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@@ "node": ">= 14" } }, + "node_modules/yargs": { + "version": "17.7.2", + "resolved": "https://registry.npmjs.org/yargs/-/yargs-17.7.2.tgz", + "integrity": "sha512-7dSzzRQ++CKnNI/krKnYRV7JKKPUXMEh61soaHKg9mrWEhzFWhFnxPxGl+69cD1Ou63C13NUPCnmIcrvqCuM6w==", + "peer": true, + "dependencies": { + "cliui": "^8.0.1", + "escalade": "^3.1.1", + "get-caller-file": "^2.0.5", + "require-directory": "^2.1.1", + "string-width": "^4.2.3", + "y18n": "^5.0.5", + "yargs-parser": "^21.1.1" + }, + "engines": { + "node": ">=12" + } + }, + "node_modules/yargs-parser": { + "version": "21.1.1", + "resolved": "https://registry.npmjs.org/yargs-parser/-/yargs-parser-21.1.1.tgz", + "integrity": "sha512-tVpsJW7DdjecAiFpbIB1e3qxIQsE6NoPc5/eTdrbbIC4h0LVsWhnoa3g+m2HclBIujHzsxZ4VJVA+GUuc2/LBw==", + "peer": true, + "engines": { + "node": ">=12" + } + }, "node_modules/yauzl": { "version": "2.10.0", "resolved": "https://registry.npmjs.org/yauzl/-/yauzl-2.10.0.tgz", diff --git a/package.json b/package.json index 71be6d5..34f67c5 100644 --- a/package.json +++ b/package.json @@ -48,6 +48,8 @@ "dependencies": { "@mdi/font": "^7.4.47", "@protobuf-ts/runtime": "^2.9.3", + "vega": "^5.27.0", + "vega-embed": "^6.24.0", "vite-plugin-css-injected-by-js": "^3.3.1", "vite-plugin-static-copy": "^1.0.1", "vue": "^3.3.11", diff --git a/src/components/GeneExpressionCard/GeneExpressionCard.spec.ts b/src/components/GeneExpressionCard/GeneExpressionCard.spec.ts new file mode 100644 index 0000000..6741529 --- /dev/null +++ b/src/components/GeneExpressionCard/GeneExpressionCard.spec.ts @@ -0,0 +1,107 @@ +import { describe, expect, it, vi } from 'vitest' + +import { setupMountedComponents } from '@/lib/testUtils' +import { GtexTissueRecord } from '@/pbs/annonars/genes/base' + +import GeneExpressionCard from './GeneExpressionCard.vue' + +// A few GtexTissueRecords as test data +const fixtureGtexTissueRecords = [ + { + tissue: 'GTEX_TISSUE_ADIPOSE_TISSUE', + tissueDetailed: 'GTEX_TISSUE_DETAILED_ADIPOSE_SUBCUTANEOUS', + tpms: [7.357, 12.695, 14.5, 16.74, 31.88] + }, + { + tissue: 'GTEX_TISSUE_ADIPOSE_TISSUE', + tissueDetailed: 'GTEX_TISSUE_DETAILED_ADIPOSE_VISCERAL_OMENTUM', + tpms: [1.562, 12.45, 15.63, 19.15, 31.99] + }, + { + tissue: 'GTEX_TISSUE_ADRENAL_GLAND', + tissueDetailed: 'GTEX_TISSUE_DETAILED_ADRENAL_GLAND', + tpms: [2.171, 10.375, 12.23, 14.1975, 32.68] + } +].map((record) => GtexTissueRecord.fromJson(record)) + +describe.concurrent('GeneExpressionCard', async () => { + it('renders the GeneExpressionCard with data', async () => { + // arrange: + // Disable warinings, because of invalid test data + console.warn = vi.fn() + const { wrapper } = await setupMountedComponents( + { component: GeneExpressionCard }, + { + props: { + geneSymbol: 'BRCA1', + expressionRecords: fixtureGtexTissueRecords, + ensemblGeneId: 'ENSG00000012048' + } + } + ) + + // act: