Merge branch 'release/0.3.1'

statgen · Oct 16, 2019 · 3037700 · 3037700
2 parents 8ea5435 + aed63e9
commit 3037700
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Showing 9 changed files with 32 additions and 19 deletions.
diff --git a/package.json b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "localzoom",
-  "version": "0.3.0",
+  "version": "0.3.1",
   "license": "MIT",
   "main": "lib/LzTabix.umd.min.js",
   "scripts": {
@@ -16,7 +16,7 @@
     "bootstrap": "^4.1.3",
     "bootstrap-vue": "^2.0.0-rc.11",
     "gwas-credible-sets": "^0.1.0",
-    "locuszoom": "https://github.com/statgen/locuszoom#develop",
+    "locuszoom": "https://github.com/statgen/locuszoom#8b06580",
     "lodash": "^4.17.11",
     "tabix-reader": "https://github.com/abought/tabix-reader",
     "tabulator-tables": "^4.1.4",

diff --git a/src/components/ExportData.vue b/src/components/ExportData.vue
@@ -36,27 +36,35 @@ export default {
             // How should the table display this set of fields? Determined once at component load.
             const base = [
                 { title: 'Chrom', field: 'chromosome' },
-                { title: 'Pos', field: 'position' },
+                { title: 'Pos', field: 'position', sorter: 'number' },
                 { title: 'Ref', field: 'ref_allele' },
                 { title: 'Alt', field: 'alt_allele' },
-                { title: '-log<sub>10</sub>(p)', field: 'log_pvalue', formatter: formatSciNotation },
+                {
+                    title: '-log<sub>10</sub>(p)',
+                    field: 'log_pvalue',
+                    formatter: formatSciNotation,
+                    sorter: 'number',
+                },
                 {
                     title: '&beta;',
                     field: 'beta',
                     formatter: 'money',
                     formatterParams: { precision: 3 },
+                    sorter: 'number',
                 },
                 {
                     title: 'SE(&beta;)',
                     field: 'stderr_beta',
                     formatter: 'money',
                     formatterParams: { precision: 3 },
+                    sorter: 'number',
                 },
                 {
                     title: 'Alt freq.',
                     field: 'alt_allele_freq',
                     formatter: 'money',
                     formatterParams: { precision: 3 },
+                    sorter: 'number',
                 },
             ];
             if (this.has_credible_sets) {

diff --git a/src/components/GwasToolbar.vue b/src/components/GwasToolbar.vue
@@ -121,7 +121,7 @@ export default {
                        @fail="showMessage" class="float-right"
                        :build="build"
                        :max_range="1000000"
-                       search_url="https://portaldev.sph.umich.edu/api_internal_dev/v1/annotation/omnisearch/" />
+                       search_url="https://portaldev.sph.umich.edu/api/v1/annotation/omnisearch/" />
         <b-dropdown v-else text="Plot options" variant="info"
                      class="float-right">
           <div class="px-3">

diff --git a/src/components/LzPlot.vue b/src/components/LzPlot.vue
@@ -57,9 +57,13 @@ export default {
          */
         createLZ(base_layout, base_sources) {
             // Create and populate the plot
+            // The layout comes from properties assigned to a vue instance, which are automatically
+            //   wrapped (deeply) with Vue observable getters/setters. This can confuse LocusZoom,
+            //   so we will deep-copy to ensure this is just pure JS primitives
+            const layout = JSON.parse(JSON.stringify(base_layout));
             const data_sources = new LocusZoom.DataSources();
             base_sources.forEach(([name, config]) => data_sources.add(name, config));
-            const plot = LocusZoom.populate(`#${this.dom_id}`, data_sources, base_layout);
+            const plot = LocusZoom.populate(`#${this.dom_id}`, data_sources, layout);
 
             if (this.show_loading) {
                 // Add loading indicator to every panel if appropriate
@@ -115,8 +119,9 @@ export default {
                 // FIXME: this component receives notifications of a value it changes, a design
                 //   quirk that risks infinite update loops
                 // Only apply new region information if it has changed
-                const diffs = Object.keys(this.region).reduce((acc, key) => {
-                    const new_val = this.region[key];
+                const region = Object.assign({}, this.region);
+                const diffs = Object.keys(region).reduce((acc, key) => {
+                    const new_val = region[key];
                     if (new_val !== this.plot.state[key]) {
                         acc[key] = new_val;
                     }

diff --git a/src/components/RegionPicker.vue b/src/components/RegionPicker.vue
@@ -27,7 +27,7 @@ export default {
         },
         search_url: {
             type: String,
-            default: 'https://portaldev.sph.umich.edu/api_internal_dev/v1/annotation/omnisearch/',
+            default: 'https://portaldev.sph.umich.edu/api/v1/annotation/omnisearch/',
         },
         build: {
             type: String,

