Pigean all traits (#807)

* defaults to all

* getting data from all groups

* getting there

* phewas data is being set but why isn't it propagating

* getting all data

* top 1500 traits

* remove superfluous watch

src/components/TraitGroupSelectPicker.vue

@@ -1,5 +1,6 @@
 <template>
     <select v-model="traitGroup" class="form-control">
+        <option value="all">All</option>
         <option value="portal">A2F</option>
         <option value="gcat_trait">GWAS Catalog</option>
         <option value="rare_v2">Orphanet</option>

src/utils/bioIndexUtils.js

@@ -140,7 +140,7 @@ async function processRequest(req, onResolve, onError, onLoad, limitWhile) {
 }
 export const DEFAULT_SIGMA = 2;
 export const DEFAULT_GENESET_SIZE = "small";
-export const DEFAULT_TRAIT_GROUP = "portal";
+export const DEFAULT_TRAIT_GROUP = "all";
 
 export default {
     query,

src/views/PIGEAN/Gene/main.js

@@ -145,7 +145,7 @@ new Vue({
         },
         plotReady() {
             return (
-                this.$store.state.pigeanGene.data.length > 0 &&
+                this.pigeanFilteredData.length > 0 &&
                 Object.keys(this.pigeanPhenotypeMap).length > 0
             );
         },
@@ -159,10 +159,15 @@ new Vue({
             return adjustedData;
         },
         pigeanFilteredData(){
-            return this.$store.state.pigeanGene.data.filter(item => item.log_bf > 0 || item.prior > 0);
+            let rawData = structuredClone(this.phewasAllData);
+            let filteredData = rawData.filter(item => item.log_bf > 0 || item.prior > 0);
+            return filteredData;
         },
         pigeanMap(){
             return this.pigeanPhenotypeMap;
+        },
+        phewasAllData(){
+            return this.$store.state.phewasData;
         }
     },
     watch: {

src/views/PIGEAN/Gene/store.js

@@ -24,7 +24,7 @@ export default new Vuex.Store({
         aliasName: null,
         traitGroup: keyParams.traitGroup || bioIndexUtils.DEFAULT_TRAIT_GROUP,
         traitGroupToQuery: null,
-
+        phewasData: [],
     },
 
     mutations: {
@@ -47,6 +47,9 @@ export default new Vuex.Store({
         setAliasName(state, aliasName) {
             state.aliasName = aliasName || state.aliasName;
         },
+        setPhewasData(state, phewasData){
+            state.phewasData = phewasData || state.phewasData;
+        }
     },
 
     getters: {
@@ -82,9 +85,24 @@ export default new Vuex.Store({
             context.commit("setTraitGroup", traitGroup);
             if (!!name) {
                 context.dispatch("gene/query", { q: name });
-                context.dispatch("pigeanGene/query", { q: 
-                    `${traitGroup},${name},${bioIndexUtils.DEFAULT_SIGMA},${genesetSize}`,
-                    limit: 1000 });
+                if (traitGroup !== 'all'){
+                    await context.dispatch("pigeanGene/query", { q: 
+                        `${traitGroup},${name},${bioIndexUtils.DEFAULT_SIGMA},${genesetSize}`});
+                    context.commit("setPhewasData", context.state.pigeanGene.data);
+                } else {
+                    // If ALL is selected, query all trait groups and get top results across all
+                    const TRAIT_GROUPS = ["portal", "gcat_trait", "rare_v2"];
+                    let traitsData = [];
+                    for (let i = 0; i < TRAIT_GROUPS.length; i++){
+                        let group = TRAIT_GROUPS[i];
+                        let traitQuery = `${group},${context.state.geneName},${
+                            bioIndexUtils.DEFAULT_SIGMA},${context.state.genesetSize}`;
+                        let groupData = await bioIndexUtils.query("pigean-gene", traitQuery);
+                        traitsData = traitsData.concat(groupData);
+                    }
+                    traitsData = traitsData.sort((a,b) => b.combined - a.combined);
+                    context.commit("setPhewasData", traitsData.slice(0,1500));
+                }
             }
         },
         async getPigeanPhenotypes(context) {