nothing, only test rendering + + // assert: + expect(wrapper.text()).toContain('Tissue-Specific Gene Expression from GTeX') + const vegaPlot = wrapper.findComponent({ name: 'VegaPlot' }) + expect(vegaPlot.exists()).toBe(true) + // Find gtex linkout + const gtexLink = wrapper.find('#expression-card-gtex-portal') + expect(gtexLink.exists()).toBe(true) + expect(gtexLink.attributes('href')).toBe('https://gtexportal.org/home/gene/ENSG00000012048') + }) + + it('renders skelleton loader if ENSEMBL gene ID is undefined', async () => { + // arrange: + // Disable warinings, because of invalid test data + console.warn = vi.fn() + const { wrapper } = await setupMountedComponents( + { component: GeneExpressionCard }, + { + props: { + geneSymbol: 'BRCA1', + expressionRecords: fixtureGtexTissueRecords, + ensemblGeneId: undefined + } + } + ) + + // act: nothing, only test rendering + + // assert: + expect(wrapper.text()).not.toContain('Tissue-Specific Gene Expression from GTeX') + const vegaPlot = wrapper.findComponent({ name: 'VegaPlot' }) + expect(vegaPlot.exists()).toBe(false) + // Find VSkeletonLoader + const skeletonLoader = wrapper.findComponent({ name: 'VSkeletonLoader' }) + expect(skeletonLoader.exists()).toBe(true) + }) + + it('does not blow up with undefined data', async () => { + // arrange: + // Disable warinings, because of invalid test data + console.warn = vi.fn() + const { wrapper } = await setupMountedComponents( + { component: GeneExpressionCard }, + { + props: { + geneSymbol: 'BRCA1', + expressionRecords: undefined, + ensemblGeneId: 'ENSG00000012048' + } + } + ) + + // act: nothing, only test rendering + + // assert: + expect(wrapper.text()).toContain('Tissue-Specific Gene Expression from GTeX') + const vegaPlot = wrapper.findComponent({ name: 'VegaPlot' }) + expect(vegaPlot.exists()).toBe(true) + // Find gtex linkout + const gtexLink = wrapper.find('#expression-card-gtex-portal') + expect(gtexLink.exists()).toBe(true) + expect(gtexLink.attributes('href')).toBe('https://gtexportal.org/home/gene/ENSG00000012048') + }) +}) diff --git a/src/components/GeneExpressionCard/GeneExpressionCard.stories.ts b/src/components/GeneExpressionCard/GeneExpressionCard.stories.ts new file mode 100644 index 0000000..210802a --- /dev/null +++ b/src/components/GeneExpressionCard/GeneExpressionCard.stories.ts @@ -0,0 +1,56 @@ +import { JsonValue } from '@protobuf-ts/runtime' +import type { Meta, StoryObj } from '@storybook/vue3' + +import { Record as GeneInfoRecord } from '../../pbs/annonars/genes/base' +import geneInfoBrca1Json from '../GenePathogenicityCard/fixture.geneInfo.BRCA1.json' +import geneInfoTgdsJson from '../GenePathogenicityCard/fixture.geneInfo.TGDS.json' +import GeneExpressionCard from './GeneExpressionCard.vue' + +// Here, fixture data is loaded via `import` from JSON file. Reading the file +// as in the tests fails with "process is not