diff --git a/src/gwas/parser_utils.js b/src/gwas/parser_utils.js
@@ -100,7 +100,7 @@ function parseAlleleFrequency({ freq, allele_count, n_samples, is_alt_effect = t
         return null;
     }
     if (freq === undefined && allele_count !== undefined) {
-        result = +allele_count / +n_samples;
+        result = +allele_count / +n_samples / 2;
     } else if (MISSING_VALUES.has(freq)) { // Frequency-based parsing
         return null;
     } else {

diff --git a/src/util/lz-helpers.js b/src/util/lz-helpers.js
@@ -1,7 +1,7 @@
 import LocusZoom from 'locuszoom';
 import 'locuszoom/dist/ext/lz-credible-sets.min'; // Import for side effects (globally register helpers)
 
-import { PORTAL_API_BASE_URL, LD_SERVER_BASE_URL, PORTAL_DEV_API_BASE_URL } from './constants';
+import { PORTAL_API_BASE_URL, LD_SERVER_BASE_URL } from './constants';
 import { makeParser } from '../gwas/parsers';
 
 const stateUrlMapping = Object.freeze({ chr: 'chrom', start: 'start', end: 'end' });
@@ -169,7 +169,7 @@ function getBasicSources(study_sources = []) {
         ['catalog', ['GwasCatalogLZ', { url: `${PORTAL_API_BASE_URL}annotation/gwascatalog/results/` }]],
         ['ld', ['LDLZ2', { url: LD_SERVER_BASE_URL, params: { source: '1000G', population: 'ALL' } }]],
         ['gene', ['GeneLZ', { url: `${PORTAL_API_BASE_URL}annotation/genes/` }]],
-        ['recomb', ['RecombLZ', { url: `${PORTAL_DEV_API_BASE_URL}annotation/recomb/results/` }]],
+        ['recomb', ['RecombLZ', { url: `${PORTAL_API_BASE_URL}annotation/recomb/results/` }]],
         // TODO: This source is broken on https; I wish we had an alternative
         ['constraint', ['GeneConstraintLZ', { url: 'http://exac.broadinstitute.org/api/constraint' }]],
     ];

diff --git a/tests/unit/parser_utils.spec.js b/tests/unit/parser_utils.spec.js
@@ -48,12 +48,12 @@ describe('parseAlleleFrequency', () => {
 
     it('calculates freq from counts', () => {
         const res = parseAlleleFrequency({ allele_count: '25', n_samples: '100' });
-        assert.equal(res, 0.25);
+        assert.equal(res, 0.125);
     });
 
     it('calculates freq from counts, and orients to alt', () => {
         const res = parseAlleleFrequency({ allele_count: '75', n_samples: '100', is_alt_effect: false });
-        assert.equal(res, 0.25);
+        assert.equal(res, 0.625);
     });
 
     it('handles missing data when working with counts', () => {

diff --git a/yarn.lock b/yarn.lock
@@ -5412,9 +5412,9 @@ locate-path@^3.0.0:
     p-locate "^3.0.0"
     path-exists "^3.0.0"
 
-locuszoom@statgen/locuszoom#develop:
-  version "0.9.1"
-  resolved "https://codeload.github.com/statgen/locuszoom/tar.gz/29328f21eea7e5a7744c51a33416e26098a653ba"
+"locuszoom@https://github.com/statgen/locuszoom#8b06580":
+  version "0.10.0-beta.1"
+  resolved "https://github.com/statgen/locuszoom#8b065804188279ff33cb30619aa555566c834d36"
   dependencies:
     d3 "3.5.17"
     promise-polyfill "^8.1.3"
@@ -8446,9 +8446,9 @@ symbol-tree@^3.2.2:
   resolved "https://registry.yarnpkg.com/symbol-tree/-/symbol-tree-3.2.4.tgz#430637d248ba77e078883951fb9aa0eed7c63fa2"
   integrity sha512-9QNk5KwDF+Bvz+PyObkmSYjI5ksVUYtjW7AU22r2NKcfLJcXp96hkDWU3+XndOsUb+AQ9QhfzfCT2O+CNWT5Tw==
 
-tabix-reader@abought/tabix-reader:
+"tabix-reader@https://github.com/abought/tabix-reader":
   version "1.0.0"
-  resolved "https://codeload.github.com/abought/tabix-reader/tar.gz/5c1fff378e2674370e910f63f9ece3af8ea6e049"
+  resolved "https://github.com/abought/tabix-reader#5c1fff378e2674370e910f63f9ece3af8ea6e049"
   dependencies:
     eslint "^5.16.0"
     jszlib dasmoth/jszlib