added prs plot

episphere · Apr 10, 2024 · 5c6605d · 5c6605d
1 parent 307a829
commit 5c6605d
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Showing 4 changed files with 374 additions and 246 deletions.
diff --git a/index.html b/index.html
@@ -94,6 +94,7 @@ <h3>PRS</h3>
             (compressed or not).</p>
 
             <div id=prsDiv>prsDiv</div>
+            <div id=prsButton></div>
 
 
     </div>
@@ -133,8 +134,12 @@ <h3>The Polygenic Score (PGS) Catalog</h3>
         <div class="tab">
             <button class="tablinks" onclick="openCity(event, 'Categories', true)">Categories</button>
             <button class="tablinks" onclick="openCity(event, 'Traits', true)">Traits</button>
+            <button class="tablinks" onclick="openCity(event, 'EFO_ids', true)">EFO_ids</button>
+
         </div>
 
+            <!--  --------------------->
+
         <div id="Categories" class="tabcontent">
 
             <h6 style="color: rgb(6, 137, 231);">Select a PGS category below:</h6>
@@ -168,7 +173,7 @@ <h6 id="pieHeader"></h6>
         </div>
         <!--  --------------------->
         <div id="Traits" class="tabcontent">
-            <h6 style="color: rgb(6, 137, 231);">Select a PGS trait below:</h6>
+            <h6 style="color: rgb(6, 137, 231);">Select a PGS category below:</h6>
         <div id="topBarTraits"></div>
         <div class="spinner-border m-5" style="display: none;" role="status" id="spinner3">
             <span class="visually-hidden">Loading...</span>
@@ -180,10 +185,24 @@ <h6 style="color: rgb(6, 137, 231);">Select a PGS trait below:</h6>
         <div id="betassecondBarTraits"></div>
     </div>
     </div>
+
+          <!--  --------------------->
+
+          <div id="EFO_ids" class="tabcontent">
+
+            <h6 style="color: rgb(6, 137, 231);">Select an EFO id below:</h6>
+            <div id="topBarEFO_ids"></div>
+            <p id="description1" style="font-size:10px;color:blue"></p>
+
+
+          </div>
+          <button id="plotbetasButton"></button>
+
+          <div id="plotbetas">plotbetas</div>
+
     <!-- scripts----------------------------------------------->
     <script src="tabs.js"></script>
     <script type="module" src="sdk/prs.js"></script>
-
     <script type="module" src="sdk/sdk.js"></script>
     <script type="module" src="sdk/main.js"></script>
     <script type="module" src="sdk/plots.js"></script>

diff --git a/sdk/main.js b/sdk/main.js
@@ -66,36 +66,38 @@ functions.filterUsers = async function(type, users) {
 }
 
 
-functions.get23 = async function(urls) {
+functions.get23 = async function(usersData) {
     let arr23Txts = []
+  //  console.log(",usersData.map(x=> x.phenotypes[Type II Diabetes])",usersData.map(x=> x.phenotypes["Type II Diabetes"]))//.phenotypes["Type II Diabetes"]))
+    let urls = usersData.map( x => x["genotype.download_url"]).slice(128,150)
+    console.log("# of users: ",urls.length)
     for (let i = 0; i < urls.length; i++) {
         let user = await openSnpDbUsers.getItem(urls[i]);
-        console.log(i)
+        console.log("user #",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 functions.parse23(user, urls[i])
+            console.log("This is a valid 23andMe file:", user.substring(0, 37))
+            let parsedUser = await functions.parse23(user, usersData[i])//urls[i])
             arr23Txts.push(parsedUser)
         } else {
             console.log("ERROR:This is NOT a valid 23andMe file:", user.substring(0, 37))
         }
     }
-    console.log("arr23Txts",arr23Txts)
     return arr23Txts
 }
 
 // create 23andme obj and data --------------------------
-functions.parse23 = async function (txt, url) {
+functions.parse23 = async function (txt, usersData) {
     // normally info is the file name
     let obj = {}
     let rows = txt.split(/[\r\n]+/g)
     obj.txt = txt
-    obj.url = url
+    obj.openSnp = usersData
 
     let n = rows.filter(r => (r[0] == '#')).length
     obj.meta = rows.slice(0, n - 1).join('\r\n')
@@ -278,7 +280,6 @@ functions.getscoreFiles = async function(pgsIds) {
 
 
 const traitFiles = (await functions.fetchAll2('https://www.pgscatalog.org/rest/trait/all')).flatMap(x => x)
-functions.removeLocalStorageValues('request', pgs)
 
 export {
     functions