added opensnp data

index.html

@@ -64,8 +64,14 @@ <h4 class="hero_title">Diseasome</h3>
         </div>
 
     </section>
+<!-- 23 and me -->
+<h5>OpenSNP</h5>
+<div id = snp></div>
+  <br>
 
     <!-- pgs scoring counts bar plot ----------------------------->
+    <h5>The Polygenic Score (PGS) Catalog</h5>
+    <p>The PGS Catalog is an open database of published polygenic scores (PGS). Each PGS in the Catalog is consistently annotated with relevant metadata; including scoring files (variants, effect alleles/weights), annotations of how the PGS was developed and applied, and evaluations of their predictive performance.</p>
     <br>
     <h6 style="color: rgb(6, 137, 231);">Select from the bar chart below, to display variant sizes for entries in a category</h6>
 

sdk/allTraits.js

@@ -17,8 +17,141 @@ let fetchAll = localforage.createInstance({
     name: "fetchAll",
     storeName: "urls"
 })
+let openSnpDbUrls = localforage.createInstance({
+    name: "openSnpDbUrls",
+    storeName: "userUrls"
+})
+let openSnpDbUsers = localforage.createInstance({
+    name: "openSnpDbUsers",
+    storeName: "usersTxt"
+})
 let output = []
+// 23andMe ///////////////////////////////////////////////////////////////////////////////////
+// get all users with genotype data (23andMe, illumina, ancestry etc)-------------------------------
+async function getUserUrls() { // opensnp user data includes ancestry, familtyTree, and 23and me genotype data
+    const newLocal = 'usersFull';
+    let dt
+    dt = await openSnpDbUrls.getItem(newLocal); // check for users in localstorage
+    if (dt == null) {
+        let url = 'https://corsproxy.io/?https://opensnp.org/users.json'
+        let users = (await (await fetch(url)).json())
+        let dt2 = users.sort((a, b) => a.id - b.id)
+        dt = openSnpDbUrls.setItem('usersFull', dt2)
+    }
+    // console.log("getUrls, dt:", dt)
+    return dt
+}
+
+// filter users without 23andme/ancestry data---------------------------------------------------------
+async function filterUsers(type) {
+    let users = await getUserUrls()
+    let dt
+    let arr = []
+    dt = await openSnpDbUrls.getItem('usersFiltered'); // check local storage for user data 
+    if (dt == null) {
+        users.filter(row => row.genotypes.length > 0).map(dt => {
+
+            // keep user with one or more 23andme files
+            dt.genotypes.map(i => {
+                if (dt.genotypes.length > 0 && i.filetype == type) {
+                    let innerObj = {};
+                    innerObj["name"] = dt["name"];
+                    innerObj["id"] = dt["id"];
+                    innerObj["genotype.id"] = i.id;
+                    innerObj["genotype.filetype"] = i.filetype;
+                    innerObj["genotype.download_url"] = i.download_url.replace("http", "https")
+                    arr.push(innerObj)
+
+                }
+            })
+        })
+        dt = arr //.filter(x=> x.genotypes.length != 0)
+        openSnpDbUrls.setItem('usersFiltered', dt)
+    }
+    //console.log("fiter, dt:", dt)
+    return dt
+}
+let users2 = await filterUsers("23andme")
+console.log("users2",users2)
+
+async function get23(urls) {
+    let arr23Txts = []
+    for (let i = 0; i < urls.length; i++) {
+        let user = await openSnpDbUsers.getItem(urls[i]);
+
+        if (user == null) {
+            let url2 = 'https://corsproxy.io/?' + urls[i]
+            user = (await (await fetch(url2)).text())
+            openSnpDbUsers.setItem(urls[i], user);
+        }
+        if (user.substring(0, 37) == '# This data file generated by 23andMe') {
+            //console.log("This is a valid 23andMe file:", user.substring(0, 37))
+            let parsedUser = await parse23(user, urls[i])
+            arr23Txts.push(parsedUser)
+        } else {
+            console.log("ERROR:This is NOT a valid 23andMe file:", user.substring(0, 37))
+        }
+    }
+
+    return arr23Txts
+}
+
+// plot opensnp data types --------------
+let users = (await getUserUrls())
+let usersFlat = users.flatMap(x=>x.genotypes)
+let datatypes = [...new Set(users.flatMap(x=>x.genotypes.flatMap(e=>e.filetype)))]
+console.log("usersFlat",usersFlat)
+var obj = {};
+var counter = {}
+
+for (var i = 0, len = usersFlat.length; i < len; i++) {
+  obj[usersFlat[i]['filetype']] = usersFlat[i];
+  counter[usersFlat[i]['filetype']] = (counter[usersFlat[i]['filetype']] || 0) + 1
+}
+let newArr = new Array();
+for (var key in obj){
+  newArr.push(extend( obj[key], {count:counter[key]}));
+}
+
+function extend(a, b){
+    for(var key in b)
+        if(b.hasOwnProperty(key))
+            a[key] = b[key];
+    return a;
+}
+console.log(newArr)
+
+
+let snpDiv = document.getElementById("snp")
+var layout = {
+
+    autosize: true,
+    title: `Counts of OpenSNP datatypes`,
+ margin: {l:150},
+    xaxis: {
+        autorange: false,
+        range: [0, 1000],
+        type: 'linear'
+    },
+}
+var dt = [{
+    x: newArr.map(x => x.count),
+    y: newArr.map(x => x.filetype),
+    type: 'bar',
+    orientation: 'h',
+    marker: {
+        color: Array(newArr.length).fill(['orange', 'green', 'red',
+            '#1f77b4', //muted blue
+            '#ff7f0e', // safety orange
+            '#2ca02c', // cooked asparagus green
+            '#d62728', //brick red
+        ]).flat().splice(0, newArr.length)
+    }
+}]
+plotly.newPlot(snpDiv, dt, layout);
 
+// top bar plot
+// PGS ///////////////////////////////////////////////////////////////////////////////////
 const traitFiles = (await fetchAll2('https://www.pgscatalog.org/rest/trait/all')).flatMap(x => x)
 const traits = Array.from(new Set(traitFiles.flatMap(x => x["trait_categories"])
     .sort().filter(e => e.length).map(JSON.stringify)), JSON.parse)

style.css

@@ -4,7 +4,7 @@
 }
 /* hero background image */
 .bgimage {
-    height:45vh;
+    height:35vh;
     background: url('dna2.jpg');
     background-size:cover;
     position:relative;