feat: adding GeneExpressionCard component

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",

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')
+  })
+})

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<typeof GeneExpressionCard>
+
+export default meta
+type Story = StoryObj<typeof meta>
+
+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
+  }
+}

src/components/GeneExpressionCard/GeneExpressionCard.vue

@@ -0,0 +1,192 @@
+<script setup lang="ts">
+/**
+ * This component displays a VCard with gene expression information from GTEx.
+ */
+import { computed, ref } from 'vue'
+
+import { GtexTissueRecord } from '../../pbs/annonars/genes/base'
+import DocsLink from '../DocsLink/DocsLink.vue'
+import VegaPlot from '../VegaPlot/VegaPlot.vue'
+import { TISSUE_DETAILED_LABELS, TISSUE_LABELS } from './constants'
+
+const props = withDefaults(
+  defineProps<{
+    /** Gene symbol */
+    geneSymbol?: string
+    /** Expression records */
+    expressionRecords?: GtexTissueRecord[]
+    /** Ensembl gene ID */
+    ensemblGeneId?: string
+  }>(),
+  {
+    geneSymbol: '',
+    expressionRecords: () => [],
+    ensemblGeneId: ''
+  }
+)
+
+// -- interactive plot configuration -------------------------------------------
+
+/** Sort order. */
+enum SortOrder {
+  /** Sort alphabetically by label */
+  ALPHA = 'alphabetical',
+  /** Sort by TPM metric */
+  TPM = 'tpm'
+}
+
+/** Sort order configuration (currently static) */
+const sortOrder = ref<SortOrder>(SortOrder.TPM)
+
+// -- data for Vega plot -------------------------------------------------------
+
+/** Interface for the plot data. */
+interface VegaData {
+  /** Tissue label */
+  tissue: string
+  /** Detailed tissue label */
+  tissueDetailed: string
+  /** Lower quantile */
+  lower: number
+  /** First quartile */
+  q1: number
+  /** Median */
+  median: number
+  /** Third quartile */
+  q3: number
+  /** Upper quantile */
+  upper: number
+}
+
+/** Compute data values for Vega plot. */
+const vegaData = computed<VegaData[]>(() => {
+  if (!props?.expressionRecords?.length) {
+    return []
+  }
+
+  const expressionRecords = Object.assign([], props?.expressionRecords)
+  if (sortOrder.value === SortOrder.ALPHA) {
+    expressionRecords.sort((a: GtexTissueRecord, b: GtexTissueRecord) => {
+      const aTissue = TISSUE_LABELS[a.tissue]
+      const bTissue = TISSUE_LABELS[b.tissue]
+      if (aTissue < bTissue) {
+        return -1
+      } else if (aTissue > bTissue) {
+        return 1
+      } else {
+        return 0
+      }
+    })
+  } else {
+    expressionRecords.sort((a: GtexTissueRecord, b: GtexTissueRecord) => {
+      if (a.tpms[2] < b.tpms[2]) {
+        return 1
+      } else if (a.tpms[2] > b.tpms[2]) {
+        return -1
+      } else {
+        return 0
+      }
+    })
+  }
+  return expressionRecords.map((record: GtexTissueRecord) => ({
+    tissue: TISSUE_LABELS[record.tissue],
+    tissueDetailed: TISSUE_DETAILED_LABELS[record.tissueDetailed],
+    lower: record.tpms[0],
+    q1: record.tpms[1],
+    median: record.tpms[2],
+    q3: record.tpms[3],
+    upper: record.tpms[4]
+  }))
+})
+
+/** The encoding for the Vega plot. */
+const vegaEncoding = {
+  x: {
+    field: 'tissueDetailed',
+    type: 'nominal',
+    title: null,
+    axis: { labelAngle: 45 }
+  }
+}
+
+/** The layer definition for the Vega plot. */
+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>
+  <!-- no ENSG => display loader -->
+  <template v-if="!ensemblGeneId?.length">
+    <v-skeleton-loader class="mt-3 mx-auto border" type="image,button" />
+  </template>
+
+  <!-- otherwise, display actual card -->
+  <template v-else>
+    <v-card class="mt-3">
+      <v-card-title class="pb-0 pr-2">
+        Expression
+        <DocsLink anchor="expression" />
+      </v-card-title>
+      <v-card-subtitle class="text-overline">
+        Tissue-Specific Gene Expression from GTeX
+      </v-card-subtitle>
+      <v-card-text class="pt-3 pb-0">
+        <v-sheet color="background" class="pa-2">
+          <VegaPlot
+            data-name="expression"
+            :data-values="vegaData"
+            :encoding="vegaEncoding"
+            :layer="vegaLayer"
+            :mark="false"
+            :height="300"
+            :width="1200"
+            background="#eeeeee"
+            renderer="svg"
+          />
+        </v-sheet>
+      </v-card-text>
+      <v-card-actions>
+        <v-btn
+          id="expression-card-gtex-portal"
+          :href="`https://gtexportal.org/home/gene/${ensemblGeneId ?? ''}`"
+          target="_blank"
+          prepend-icon="mdi-launch"
+        >
+          GTeX Portal
+        </v-btn>
+      </v-card-actions>
+    </v-card>
+  </template>
+</template>
+./constants