Merge branch 'release/0.9.4'

statgen · Dec 14, 2021 · 46394fd · 46394fd
2 parents 83f5181 + 1c69c0b
commit 46394fd
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Showing 7 changed files with 229 additions and 152 deletions.
diff --git a/package-lock.json b/package-lock.json
diff --git a/package.json b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "localzoom",
-  "version": "0.9.3",
+  "version": "0.9.4",
   "license": "MIT",
   "engines": {
     "node": ">=10.13.0"
@@ -20,7 +20,7 @@
     "@sentry/browser": "^4.5.2",
     "bootstrap": "^4.4.1",
     "bootstrap-vue": "^2.21.2",
-    "locuszoom": "git+https://github.com/statgen/locuszoom.git#71720de",
+    "locuszoom": "git+https://github.com/statgen/locuszoom.git#33316cd",
     "lodash": "^4.17.11",
     "tabulator-tables": "^5.0.7",
     "vue": "^2.6.14",

diff --git a/src/App.vue b/src/App.vue
@@ -38,8 +38,6 @@ export default {
             // State to be tracked across all components
             genome_build: 'GRCh37',
             known_tracks: [],
-            // Control specific display options
-            has_credible_sets: true,
         };
     },
     computed: {
@@ -295,7 +293,6 @@ export default {
     <div class="row">
       <div class="col-md-12">
         <gwas-toolbar
-          :has_credible_sets.sync="has_credible_sets"
           :genome_build.sync="genome_build"
           :max_studies="6"
           :known_tracks="known_tracks"
@@ -312,7 +309,6 @@ export default {
           :base_sources="base_sources"
           :dynamic_urls="true"
           :genome_build="genome_build"
-          :has_credible_sets="has_credible_sets"
           :known_tracks="known_tracks"
           :chr="chr"
           :start="start"

diff --git a/src/components/ExportData.vue b/src/components/ExportData.vue
@@ -24,7 +24,6 @@ export default {
     components: { TabulatorTable },
     props: {
         known_tracks: { type: Array, default: () => [] },
-        has_credible_sets: { type: Boolean, default: true },
         table_data: { type: Array, default: () => [] },
     },
     data() {
@@ -78,13 +77,9 @@ export default {
                     formatterParams: { precision: 3 },
                     sorter: 'number',
                 },
+                { title: 'Cred. set', field: 'credset:is_member', formatter: 'tickCross' },
+                { title: 'Posterior probability', field: 'credset:posterior_prob', formatter: formatSciNotation },
             ];
-            if (this.has_credible_sets) {
-                base.push(
-                    { title: 'Cred. set', field: 'credset:is_member', formatter: 'tickCross' },
-                    { title: 'Posterior probability', field: 'credset:posterior_prob', formatter: formatSciNotation },
-                );
-            }
             return base;
         },
     },

diff --git a/src/components/GwasToolbar.vue b/src/components/GwasToolbar.vue
@@ -26,10 +26,6 @@ export default {
             type: String,
             default: 'GRCh37',
         },
-        has_credible_sets: {
-            type: Boolean,
-            default: true,
-        },
         // Limit how many studies can be added (due to browser performance)
         max_studies: {
             type: Number,
@@ -53,9 +49,6 @@ export default {
             message: '',
             message_class: '',
 
-            // Allow the user to customize the plot and select featured annotations.
-            has_gwas_catalog: true,
-
             // Controls for "batch view" mode
             batch_mode_active: false,
             batch_mode_regions: [],
@@ -75,14 +68,6 @@ export default {
                 this.$emit('update:genome_build', newValue);
             },
         },
-        i_has_credible_sets: {
-            get: function() {
-                return this.has_credible_sets;
-            },
-            set: function(newValue) {
-                this.$emit('update:has_credible_sets', newValue);
-            },
-        },
     },
     methods: {
         reset() {
@@ -116,11 +101,11 @@ export default {
                 return;
             }
 
-            const { genome_build, has_gwas_catalog, has_credible_sets } = this;
+            const { genome_build } = this;
 
 
             const track_sources = createStudySources(data_type, reader, filename, parser_func);
-            const panel_layouts = createStudyLayouts(data_type, filename, display_name, {has_gwas_catalog, has_credible_sets});
+            const panel_layouts = createStudyLayouts(data_type, filename, display_name);
             const new_plot_state = { genome_build, ...metadata };
 
             this.$emit('add-tabix-track', data_type, filename, display_name, track_sources, panel_layouts, new_plot_state);
@@ -172,32 +157,10 @@ export default {
         </div>
         <b-dropdown
           v-else
-          text="Plot options"
+          text="Genome Build"
           variant="info"
           class="float-right">
           <div class="px-3">
-            <strong>Annotations</strong><br>
-            <div class="form-check form-check-inline">
-              <input
-                id="show-catalog"
-                v-model="has_gwas_catalog"
-                class="form-check-input"
-                type="checkbox">
-              <label
-                class="form-check-label"
-                for="show-catalog">GWAS Catalog</label>
-            </div>
-            <div class="form-check form-check-inline">
-              <input
-                id="show-credible-set"
-                v-model="i_has_credible_sets"
-                class="form-check-input"
-                type="checkbox">
-              <label
-                class="form-check-label"
-                for="show-credible-set">95% credible set</label>
-            </div>
-            <strong>Genome Build</strong><br>
             <div class="form-check">
               <input
                 id="build-37"

diff --git a/src/components/PlotPanes.vue b/src/components/PlotPanes.vue
@@ -34,7 +34,6 @@ export default {
 
         // Control optional features (this could be done more nicely)
         dynamic_urls: { type: Boolean, default: false }, // Change URL when plot updates
-        has_credible_sets: { type: Boolean, default: true }, // export tool
     },
     data() {
         return {
@@ -167,7 +166,6 @@ export default {
           :disabled="!has_studies"
           title="Export">
           <export-data
-            :has_credible_sets="has_credible_sets"
             :known_tracks="known_tracks"
             :table_data="table_data"
             @requested-data="subscribeToData"/>