Assembly:
@@ -422,12 +439,12 @@ import useFormatters from '@/composition/formatters'
import useItem from '@/composition/item'
import useRemoteData from '@/composition/remote-data'
import config from '@/config'
+import { textForTargetGeneCategory } from '@/lib/target-genes';
import {saveChartAsFile} from '@/lib/chart-export'
import { parseScoresOrCounts } from '@/lib/scores'
-import { variantNotNullOrNA } from '@/lib/mave-hgvs';
+import { preferredVariantLabel, variantNotNullOrNA } from '@/lib/mave-hgvs';
import { mapState } from 'vuex'
import { ref } from 'vue'
-import items from '@/composition/items'
export default {
name: 'ScoreSetView',
@@ -439,6 +456,40 @@ export default {
['familyName', 'givenName', 'orcidId']
)
},
+ evidenceStrengths: function() {
+ if (config.CLINICAL_FEATURES_ENABLED) {
+ return {
+ 'urn:mavedb:00000050-a-1': {
+ oddsOfPathogenicity: {
+ abnormal: 24.9,
+ normal: 0.043
+ },
+ evidenceCodes: {
+ abnormal: 'PS3_Strong',
+ normal: 'BS3_Strong'
+ },
+ source: 'https://pubmed.ncbi.nlm.nih.gov/36550560/'
+ },
+ 'urn:mavedb:00000097-0-1': {
+ oddsOfPathogenicity: {
+ abnormal: 52.4,
+ normal: 0.02
+ },
+ evidenceCodes: {
+ abnormal: 'PS3_Strong',
+ normal: 'BS3_Strong'
+ },
+ source: 'https://pubmed.ncbi.nlm.nih.gov/34793697/',
+ exampleVariant: {
+ urn: 'urn:mavedb:00000097-0-1#1697',
+ name: 'NM_007294.4(BRCA1):c.5237A>C (p.His1746Pro)'
+ }
+ }
+ }[this.item.urn] || null
+ } else {
+ return null
+ }
+ },
isMetaDataEmpty: function() {
//If extraMetadata is empty, return value will be true.
return Object.keys(this.item.extraMetadata).length === 0
@@ -459,6 +510,9 @@ export default {
// While a user is autocompleting, `this.selectedVariant` is a string. Once selected, it will become an object and we can pass it as a prop.
return typeof this.selectedVariant === 'object' ? this.selectedVariant : null
},
+ urlVariant: function() {
+ return this.$route.query.variant
+ },
...mapState({
galaxyUrl: state => state.routeProps.galaxyUrl,
toolId: state => state.routeProps.toolId,
@@ -481,6 +535,7 @@ export default {
setScoresDataUrl: scoresRemoteData.setDataUrl,
ensureScoresDataLoaded: scoresRemoteData.ensureDataLoaded,
variantSearchSuggestions,
+ textForTargetGeneCategory: textForTargetGeneCategory
}
},
props: {
@@ -531,8 +586,16 @@ export default {
scoresData: {
handler: function(newValue) {
this.scores = newValue ? Object.freeze(parseScoresOrCounts(newValue)) : null
+ this.applyUrlState()
}
- }
+ },
+ selectedVariant: {
+ handler: function(newValue) {
+ this.$router.push({query: {
+ ...(this.selectedVariant && this.selectedVariant.accession) ? {variant: this.selectedVariant.accession} : {},
+ }})
+ }
+ },
},
methods: {
variantNotNullOrNA,
@@ -780,37 +843,36 @@ export default {
variantSearch: function(event) {
const matches = []
for (const variant of this.scores) {
- if (
- (variantNotNullOrNA(variant.hgvs_pro) && variant.hgvs_pro.toLowerCase().includes(event.query.toLowerCase()))
- || (variantNotNullOrNA(variant.hgvs_nt) && variant.hgvs_nt.toLowerCase().includes(event.query.toLowerCase()))
- || (variantNotNullOrNA(variant.hgvs_splice) && variant.hgvs_splice.toLowerCase().includes(event.query.toLowerCase()))
- ) {
- matches.push(variant)
+ if (variantNotNullOrNA(variant.hgvs_nt) && variant.hgvs_nt.toLowerCase().includes(event.query.toLowerCase())) {
+ matches.push(Object.assign(variant, {mavedb_label: variant.hgvs_nt}))
+ } else if (variantNotNullOrNA(variant.hgvs_splice) && variant.hgvs_splice.toLowerCase().includes(event.query.toLowerCase())) {
+ matches.push(Object.assign(variant, {mavedb_label: variant.hgvs_splice}))
+ } else if (variantNotNullOrNA(variant.hgvs_pro) && variant.hgvs_pro.toLowerCase().includes(event.query.toLowerCase())) {
+ matches.push(Object.assign(variant, {mavedb_label: variant.hgvs_pro}))
+ } else if (variantNotNullOrNA(variant.accession) && variant.accession.toLowerCase().includes(event.query.toLowerCase())) {
+ matches.push(Object.assign(variant, {mavedb_label: variant.accession}))
}
}
this.variantSearchSuggestions = matches
},
- variantSearchLabel: function(selectedVariant) {
- var displayStr = ""
