Added p-values to geneset table (#763)

* Added p-values to geneset table * passing gene sets parameter
broadinstitute · Oct 23, 2024 · faf12e3 · faf12e3
1 parent 82d0f79
commit faf12e3
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Showing 3 changed files with 32 additions and 13 deletions.
diff --git a/src/views/Factorization/Template.vue b/src/views/Factorization/Template.vue
@@ -41,7 +41,7 @@
                                         Gene Sets
                                     </div>
                                     <select class="form-control"
-                                        :v-model="$parent.genesetParam"
+                                        v-model="$parent.genesetParam"
                                     >
                                         <option v-for=" o in $store.state.genesetOptions"
                                             :value="o">

diff --git a/src/views/Factorization/main.js b/src/views/Factorization/main.js
@@ -78,9 +78,15 @@ new Vue({
             ],
             extraGenesetFields: [
                 {
-                    key: "gene_Set",
+                    key: "gene_set",
                     label: "Gene set",
                     sortable: true
+                },
+                {
+                    key: "p_value",
+                    label: "P-value",
+                    formatter: Formatters.pValueFormatter,
+                    sortable: true
                 }
             ],
             extraGeneFields: [
@@ -162,13 +168,22 @@ new Vue({
         },
         genesetFactor() {
             let data = this.flatData(this.$store.state.genesetFactor);
+            data.forEach(item => item["p_value"] = this.pValueLookup[item.gene_set]);
             return this.formatLabels(data);
         },
         genesetFields(){
             return this.baseFields.concat(this.extraGenesetFields);
         },
         geneFields(){
             return this.baseFields.concat(this.extraGeneFields);
+        },
+        pValueLookup(){
+            let pValueList = this.$store.state.genesetPValues;
+            let lookup = {};
+            pValueList.forEach(item =>
+                lookup[item.gene_set] = item.p_value
+            );
+            return lookup;
         }
     },
     watch: {
@@ -188,7 +203,11 @@ new Vue({
             if (this.geneInput) {
                 let genes = this.geneInput.trim().split(/[\n, ]+/);
                 let geneSets = this.genesetParam;
-                this.$store.dispatch("queryBayesGenes", genes, geneSets);
+                let queryString = JSON.stringify({
+                    "genes": genes,
+                    "gene_sets": geneSets
+                });
+                this.$store.dispatch("queryBayesGenes", queryString);
             }
         },
         flatData(data){

diff --git a/src/views/Factorization/store.js b/src/views/Factorization/store.js
@@ -21,6 +21,7 @@ export default new Vuex.Store({
         genesetFactor: [],
         roundTripInputGenes: [],
         genesetOptions: [],
+        genesetPValues: [],
     },
 
     mutations: {
@@ -37,40 +38,39 @@ export default new Vuex.Store({
             state.roundTripInputGenes = data || state.roundTripInputGenes;
         },
         setGenesetOptions(state, data){
-            state.genesetOptions = data || state.genesetOptions
+            state.genesetOptions = data || state.genesetOptions;
+        },
+        setGenesetPValues(state, data){
+            state.genesetPValues = data || state.genesetPValues;
         },
         clearAllData(state){
             state.pigeanFactor = [];
             state.geneFactor = [];
             state.genesetFactor = [];
             state.roundTripInputGenes = [];
+            state.genesetPValues = [];
         }
     },
 
     getters: {
     },
 
     actions: {
-        async queryBayesGenes(context, genesList, geneSets){
+        async queryBayesGenes(context, queryString){
             context.commit("clearAllData");
             let address = "https://translator.broadinstitute.org/genetics_provider/bayes_gene/pigean";
-            let genesQuery = JSON.stringify(
-                { 
-                    "genes": genesList,
-                    "gene_sets": geneSets,
-                }
-            );
             let json = await fetch(address, {
                 method: "POST",
                 headers: {
                     'Content-Type': 'application/json'
                 },
-                body: genesQuery
+                body: queryString
             }).then(resp => resp.json());
             context.commit("setRoundTripInputGenes", json.input_genes);
             context.commit("setPigeanFactor", json["pigean-factor"].data);
             context.commit("setGeneFactor", json["gene-factor"]);
             context.commit("setGenesetFactor", json["gene-set-factor"]);
+            context.commit("setGenesetPValues", json["gene_sets"]);
         },
         async queryGenesetOptions(context){
             let address = "https://translator.broadinstitute.org/genetics_provider/bayes_gene/heartbeat";
@@ -81,6 +81,6 @@ export default new Vuex.Store({
                 }
             }).then(resp => resp.json());
             context.commit("setGenesetOptions", json.gene_sets);
-        }
+        },
     },
 });