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feat: Integrate new GTEx and clinvar information as done for VarFish (#…
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,136 @@ | ||
| <script setup lang="ts"> | ||
| import { computed } from 'vue' | ||
| import VegaPlot from '@/components/VegaPlot.vue' | ||
| const coarseClinsigLabels = ['benign', 'uncertain', 'pathogenic'] | ||
| const bucketLabels = [ | ||
| 'no frequency', | ||
| '<0.00001', | ||
| '<0.00025', | ||
| '<0.0005', | ||
| '<0.0001', | ||
| '<0.00025', | ||
| '<0.0005', | ||
| '<0.001', | ||
| '<0.0025', | ||
| '<0.005', | ||
| '<0.01', | ||
| '<0.025', | ||
| '<0.05', | ||
| '<0.1', | ||
| '<0.25', | ||
| '<0.5', | ||
| '<1.0' | ||
| ] | ||
| export interface CountsRecord { | ||
| /** Coarse clinical significance ID */ | ||
| coarse_clinsig: number | ||
| /** Counts per bucket */ | ||
| counts: number[] | ||
| } | ||
| export interface Props { | ||
| /** Gene symbol */ | ||
| geneSymbol: string | ||
| /** Expression records */ | ||
| perFreqCounts: CountsRecord[] | ||
| } | ||
| const props = withDefaults(defineProps<Props>(), {}) | ||
| const vegaData = computed(() => { | ||
| const values = [] | ||
| for (const record of props?.perFreqCounts || []) { | ||
| for (let i = 0; i < record.counts.length; i++) { | ||
| if (record.counts[i] > 0) { | ||
| values.push({ | ||
| coarseClinsig: coarseClinsigLabels[record.coarse_clinsig], | ||
| coarseClinsigNo: record.coarse_clinsig, | ||
| freqBucket: bucketLabels[i], | ||
| freqBucketNo: i, | ||
| value: record.counts[i] | ||
| }) | ||
| } | ||
| } | ||
| } | ||
| if (values.length) { | ||
| return values | ||
| } else { | ||
| return null | ||
| } | ||
| }) | ||
| const vegaLayer = [ | ||
| { | ||
| mark: { type: 'bar', tooltip: true } | ||
| }, | ||
| { | ||
| mark: { | ||
| type: 'text', | ||
| align: 'center', | ||
| baseline: 'middle', | ||
| dy: -10 | ||
| }, | ||
| encoding: { | ||
| text: { field: 'value', type: 'quantitative', fontSize: 8 } | ||
| } | ||
| } | ||
| ] | ||
| const vegaEncoding = { | ||
| x: { | ||
| field: 'freqBucket', | ||
| title: 'population frequency', | ||
| type: 'nominal', | ||
| sort: bucketLabels, | ||
| axis: { labelAngle: 45 } | ||
| }, | ||
| y: { | ||
| field: 'value', | ||
| scale: { type: 'log' }, | ||
| title: 'variant count', | ||
| axis: { | ||
| grid: false, | ||
| tickExtra: false | ||
| } | ||
| }, | ||
| xOffset: { | ||
| field: 'coarseClinsig', | ||
| type: 'nominal', | ||
| sort: coarseClinsigLabels | ||
| }, | ||
| color: { | ||
| field: 'coarseClinsig', | ||
| title: 'clinical sig.', | ||
| type: 'nominal', | ||
| sort: coarseClinsigLabels, | ||
| scale: { | ||
| domain: coarseClinsigLabels, | ||
| range: ['#5d9936', '#f5c964', '#b05454'] | ||
| } | ||
| } | ||
| } | ||
| /** Ref to the VegaPlot (for testing). */ | ||
| // const vegaPlotRef = ref(null) | ||
| </script> | ||
|
|
||
| <template> | ||
| <figure class="figure border rounded pl-2 pt-2 mr-3 w-100 col"> | ||
| <figcaption class="figure-caption text-center"> | ||
| Population frequency of ClinVar variants | ||
| </figcaption> | ||
| <VegaPlot | ||
| :data-values="vegaData as any" | ||
| :encoding="vegaEncoding" | ||
| :mark="false" | ||
| :layer="vegaLayer" | ||
| :width="800" | ||
| :height="300" | ||
| renderer="svg" | ||
| /> | ||
| </figure> | ||
| </template> |
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