Highlight high LOF OEs in mitochondrial constraint table

broadinstitute · Feb 26, 2025 · 5c52b3c · 5c52b3c
1 parent 583ecc8
commit 5c52b3c
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Showing 4 changed files with 2,657 additions and 80 deletions.
diff --git a/browser/src/ConstraintTable/ConstraintTable.spec.tsx b/browser/src/ConstraintTable/ConstraintTable.spec.tsx
@@ -118,6 +118,22 @@ forAllDatasets('ConstraintTable with "%s" dataset selected', (datasetId) => {
       )
       expect(tree).toMatchSnapshot()
     })
+
+    test('highlights upper LOF OE CI if below 0.058', () => {
+      const constraint = proteinMitochondrialConstraintFactory.build({ oe_lof_upper: 0.057999999 })
+      const tree = renderer.create(
+        <BrowserRouter>
+          <ConstraintTable
+            datasetId={datasetId}
+            geneOrTranscript={geneFactory.build({
+              chrom: 'M',
+              mitochondrial_constraint: constraint,
+            })}
+          />
+        </BrowserRouter>
+      )
+      expect(tree).toMatchSnapshot()
+    })
   })
 
   describe('with a mitochondrial RNA gene', () => {
@@ -136,6 +152,22 @@ forAllDatasets('ConstraintTable with "%s" dataset selected', (datasetId) => {
       )
       expect(tree).toMatchSnapshot()
     })
+
+    test('highlights upper LOF OE CI if below 0.27', () => {
+      const constraint = rnaMitochondrialConstraintFactory.build({ oe_upper: 0.2699999 })
+      const tree = renderer.create(
+        <BrowserRouter>
+          <ConstraintTable
+            datasetId={datasetId}
+            geneOrTranscript={geneFactory.build({
+              chrom: 'M',
+              mitochondrial_constraint: constraint,
+            })}
+          />
+        </BrowserRouter>
+      )
+      expect(tree).toMatchSnapshot()
+    })
   })
 
   describe('with a mitochondrial gene missing constraint data', () => {

diff --git a/browser/src/ConstraintTable/MitochondrialConstraintTable.tsx b/browser/src/ConstraintTable/MitochondrialConstraintTable.tsx
@@ -5,36 +5,66 @@ import {
   RNAMitochondrialGeneConstraint,
 } from '../GenePage/GenePage'
 import { BaseTable, TooltipAnchor } from '@gnomad/ui'
+import { ConstraintHighlight } from './constraintMetrics'
 
 const isProteinMitochondrialGeneConstraint = (
   constraint: MitochondrialGeneConstraint
 ): constraint is ProteinMitochondrialGeneConstraint =>
   Object.prototype.hasOwnProperty.call(constraint, 'exp_lof')
 
+type Highlight = {
+  threshold: number
+  color: string
+}
+
+type ConstraintRowProps = {
+  category: string
+  expected: number
+  observed: number
+  oe: number
+  oeLower: number
+  oeUpper: number
+  highlight?: Highlight
+}
+
+const PROTEIN_GENE_HIGHLIGHT: Highlight = {
+  threshold: 0.058,
+  color: '#ff2600',
+}
+
+const RNA_GENE_HIGHLIGHT: Highlight = {
+  threshold: 0.27,
+  color: PROTEIN_GENE_HIGHLIGHT.color,
+}
+
 const ConstraintRow = ({
   category,
   expected,
   observed,
   oe,
   oeLower,
   oeUpper,
-}: {
-  category: string
-  expected: number
-  observed: number
-  oe: number
-  oeLower: number
-  oeUpper: number
-}) => (
-  <tr>
-    <th scope="row">{category}</th>
-    <td>{expected < 10 ? expected.toFixed(2) : expected.toFixed(1)}</td>
-    <td>{observed < 10 ? observed.toFixed(2) : observed.toFixed(1)}</td>
-    <td>
-      o/e = {oe.toFixed(2)} ({oeLower.toFixed(2)} - {oeUpper.toFixed(2)})
-    </td>
-  </tr>
-)
+  highlight,
+}: ConstraintRowProps) => {
+  const oeUpperFixed = oeUpper.toFixed(2)
+  const oeUpperContent =
+    highlight && oeUpper < highlight.threshold ? (
+      <ConstraintHighlight highlightColor={highlight.color}>{oeUpperFixed}</ConstraintHighlight>
+    ) : (
+      oeUpperFixed
+    )
+
+  return (
+    <tr>
+      <th scope="row">{category}</th>
+      <td>{expected < 10 ? expected.toFixed(2) : expected.toFixed(1)}</td>
+      <td>{observed < 10 ? observed.toFixed(2) : observed.toFixed(1)}</td>
+      <td>
+        o/e = {oe.toFixed(2)} ({oeLower.toFixed(2)} - {oeUpperContent})
+      </td>
+    </tr>
+  )
+}
 
 const ProteinConstraintMetrics = ({
   constraint,
@@ -83,6 +113,7 @@ const ProteinConstraintMetrics = ({
         oe={oe_lof}
         oeLower={oe_lof_lower}
         oeUpper={oe_lof_upper}
+        highlight={PROTEIN_GENE_HIGHLIGHT}
       />
     </tbody>
   )
@@ -99,6 +130,7 @@ const RNAConstraintMetrics = ({ constraint }: { constraint: RNAMitochondrialGene
         oe={oe}
         oeLower={oe_lower}
         oeUpper={oe_upper}
+        highlight={RNA_GENE_HIGHLIGHT}
       />
     </tbody>
   )