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added trait drop down
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lorenasandoval88 committed Oct 11, 2023
1 parent 621638a commit 0646aa7
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116 changes: 72 additions & 44 deletions index.html
Original file line number Diff line number Diff line change
Expand Up @@ -60,8 +60,6 @@
</nav>

<!-- side panel -->

<!-- main banner -->
<section class="bgimage" id="home">
<div class="container-fluid">
<div class="col-lg-12 col-md-12 col-sm-12 col-xs-12 hero-text">
Expand All @@ -74,53 +72,83 @@ <h2 class="hero_title">Diseasome</h2>
</div>

</section>

<h5 >PGS catalog Traits</h5>

<div id = "pgsBar" >
</div>
<!-- pgs scoring counts bar plot -->
<h5>PGS catalog Traits</h5>
<div class="spinner-border m-5" role="status" id="spinner">
<span class="visually-hidden">Loading...</span>
</div>

<div id="pgsBar"></div>

<!-- calc section-->
<section id="calculator">
<h5 >Polygenic Risk Score Calculator</h5>
<div id="calcDiv">
<script>
(async () => {
pgs23 = await import('http://127.0.0.1:5500/main.js')
//pgs23 = await import(location.href+'/export.js')
//pgs23 = await import('https://episphere.github.io/diseasome/main.js')
pgs23.ui()
})()
</script>

<!-- input to select pgs trait and variant number-->
<h5>Select trait</h5>
<!--Make sure the form has the autocomplete function switched off:-->
<form autocomplete="off" action="javascript:alert(`${traitInput.value} submitted`);">
<div class="autocomplete" style="width:300px;">
<input id="traitInput" type="text" name="traitInput" placeholder="Cancer">
</div>
</section>
<input type="submit">
</form>
<br>

<script type="module" src="sdk/plot.js"></script>
<script type="module" src="main.js"></script>
<script type="module" src="dependencies.js"></script>
<script type="module" src="pgs.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjs/3.3.0/math.min.js"></script>


<!-- privacy section-->
<section id="notices">
<span style="font-size:large;">Privacy:</span><br>
<span style="font-size:small;color:black;font-weight:normal">
All data and calculations take place in the browser. No data or calculations circulate by a server. This
application is, foremost, an exercise in privacy-preserving biomedical informatics for consumer genomics
data.
</span><br>
<span style="font-size:large;">Scope/Limitations:</span><br>
<span style="font-size:small;color:black;font-weight:normal">
This calculator was devised as an implementation proof of concept. It has a number of important limitations
for epidemiology research and it does not meet criteria for clinical use. The current tool uses
pre-imputation genotype data and thus results in a low number of SNP matches. Most important, only the
relative risk model <a href='https://www.nature.com/articles/nrg.2016.27#Sec5' target="_blank">(Box 1, eq
2)</a> is calculated, with no effort to determine absolute risk of disease. Finally, the risk
calculation will only be attempted for PGS catalog entries reporting effects as beta values under
"effect_weight".</span>
</section>
<form>
<h5>Select max number of variants in a scoring file</h5>
<select id="myList" >

<option> ---Choose a size--- </option>
<option> 10 </option>
<option> 100 </option>
<option> 500 </option>
<option> 1000 </option>
</select>

</form>

<!-- calc section-->
<section id="calculator">
<h5>Polygenic Risk Score Calculator</h5>
<div id="calcDiv">
<script>
(async () => {
pgs23 = await import('http://127.0.0.1:5500/main.js')
//pgs23 = await import(location.href+'/export.js')
//pgs23 = await import('https://episphere.github.io/diseasome/main.js')
pgs23.ui()
})()
</script>
</div>
</section>

<script type="module" src="./input.js" ></script>
<script type="module" src="sdk/plot.js"></script>
<script type="module" src="main.js"></script>
<script type="module" src="dependencies.js"></script>
<script type="module" src="pgs.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjs/3.3.0/math.min.js"></script>


<!-- privacy section-->
<section id="notices">
<span style="font-size:large;">Privacy:</span><br>
<span style="font-size:small;color:black;font-weight:normal">
All data and calculations take place in the browser. No data or calculations circulate by a server. This
application is, foremost, an exercise in privacy-preserving biomedical informatics for consumer genomics
data.
</span><br>
<span style="font-size:large;">Scope/Limitations:</span><br>
<span style="font-size:small;color:black;font-weight:normal">
This calculator was devised as an implementation proof of concept. It has a number of important
limitations
for epidemiology research and it does not meet criteria for clinical use. The current tool uses
pre-imputation genotype data and thus results in a low number of SNP matches. Most important, only the
relative risk model <a href='https://www.nature.com/articles/nrg.2016.27#Sec5' target="_blank">(Box 1,
eq
2)</a> is calculated, with no effort to determine absolute risk of disease. Finally, the risk
calculation will only be attempted for PGS catalog entries reporting effects as beta values under
"effect_weight".</span>
</section>


