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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" | ||
| :encoding="vegaEncoding" | ||
| :mark="false" | ||
| :layer="vegaLayer" | ||
| :width="800" | ||
| :height="300" | ||
| renderer="svg" | ||
| /> | ||
| </figure> | ||
| </template> |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,188 @@ | ||
| <script setup lang="ts"> | ||
| import { computed } from 'vue' | ||
| import VegaPlot from '@/components/VegaPlot.vue' | ||
| export interface ExpressionRecord { | ||
| /** Tissue id */ | ||
| tissue: number | ||
| /** Detailed tissue id */ | ||
| tissue_detailed: number | ||
| /** TPM quantiles (0, 0.25, 0.5, 0.75, 1.0) */ | ||
| tpms: number[] | ||
| } | ||
| export interface Props { | ||
| /** Gene symbol */ | ||
| geneSymbol: string | ||
| /** Expression records */ | ||
| expressionRecords: ExpressionRecord[] | ||
| } | ||
| const props = withDefaults(defineProps<Props>(), {}) | ||
| const tissueLabels = [ | ||
| 'Adipose Tissue', | ||
| 'Adrenal Gland', | ||
| 'Bladder', | ||
| 'Blood', | ||
| 'Blood Vessel', | ||
| 'Bone Marrow', | ||
| 'Brain', | ||
| 'Breast', | ||
| 'Cervix Uteri', | ||
| 'Colon', | ||
| 'Esophagus', | ||
| 'Fallopian Tube', | ||
| 'Heart', | ||
| 'Kidney', | ||
| 'Liver', | ||
| 'Lung', | ||
| 'Muscle', | ||
| 'Nerve', | ||
| 'Ovary', | ||
| 'Pancreas', | ||
| 'Pituitary', | ||
| 'Prostate', | ||
| 'Salivary Gland', | ||
| 'Skin', | ||
| 'Small Intestine', | ||
| 'Spleen', | ||
| 'Stomach', | ||
| 'Testis', | ||
| 'Thyroid', | ||
| 'Uterus', | ||
| 'Vagina' | ||
| ] | ||
| const tissueDetailedLabels = [ | ||
| 'Adipose - Subcutaneous', | ||
| 'Adipose - Visceral (Omentum)', | ||
| 'Adrenal Gland', | ||
| 'Artery - Aorta', | ||
| 'Artery - Coronary', | ||
| 'Artery - Tibial', | ||
| 'Bladder', | ||
| 'Brain - Amygdala', | ||
| 'Brain - Anterior cingulate cortex (BA24)', | ||
| 'Brain - Caudate (basal ganglia)', | ||
| 'Brain - Cerebellar Hemisphere', | ||
| 'Brain - Cerebellum', | ||
| 'Brain - Cortex', | ||
| 'Brain - Frontal Cortex (BA9)', | ||
| 'Brain - Hippocampus', | ||
| 'Brain - Hypothalamus', | ||
| 'Brain - Nucleus accumbens (basal ganglia)', | ||
| 'Brain - Putamen (basal ganglia)', | ||
| 'Brain - Spinal cord (cervical c-1)', | ||
| 'Brain - Substantia nigra', | ||
| 'Breast - Mammary Tissue', | ||
| 'Cells - Cultured fibroblasts', | ||
| 'Cells - EBV-transformed lymphocytes', | ||
| 'Cells - Leukemia cell line (CML)', | ||
| 'Cervix - Ectocervix', | ||
| 'Cervix - Endocervix', | ||
| 'Colon - Sigmoid', | ||
| 'Colon - Transverse', | ||
| 'Esophagus - Gastroesophageal Junction', | ||
| 'Esophagus - Mucosa', | ||
| 'Esophagus - Muscularis', | ||
| 'Fallopian Tube', | ||
| 'Heart - Atrial Appendage', | ||
| 'Heart - Left Ventricle', | ||
| 'Kidney - Cortex', | ||
| 'Kidney - Medulla', | ||
| 'Liver', | ||
| 'Lung', | ||
| 'Minor Salivary Gland', | ||
| 'Muscle - Skeletal', | ||
| 'Nerve - Tibial', | ||
| 'Ovary', | ||
| 'Pancreas', | ||
| 'Pituitary', | ||
| 'Prostate', | ||
| 'Salivary Gland', | ||
| 'Skin - Not Sun Exposed (Suprapubic)', | ||
| 'Skin - Sun Exposed (Lower leg)', | ||
| 'Small Intestine - Terminal Ileum', | ||
| 'Spleen', | ||
| 'Stomach', | ||
| 'Testis', | ||
| 'Thyroid', | ||
| 'Uterus', | ||
| 'Vagina', | ||
| 'Whole Blood' | ||
| ] | ||
| const vegaData = computed(() => { | ||
| return props?.expressionRecords?.map((record) => ({ | ||
| tissue: tissueLabels[record.tissue], | ||
| tissueDetailed: tissueDetailedLabels[record.tissue_detailed], | ||
| lower: record.tpms[0], | ||
| q1: record.tpms[1], | ||
| median: record.tpms[2], | ||
| q3: record.tpms[3], | ||
| upper: record.tpms[4] | ||
| })) | ||
| }) | ||
| const vegaEncoding = { | ||
| x: { | ||
| field: 'tissueDetailed', | ||
| type: 'nominal', | ||
| title: null, | ||
| axis: { labelAngle: 45 } | ||
| } | ||
| } | ||
| const vegaLayer = [ | ||
| { | ||
| mark: { type: 'rule', tooltip: { content: 'data' } }, | ||
| encoding: { | ||
| y: { | ||
| field: 'lower', | ||
| type: 'quantitative', | ||
| scale: { zero: false }, | ||
| title: 'TPM' | ||
| }, | ||
| y2: { field: 'upper' } | ||
| } | ||
| }, | ||
| { | ||
| mark: { type: 'bar', size: 14, tooltip: { content: 'data' } }, | ||
| encoding: { | ||
| y: { field: 'q1', type: 'quantitative' }, | ||
| y2: { field: 'q3' }, | ||
| color: { field: 'tissue', type: 'nominal', legend: null } | ||
| } | ||
| }, | ||
| { | ||
| mark: { | ||
| type: 'tick', | ||
| color: 'white', | ||
| size: 14, | ||
| tooltip: { content: 'data' } | ||
| }, | ||
| encoding: { | ||
| y: { field: 'median', type: 'quantitative' } | ||
| } | ||
| } | ||
| ] | ||
| </script> | ||
|
|
||
| <template> | ||
| <figure class="figure border rounded pl-2 pt-2 mr-3 w-100 col"> | ||
| <figcaption class="figure-caption text-center"> | ||
| Bulk tissue gene expression for gene {{ props.geneSymbol }} | ||
| </figcaption> | ||
| <VegaPlot | ||
| :data-values="vegaData" | ||
| :encoding="vegaEncoding" | ||
| :layer="vegaLayer" | ||
| :mark="false" | ||
| :width="1000" | ||
| :height="300" | ||
| renderer="svg" | ||
| /> | ||
| </figure> | ||
| </template> |
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