; font-size: 16px;">
</select>
<button id="geneTraitSearchLaunch" class="btn btn-primary btn-sm" type="button" style="width:15%; height: 35px; background-color:#fff; color: #000; border:none; border-radius: 5px; margin:0; background-image:url(${resource(dir: 'images', file: 'button_arrow.svg')}); background-repeat: no-repeat; background-position: center right;"><g:message code="mainpage.button.imperative"/>&nbsp;&nbsp;&nbsp;</button>
<div class="form-inline gene-association-ui-wrapper" style="display:none;">
<div class="gene-association-ui">
<select name="" id="gene-trait-input" class="form-control input-sm selectpicker" data-live-search="true" style="width: 83%; height: 35px; background-color:#fff; border:none; border-radius: 0; border-top-left-radius: 3px; border-bottom-left-radius: 3px; margin:0; font-size: 16px;">
</select>
<button id="geneTraitSearchLaunch" class="btn btn-primary btn-sm" type="button" style="width:15%; height: 35px; background-color:#fff; color: #000; border:none; border-radius: 5px; margin:0; background-image:url(${resource(dir: 'images', file: 'button_arrow.svg')}); background-repeat: no-repeat; background-position: center right;"><g:message code="mainpage.button.imperative"/>&nbsp;&nbsp;&nbsp;</button>
</div>
</div>
</g:if>
</div>
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8 changes: 8 additions & 0 deletions web-app/css/lib/dkstyle.css
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Expand Up @@ -1226,4 +1226,12 @@ span.new-dataset-flag {

.analysis-modules-btn:hover ul {
display: block;
}

.variant-association-ui > .btn-group, .gene-association-ui > .btn-group {
width: 84% !important; height: 35px;
}

.variant-association-ui > .btn-group > button, .gene-association-ui > .btn-group > button {
height: 35px; border-radius: 5px; border: none;
}
117 changes: 62 additions & 55 deletions web-app/js/lib/dport/genePrioritization.js
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Expand Up @@ -102,8 +102,11 @@ var mpgSoftware = mpgSoftware || {};
var dataSetRecordsForPhenotype = _.uniqBy(matchingPhenotypeRecords,'systemId');
if (dataSetRecordsForPhenotype.length > 0){
_.forEach (dataSetRecordsForPhenotype, function (oneElement){
options.append($("<option />").val(oneElement.systemId)
.html(oneElement.translatedSystemId));
if(oneElement.technology == "ExSeq"){
options.append($("<option />").val(oneElement.systemId)
.html(oneElement.translatedSystemId));
}

});
}

Expand Down Expand Up @@ -203,9 +206,9 @@ var mpgSoftware = mpgSoftware || {};
}

}
if (!skipIt){
collector.push(d);
}

collector.push(d);


}

Expand All @@ -217,57 +220,61 @@ var mpgSoftware = mpgSoftware || {};
$('#manhattanSampleGroupChooser').val(data.variant.dataset);
}

var margin = {top: 0, right: 20, bottom: 0, left: 70},
width = 1050 - margin.left - margin.right,
height = 600 - margin.top - margin.bottom;

var manhattan = baget.manhattan()
.width(width)
.height(height)
.dataHanger("#manhattanPlot1", collector)
.crossChromosomePlot(true)
// .overrideYMinimum (0)
// .overrideYMaximum (10)
// .overrideXMinimum (0)
// .overrideXMaximum (1000000000)
.dotRadius(3)
//.blockColoringThreshold(0.5)
.significanceThreshold(undefined)
.xAxisAccessor(function (d) {
return d.POS
})
.yAxisAccessor(function (d) {
var retVal;
// if (d.P_VALUE > 0) {
// return (0 - Math.log10(d.P_VALUE));
// } else {
// return 0
// }
if (d.P_VALUE > 0) {
retVal = (0 - Math.log10(d.P_VALUE));
} else {
retVal = 0;
}
if (isNaN(retVal)){
console.log('isNaN=true for Manhattan data!');
return 0;
} else {
return retVal;
}
//HACK - Do this only when the portal type is T2D - you can create a portalVersionBean