defined" error in the browser. + +// @ts-ignore +const geneInfoTgds = GeneInfoRecord.fromJson(geneInfoTgdsJson as JsonValue) +// @ts-ignore +const geneInfoBrca1 = GeneInfoRecord.fromJson(geneInfoBrca1Json as JsonValue) + +const meta = { + title: 'Gene/GeneExpressionCard', + component: GeneExpressionCard, + tags: ['autodocs'], + argTypes: { + geneSymbol: { control: 'text' }, + expressionRecords: { control: 'object' }, + ensemblGeneId: { control: 'text' } + }, + args: { + geneSymbol: geneInfoBrca1.hgnc!.symbol, + expressionRecords: geneInfoBrca1.gtex!.records, + ensemblGeneId: geneInfoBrca1.hgnc!.ensemblGeneId + } +} satisfies Meta + +export default meta +type Story = StoryObj + +export const TGDS: Story = { + args: { + geneSymbol: geneInfoTgds.hgnc!.symbol, + expressionRecords: geneInfoTgds.gtex!.records, + ensemblGeneId: geneInfoTgds.hgnc!.ensemblGeneId + } +} + +export const BRCA1: Story = { + args: { + geneSymbol: geneInfoBrca1.hgnc!.symbol, + expressionRecords: geneInfoBrca1.gtex!.records, + ensemblGeneId: geneInfoBrca1.hgnc!.ensemblGeneId + } +} + +export const UndefinedGeneSymbol: Story = { + args: { + ensemblGeneId: undefined + } +} diff --git a/src/components/GeneExpressionCard/GeneExpressionCard.vue b/src/components/GeneExpressionCard/GeneExpressionCard.vue new file mode 100644 index 0000000..f2f6b3e --- /dev/null +++ b/src/components/GeneExpressionCard/GeneExpressionCard.vue @@ -0,0 +1,192 @@ + + + +./constants diff --git a/src/components/GeneExpressionCard/constants.ts b/src/components/GeneExpressionCard/constants.ts new file mode 100644 index 0000000..e42c809 --- /dev/null +++ b/src/components/GeneExpressionCard/constants.ts @@ -0,0 +1,109 @@ +import { GtexTissue, GtexTissueDetailed } from '../../pbs/annonars/genes/base' + +export const TISSUE_LABELS: { [Key in GtexTissue]: string } = { + [GtexTissue.GTEX_TISSUE_UNKNOWN]: 'Unknown', + [GtexTissue.GTEX_TISSUE_ADIPOSE_TISSUE]: 'Adipose Tissue', + [GtexTissue.GTEX_TISSUE_ADRENAL_GLAND]: 'Adrenal Gland', + [GtexTissue.GTEX_TISSUE_BLADDER]: 'Bladder', + [GtexTissue.GTEX_TISSUE_BLOOD]: 'Blood', + [GtexTissue.GTEX_TISSUE_BLOOD_VESSEL]: 'Blood Vessel', + [GtexTissue.GTEX_TISSUE_BONE_MARROW]: 'Bone Marrow', + [GtexTissue.GTEX_TISSUE_BRAIN]: 'Brain', + [GtexTissue.GTEX_TISSUE_BREAST]: 'Breast', + [GtexTissue.GTEX_TISSUE_CERVIX_UTERI]: 'Cervix Uteri', + [GtexTissue.GTEX_TISSUE_COLON]: 'Colon', + [GtexTissue.GTEX_TISSUE_ESOPHAGUS]: 'Esophagus', + [GtexTissue.GTEX_TISSUE_FALLOPIAN_TUBE]: 'Fallopian Tube', + [GtexTissue.GTEX_TISSUE_HEART]: 'Heart', + [GtexTissue.GTEX_TISSUE_KIDNEY]: 'Kidney', + [GtexTissue.GTEX_TISSUE_LIVER]: 'Liver', + [GtexTissue.GTEX_TISSUE_LUNG]: 'Lung', + [GtexTissue.GTEX_TISSUE_MUSCLE]: 'Muscle', + [GtexTissue.GTEX_TISSUE_NERVE]: 'Nerve', + [GtexTissue.GTEX_TISSUE_OVARY]: 'Ovary', + [GtexTissue.GTEX_TISSUE_PANCREAS]: 'Pancreas', + [GtexTissue.GTEX_TISSUE_PITUITARY]: 