Pigean x hpo (#965)

* working

* working on geneset

* made all but HPO default

* show trait group in header

Author: moriondo2022

src/components/TraitGroupSelectPicker.vue

@@ -1,6 +1,7 @@
 <template>
     <select v-model="traitGroup" class="form-control">
         <option value="all">All</option>
+        <option value="all_but_hpo">All but HPO</option>
         <option v-for="group in groups" :value="group[0]">
             {{ group[1] }}
         </option>
@@ -42,6 +43,7 @@ export default Vue.component("trait-group-selectpicker", {
         keyParamsTraitGroup(newKey) {
             // do we need this?
             if (this.size === null) {
+                console.log("Is this thing firing?");
                 this.size = newKey;
             }
         },

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 = "all";
+export const DEFAULT_TRAIT_GROUP = "all_but_hpo";
 export const TRAIT_GROUPS = {
     "portal": "A2F", 
     "gcat_trait": "GWAS Catalog",

src/views/PIGEAN/Gene/Template.vue

@@ -1,3 +1,8 @@
+<script setup lang="ts">
+import bioIndexUtils from '../../../utils/bioIndexUtils';
+
+</script>
+
 <template>
     <div>
         <!-- Header -->
@@ -89,7 +94,10 @@
 
             <div class="card mdkp-card">
                 <div class="card-body pigean-title">
-                    <h4 class="card-title">Traits with genetic support</h4>
+                    <h4 class="card-title">Traits with genetic support 
+                        (trait group: {{ !!bioIndexUtils.TRAIT_GROUPS[$store.state.traitGroup] 
+                            ? bioIndexUtils.TRAIT_GROUPS[$store.state.traitGroup]
+                            : $parent.tissueFormatter($store.state.traitGroup).toUpperCase()}})</h4>
                     <div>
                         Combined genetic support is composed of direct support
                         (from GWAS associations near the gene) and indirect

src/views/PIGEAN/Gene/main.js

@@ -196,6 +196,7 @@ new Vue({
             pigeanUtils.mapPhenotypes(this.$store.state.pigeanAllPhenotypes.data);
     },
     methods: {
+        tissueFormatter: Formatters.tissueFormatter,
         // go to region page
         exploreRegion(expanded = 0) {
             let r = this.region;

src/views/PIGEAN/Gene/store.js

@@ -86,14 +86,17 @@ export default new Vuex.Store({
             context.commit("setTraitGroup", traitGroup);
             if (!!name) {
                 context.dispatch("gene/query", { q: name });
-                if (traitGroup !== 'all'){
+                if (!traitGroup.startsWith('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
                     let traitsData = [];
                     let traits = Object.keys(bioIndexUtils.TRAIT_GROUPS);
+                    if (traitGroup === 'all_but_hpo'){
+                        traits = traits.filter(t => t !== 'hpo');
+                    }
                     for (let i = 0; i < traits.length; i++){
                         let group = traits[i];
                         let traitQuery = `${group},${context.state.geneName},${

src/views/PIGEAN/GeneSet/store.js

@@ -58,15 +58,19 @@ export default new Vuex.Store({
             context.commit("setGenesetSize", genesetSize);
             context.commit("setTraitGroup", traitGroup);
 
-            if (traitGroup !== 'all'){
+            if (!traitGroup.startsWith('all')){
                 await context.dispatch("pigeanGeneset/query", { q: 
                     `${traitGroup},${name},${bioIndexUtils.DEFAULT_SIGMA},${genesetSize}`});
                 context.commit("setPhewasData", context.state.pigeanGeneset.data);
             } else {
                 // If ALL is selected, query all trait groups and get top results across all
+                let traits = Object.keys(bioIndexUtils.TRAIT_GROUPS);
+                if (traitGroup === 'all_but_hpo'){
+                    traits = traits.filter(t => t !== 'hpo');
+                }
                 let traitsData = [];
-                for (let i = 0; i < bioIndexUtils.TRAIT_GROUPS.length; i++){
-                    let group = bioIndexUtils.TRAIT_GROUPS[i];
+                for (let i = 0; i < traits.length; i++){
+                    let group = traits[i];
                     let traitQuery = `${group},${name},${
                         bioIndexUtils.DEFAULT_SIGMA},${genesetSize}`;
                     let groupData = await bioIndexUtils.query("pigean-gene-set", traitQuery);