// var margin = {top: 0, right: 20, bottom: 0, left: 70},
// width = 1050 - margin.left - margin.right,
// height = 600 - margin.top - margin.bottom;
//
// var manhattan = baget.manhattan()
// .width(width)
// .height(height)
// .dataHanger("#manhattanPlot1", collector)
// .crossChromosomePlot(true)
// // .overrideYMinimum (0)
// // .overrideYMaximum (10)
// // .overrideXMinimum (0)
// // .overrideXMaximum (1000000000)
// .dotRadius(3)
// //.blockColoringThreshold(0.5)
// .significanceThreshold(undefined)
// .xAxisAccessor(function (d) {
// return d.POS
// })
// .yAxisAccessor(function (d) {
// var retVal;
// // if (d.P_VALUE > 0) {
// // return (0 - Math.log10(d.P_VALUE));
// // } else {
// // return 0
// // }
// if (d.P_VALUE > 0) {
// retVal = (0 - Math.log10(d.P_VALUE));
// } else {
// retVal = 0;
// }
// if (isNaN(retVal)){
// console.log('isNaN=true for Manhattan data!');
// return 0;
// } else {
// return retVal;
// }
//
// })
// .nameAccessor(function (d) {
// return d.GENE
// })
// .chromosomeAccessor(function (d) {
// return d.CHROM
// })
// .includeXChromosome(true)
// .includeYChromosome(false)
// .dotClickLink(savedVar.variantInfoUrl)
// ;

//d3.select("#manhattanPlot1").call(manhattan.render);

})
.nameAccessor(function (d) {
return d.GENE
})
.chromosomeAccessor(function (d) {
return d.CHROM
})
.includeXChromosome(true)
.includeYChromosome(false)
.dotClickLink(savedVar.variantInfoUrl)
;

d3.select("#manhattanPlot1").call(manhattan.render);
var mySavedVariables = getMySavedVariables();
iterativeTableFiller(collector,
effectType,
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27 changes: 21 additions & 6 deletions web-app/js/lib/dport/portalHome.js
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Expand Up @@ -191,9 +191,9 @@ var mpgSoftware = mpgSoftware || {};
}
}

console.log(data)
//console.log(data)

mpgSoftware.traitsFilter.setTraitsFilter(data.datasets,"home");
//mpgSoftware.traitsFilter.setTraitsFilter(data.datasets,"home");
},
error: function (jqXHR, exception) {
loading.hide();
Expand Down Expand Up @@ -233,8 +233,12 @@ var mpgSoftware = mpgSoftware || {};
if (groupContents.length > 0){
options.append("<optgroup label='"+key+"'>");
_.forEach (groupContents, function (oneElement){
options.append($("<option />").val(oneElement.name)
.html("&nbsp;&nbsp;&nbsp;" + oneElement.translatedPhenotype));
if(oneElement.technology == "GEN"){
options.append($("<option />").val(oneElement.name)
.html("&nbsp;&nbsp;&nbsp;" + oneElement.translatedPhenotype));
}
// options.append($("<option />").val(oneElement.name)
// .html("&nbsp;&nbsp;&nbsp;" + oneElement.translatedPhenotype));
});
options.append("</optgroup label='"+key+"'>");;
}
Expand All @@ -261,7 +265,6 @@ var mpgSoftware = mpgSoftware || {};
( typeof data !== 'undefined') &&
( typeof data.is_error !== 'undefined' ) &&
( !data.is_error ) ) {

fillGenePhenotypeCompoundDropdown(data,homePageVars.geneTraitInput,undefined,undefined,homePageVars.defaultPhenotype);
var availPhenotypes = [];
_.forEach( $("select"+homePageVars.geneTraitInput+" option"), function(a){
Expand Down Expand Up @@ -388,6 +391,17 @@ var mpgSoftware = mpgSoftware || {};

};

var switchVisibility = function( TOVISIBLE, TOINVISIBLE) {

$.each(TOVISIBLE, function(index, value) {
$("."+value).css("display","block");
})

$.each(TOINVISIBLE, function(index, value) {
$("."+value).css("display","none");
})
}


return {
initializeInputFields:initializeInputFields,
Expand All @@ -396,7 +410,8 @@ var mpgSoftware = mpgSoftware || {};
setSlideWindows: setSlideWindows,
setHomePageVariables:setHomePageVariables,
retrieveGenePhenotypes:retrieveGenePhenotypes,
retrievePhenotypes:retrievePhenotypes
retrievePhenotypes:retrievePhenotypes,
switchVisibility:switchVisibility,
}
})();
})();