'Pituitary', + [GtexTissue.GTEX_TISSUE_PROSTATE]: 'Prostate', + [GtexTissue.GTEX_TISSUE_SALIVARY_GLAND]: 'Salivary Gland', + [GtexTissue.GTEX_TISSUE_SKIN]: 'Skin', + [GtexTissue.GTEX_TISSUE_SMALL_INTESTINE]: 'Small Intestine', + [GtexTissue.GTEX_TISSUE_SPLEEN]: 'Spleen', + [GtexTissue.GTEX_TISSUE_STOMACH]: 'Stomach', + [GtexTissue.GTEX_TISSUE_TESTIS]: 'Testis', + [GtexTissue.GTEX_TISSUE_THYROID]: 'Thyroid', + [GtexTissue.GTEX_TISSUE_UTERUS]: 'Uterus', + [GtexTissue.GTEX_TISSUE_VAGINA]: 'Vagina' +} + +export const TISSUE_DETAILED_LABELS: { [Key in GtexTissueDetailed]: string } = { + [GtexTissueDetailed.GTEX_TISSUE_DETAILED_UNKNOWN]: 'Unknown', + [GtexTissueDetailed.GTEX_TISSUE_DETAILED_ADIPOSE_SUBCUTANEOUS]: 'Adipose - Subcutaneous', + [GtexTissueDetailed.GTEX_TISSUE_DETAILED_ADIPOSE_VISCERAL_OMENTUM]: + 'Adipose - Visceral (Omentum)', + [GtexTissueDetailed.GTEX_TISSUE_DETAILED_ADRENAL_GLAND]: 'Adrenal Gland', + [GtexTissueDetailed.GTEX_TISSUE_DETAILED_ARTERY_AORTA]: 'Artery - Aorta', + [GtexTissueDetailed.GTEX_TISSUE_DETAILED_ARTERY_CORONARY]: 'Artery - Coronary', + [GtexTissueDetailed.GTEX_TISSUE_DETAILED_ARTERY_TIBIAL]: 'Artery - Tibial', + [GtexTissueDetailed.GTEX_TISSUE_DETAILED_BLADDER]: 'Bladder', + [GtexTissueDetailed.GTEX_TISSUE_DETAILED_BRAIN_AMYGDALA]: 'Brain - Amygdala', + [GtexTissueDetailed.GTEX_TISSUE_DETAILED_BRAIN_ANTERIOR_CINGULATE_CORTEX]: + 'Brain - Anterior cingulate cortex (BA24)', + [GtexTissueDetailed.GTEX_TISSUE_DETAILED_BRAIN_CAUDATE_BASAL_GANGLIA]: + 'Brain - Caudate (basal ganglia)', + [GtexTissueDetailed.GTEX_TISSUE_DETAILED_BRAIN_CEREBELLAR_HEMISPHERE]: + 'Brain - Cerebellar Hemisphere', + [GtexTissueDetailed.GTEX_TISSUE_DETAILED_BRAIN_CEREBELLUM]: 'Brain - Cerebellum', + [GtexTissueDetailed.GTEX_TISSUE_DETAILED_BRAIN_CORTEX]: 'Brain - Cortex', + [GtexTissueDetailed.GTEX_TISSUE_DETAILED_BRAIN_FRONTAL_CORTEX]: 'Brain - Frontal Cortex (BA9)', + [GtexTissueDetailed.GTEX_TISSUE_DETAILED_BRAIN_HIPPOCAMPUS]: 'Brain - Hippocampus', + [GtexTissueDetailed.GTEX_TISSUE_DETAILED_BRAIN_HYPOTHALAMUS]: 'Brain - Hypothalamus', + [GtexTissueDetailed.GTEX_TISSUE_DETAILED_BRAIN_NUCLEUS_ACCUMBENS]: + 'Brain - Nucleus accumbens (basal ganglia)', + [GtexTissueDetailed.GTEX_TISSUE_DETAILED_BRAIN_PUTAMEN_BASAL_GANGLIA]: + 'Brain - Putamen (basal ganglia)', + [GtexTissueDetailed.GTEX_TISSUE_DETAILED_BRAIN_SPINAL_CORD]: 'Brain - Spinal cord (cervical c-1)', + [GtexTissueDetailed.GTEX_TISSUE_DETAILED_BRAIN_SUBSTANTIA_NIGRA]: 'Brain - Substantia nigra', + [GtexTissueDetailed.GTEX_TISSUE_DETAILED_BREAST_MAMMARY_TISSUE]: 'Breast - Mammary Tissue', + [GtexTissueDetailed.GTEX_TISSUE_DETAILED_CELLS_CULTURED_FIBROBLASTS]: + 'Cells - Cultured fibroblasts', + [GtexTissueDetailed.GTEX_TISSUE_DETAILED_CELLS_EBV_TRANSFORMED_LYMPHOCYTES]: + 'Cells - EBV-transformed lymphocytes', + [GtexTissueDetailed.GTEX_TISSUE_DETAILED_CELLS_LEUKEMIA_CELL_LINE]: + 'Cells - Leukemia cell