</body>
109 changes: 109 additions & 0 deletions input.js
Original file line number Diff line number Diff line change
@@ -0,0 +1,109 @@
import { plot} from './sdk/plot.js'

/*An array containing all the country names in the world:*/
let traits = plot.dt.pgsIds.map( x => x.trait)
//console.log(traits)

function autocomplete(inp, arr) {
/*the autocomplete function takes
two arguments,
the text field element and an array of possible autocompleted values:*/
var currentFocus;
/*execute a function when someone writes in the text field:*/
inp.addEventListener("input", function(e) {
var a, b, i, val = this.value;
/*close any already open lists of autocompleted values*/
closeAllLists();
if (!val) { return false;}
currentFocus = -1;
/*create a DIV element that will contain the items (values):*/
a = document.createElement("DIV");
a.setAttribute("id", this.id + "autocomplete-list");
a.setAttribute("class", "autocomplete-items");
/*append the DIV element as a child of the autocomplete container:*/
this.parentNode.appendChild(a);
/*for each item in the array...*/
for (i = 0; i < arr.length; i++) {
/*check if the item starts with the same letters as the text field value:*/
if (arr[i].substr(0, val.length).toUpperCase() == val.toUpperCase()) {
/*create a DIV element for each matching element:*/
b = document.createElement("DIV");
/*make the matching letters bold:*/
b.innerHTML = "<strong>" + arr[i].substr(0, val.length) + "</strong>";
b.innerHTML += arr[i].substr(val.length);
/*insert a input field that will hold the current array item's value:*/
b.innerHTML += "<input type='hidden' value='" + arr[i] + "'>";
/*execute a function when someone clicks on the item value (DIV element):*/
b.addEventListener("click", function(e) {
/*insert the value for the autocomplete text field:*/
inp.value = this.getElementsByTagName("input")[0].value;
/*close the list of autocompleted values,
(or any other open lists of autocompleted values:*/
closeAllLists();
});
a.appendChild(b);
}
}
});
/*execute a function presses a key on the keyboard:*/
inp.addEventListener("keydown", function(e) {
var x = document.getElementById(this.id + "autocomplete-list");
if (x) x = x.getElementsByTagName("div");
if (e.keyCode == 40) {
/*If the arrow DOWN key is pressed,
increase the currentFocus variable:*/
currentFocus++;
/*and and make the current item more visible:*/
addActive(x);
} else if (e.keyCode == 38) { //up
/*If the arrow UP key is pressed,
decrease the currentFocus variable:*/
currentFocus--;
/*and and make the current item more visible:*/
addActive(x);
} else if (e.keyCode == 13) {
/*If the ENTER key is pressed, prevent the form from being submitted,*/
e.preventDefault();
if (currentFocus > -1) {
/*and simulate a click on the "active" item:*/
if (x) x[currentFocus].click();
}
}
});
function addActive(x) {
/*a function to classify an item as "active":*/
if (!x) return false;
/*start by removing the "active" class on all items:*/
removeActive(x);
if (currentFocus >= x.length) currentFocus = 0;
if (currentFocus < 0) currentFocus = (x.length - 1);
/*add class "autocomplete-active":*/
x[currentFocus].classList.add("autocomplete-active");
}
function removeActive(x) {
/*a function to remove the "active" class from all autocomplete items:*/
for (var i = 0; i < x.length; i++) {
x[i].classList.remove("autocomplete-active");
}
}
function closeAllLists(elmnt) {
/*close all autocomplete lists in the document,
except the one passed as an argument:*/
var x = document.getElementsByClassName("autocomplete-items");
for (var i = 0; i < x.length; i++) {
if (elmnt != x[i] && elmnt != inp) {
x[i].parentNode.removeChild(x[i]);
}
}
}
/*execute a function when someone clicks in the document:*/
document.addEventListener("click", function (e) {
closeAllLists(e.target);
});
}


/*initiate the autocomplete function on the "myInput" element, and pass along the countries array as possible autocomplete values:*/
autocomplete(document.getElementById("traitInput"), traits);


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