- if (variantNotNullOrNA(selectedVariant.hgvs_nt)) {
- displayStr += `Nucleotide variant: ${selectedVariant.hgvs_nt}; `
- }
- if (variantNotNullOrNA(selectedVariant.hgvs_pro)) {
- displayStr += `Protein variant: ${selectedVariant.hgvs_pro}; `
- }
- if (variantNotNullOrNA(selectedVariant.hgvs_splice)) {
- displayStr += `Splice variant: ${selectedVariant.hgvs_splice}`
+ childComponentSelectedVariant: function(variant) {
+ if (variant == null) {
+ this.selectedVariant = null
}
- return displayStr.trim().replace(/;$/, '')
- },
- childComponentSelectedVariant: function(variant) {
if (!variant?.accession) {
return
}
- this.selectedVariant = this.scores.find((v) => v.accession == variant.accession)
+ const selectedVariant = this.scores.find((v) => v.accession == variant.accession)
+ this.selectedVariant = Object.assign(selectedVariant, preferredVariantLabel(selectedVariant))
+ },
+ applyUrlState: function() {
+ if (this.$route.query.variant) {
+ const selectedVariant = this.scores.find((v) => v.accession == this.$route.query.variant)
+ this.selectedVariant = Object.assign(selectedVariant, preferredVariantLabel(selectedVariant))
+ }
},
heatmapVisibilityUpdated: function(visible) {
this.heatmapExists = visible
@@ -886,8 +948,17 @@ export default {
}
.mave-score-set-variant-search {
- margin: 10px 0;
+ margin-top: 40px;
+ margin-bottom: 8px;
+ display: flex;
+ justify-content: center;
+}
+
+.mave-score-set-variant-search > span {
+ width: 50%;
display: flex;
+ align-items: center;
+ column-gap: .5em;
}
.p-float-label {
@@ -911,13 +982,40 @@ export default {
}
.mave-score-set-urn {
- /*font-family: Helvetica, Verdana, Arial, sans-serif;*/
+ font-size: 20px;
+ color: gray;
+ margin-left: 12px;
}
.mave-contributor {
margin: 0 0.5em;
}
+/* Evidence strength */
+
+table.mave-odds-path-table {
+ border-collapse: collapse;
+ margin: 1em auto 0.5em auto;
+}
+
+table.mave-odds-path-table td,
+table.mave-odds-path-table th {
+ border: 1px solid gray;
+ padding: 0.5em 1em;
+ text-align: center;
+}
+
+table.mave-odds-path-table td.mave-evidence-code-PS3_Strong {
+ background-color: #b02418;
+ color: white;
+ font-weight: bold;
+}
+table.mave-odds-path-table td.mave-evidence-code-BS3_Strong {
+ background-color: #385492;
+ color: white;
+ font-weight: bold;
+}
+
/* Formatting in Markdown blocks */
.mave-score-set-abstract {
diff --git a/src/components/screens/SearchView.vue b/src/components/screens/SearchView.vue
index 79fd428e..56426448 100644
--- a/src/components/screens/SearchView.vue
+++ b/src/components/screens/SearchView.vue
@@ -16,7 +16,7 @@
-
+
@@ -59,6 +59,7 @@ import { defineComponent } from 'vue'
import { paths, components } from '@/schema/openapi'
import type {LocationQueryValue} from "vue-router";
+import { textForTargetGeneCategory } from '@/lib/target-genes'
type ShortScoreSet = components['schemas']['ShortScoreSet']
type ShortTargetGene = components['schemas']['ShortTargetGene']
@@ -131,6 +132,7 @@ export default defineComponent({
language: {
emptyTable: 'Type in the search box above or use the filters to find a data set.'
},
+ textForTargetGeneCategory: textForTargetGeneCategory,
}
},
computed: {
diff --git a/src/components/screens/VariantScreen.vue b/src/components/screens/VariantScreen.vue
new file mode 100644
index 00000000..f1ea61d4
--- /dev/null
+++ b/src/components/screens/VariantScreen.vue
@@ -0,0 +1,220 @@
+
+
+
+
+
+ Variant: NM_007294.4(BRCA1):c.5237A>C (p.His1746Pro)
+
+
+ Functionally Abnormal
+
+
+
+ | ClinVar allele ID: |
+
+ 235927
+ |
+ |
+
+
+ | Variant type: |
+ Single nucleotide variant |
+ |
+ Functional consequence: |
+ Functionally Abnormal |
+
+
+ | Genomic location: |
+ 17:43057092 (GRCh38)
17:41209109 (GRCh37) |
+ |
+ Functional score: |
+ 2.57 |
+
+
+
+
+
+
+
+
+ BRCA1 Locus
+
+ Score set: {{ item.title }}
+
+
+
+
+
+ | Odds Path Abnormal* |
+ Odds Path Normal* |
+
+
+ | {{ evidenceStrengths.oddsOfPathogenicity.abnormal }} |
+ {{ evidenceStrengths.oddsOfPathogenicity.normal }} |
+
+
+ | {{ evidenceStrengths.evidenceCodes.abnormal }} |
+ {{ evidenceStrengths.evidenceCodes.normal }} |
+
+
+
+
+
+
+