line (CML)', + [GtexTissueDetailed.GTEX_TISSUE_DETAILED_CERVIX_ECTOCERVIX]: 'Cervix - Ectocervix', + [GtexTissueDetailed.GTEX_TISSUE_DETAILED_CERVIX_ENDOCERVIX]: 'Cervix - Endocervix', + [GtexTissueDetailed.GTEX_TISSUE_DETAILED_COLON_SIGMOID]: 'Colon - Sigmoid', + [GtexTissueDetailed.GTEX_TISSUE_DETAILED_COLON_TRANSVERSE]: 'Colon - Transverse', + [GtexTissueDetailed.GTEX_TISSUE_DETAILED_ESOPHAGUS_GASTROESOPHAGEAL_JUNCTION]: + 'Esophagus - Gastroesophageal Junction', + [GtexTissueDetailed.GTEX_TISSUE_DETAILED_ESOPHAGUS_MUCOSA]: 'Esophagus - Mucosa', + [GtexTissueDetailed.GTEX_TISSUE_DETAILED_ESOPHAGUS_MUSCULARIS]: 'Esophagus - Muscularis', + [GtexTissueDetailed.GTEX_TISSUE_DETAILED_FALLOPIAN_TUBE]: 'Fallopian Tube', + [GtexTissueDetailed.GTEX_TISSUE_DETAILED_HEART_ATRIAL_APPENDAGE]: 'Heart - Atrial Appendage', + [GtexTissueDetailed.GTEX_TISSUE_DETAILED_HEART_LEFT_VENTRICLE]: 'Heart - Left Ventricle', + [GtexTissueDetailed.GTEX_TISSUE_DETAILED_KIDNEY_CORTEX]: 'Kidney - Cortex', + [GtexTissueDetailed.GTEX_TISSUE_DETAILED_KIDNEY_MEDULLA]: 'Kidney - Medulla', + [GtexTissueDetailed.GTEX_TISSUE_DETAILED_LIVER]: 'Liver', + [GtexTissueDetailed.GTEX_TISSUE_DETAILED_LUNG]: 'Lung', + [GtexTissueDetailed.GTEX_TISSUE_DETAILED_MINOR_SALIVARY_GLAND]: 'Minor Salivary Gland', + [GtexTissueDetailed.GTEX_TISSUE_DETAILED_MUSCLE_SKELETAL]: 'Muscle - Skeletal', + [GtexTissueDetailed.GTEX_TISSUE_DETAILED_NERVE_TIBIAL]: 'Nerve - Tibial', + [GtexTissueDetailed.GTEX_TISSUE_DETAILED_OVARY]: 'Ovary', + [GtexTissueDetailed.GTEX_TISSUE_DETAILED_PANCREAS]: 'Pancreas', + [GtexTissueDetailed.GTEX_TISSUE_DETAILED_PITUITARY]: 'Pituitary', + [GtexTissueDetailed.GTEX_TISSUE_DETAILED_PROSTATE]: 'Prostate', + [GtexTissueDetailed.GTEX_TISSUE_DETAILED_SALIVARY_GLAND]: 'Salivary Gland', + [GtexTissueDetailed.GTEX_TISSUE_DETAILED_SKIN_NOT_SUN_EXPOSED_SUPRAPUBIC]: + 'Skin - Not Sun Exposed (Suprapubic)', + [GtexTissueDetailed.GTEX_TISSUE_DETAILED_SKIN_SUN_EXPOSED_LOWER_LEG]: + 'Skin - Sun Exposed (Lower leg)', + [GtexTissueDetailed.GTEX_TISSUE_DETAILED_SMALL_INTESTINE_TERMINAL_ILEUM]: + 'Small Intestine - Terminal Ileum', + [GtexTissueDetailed.GTEX_TISSUE_DETAILED_SPLEEN]: 'Spleen', + [GtexTissueDetailed.GTEX_TISSUE_DETAILED_STOMACH]: 'Stomach', + [GtexTissueDetailed.GTEX_TISSUE_DETAILED_TESTIS]: 'Testis', + [GtexTissueDetailed.GTEX_TISSUE_DETAILED_THYROID]: 'Thyroid', + [GtexTissueDetailed.GTEX_TISSUE_DETAILED_UTERUS]: 'Uterus', + [GtexTissueDetailed.GTEX_TISSUE_DETAILED_VAGINA]: 'Vagina', + [GtexTissueDetailed.GTEX_TISSUE_DETAILED_WHOLE_BLOOD]: 'Whole Blood' +} diff --git a/src/components/GenePathogenicityCard/GenePathogenicityCard.vue b/src/components/GenePathogenicityCard/GenePathogenicityCard.vue index 9a47dcf..07c9109 100644 --- a/src/components/GenePathogenicityCard/GenePathogenicityCard.vue +++ b/src/components/GenePathogenicityCard/GenePathogenicityCard.vue @@ -1,4 +1,7 @@ + + + +