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Add mitochondrial regional constraint visualizations
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46 changes: 46 additions & 0 deletions
46
browser/src/GenePage/MitochondrialRegionConstraintTrack.spec.tsx
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,46 @@ | ||
| import React from 'react' | ||
| import renderer from 'react-test-renderer' | ||
| import { expect, test } from '@jest/globals' | ||
| import MitochondrialRegionConstraintTrack, { | ||
| MitochondrialConstraintRegion, | ||
| } from './MitochondrialRegionConstraintTrack' | ||
| import { Exon } from '../TranscriptPage/TranscriptPage' | ||
| // @ts-expect-error | ||
| import { RegionViewerContext } from '@gnomad/region-viewer' | ||
|
|
||
| const childProps = { | ||
| centerPanelWidth: 3, | ||
| isPositionDefined: true, | ||
| leftPanelWidth: 4, | ||
| regions: [], | ||
| rightPanelWidth: 5, | ||
| scalePosition: (i: number) => i, | ||
| } | ||
|
|
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| const exons: Exon[] = [ | ||
| { feature_type: 'CDS', start: 123, stop: 234 }, | ||
| { feature_type: 'UTR', start: 235, stop: 999 }, | ||
| { feature_type: 'CDS', start: 1000, stop: 1999 }, | ||
| ] | ||
|
|
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| test('track has no unexpected changes when gene has constraint', () => { | ||
| const constraintRegions: MitochondrialConstraintRegion[] = [ | ||
| { start: 555, stop: 666, oe: 0.45, oe_lower: 0.37, oe_upper: 0.47 }, | ||
| { start: 777, stop: 888, oe: 0.56, oe_lower: 0.52, oe_upper: 0.59 }, | ||
| ] | ||
| const tree = renderer.create( | ||
| <RegionViewerContext.Provider value={childProps}> | ||
| <MitochondrialRegionConstraintTrack constraintRegions={constraintRegions} exons={exons} /> | ||
| </RegionViewerContext.Provider> | ||
| ) | ||
| expect(tree).toMatchSnapshot() | ||
| }) | ||
|
|
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| test('track has no unexpected changes when no constraint for gene', () => { | ||
| const tree = renderer.create( | ||
| <RegionViewerContext.Provider value={childProps}> | ||
| <MitochondrialRegionConstraintTrack constraintRegions={null} exons={exons} /> | ||
| </RegionViewerContext.Provider> | ||
| ) | ||
| expect(tree).toMatchSnapshot() | ||
| }) |
74 changes: 74 additions & 0 deletions
74
browser/src/GenePage/MitochondrialRegionConstraintTrack.tsx
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,74 @@ | ||
| import React from 'react' | ||
| import { Exon } from '../TranscriptPage/TranscriptPage' | ||
| import ConstraintTrack, { regionsInExons, RegionAttributeList } from '../ConstraintTrack' | ||
|
|
||
| export type MitochondrialConstraintRegion = { | ||
| start: number | ||
| stop: number | ||
| oe: number | ||
| oe_upper: number | ||
| oe_lower: number | ||
| } | ||
|
|
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| type Props = { | ||
| constraintRegions: MitochondrialConstraintRegion[] | null | ||
| exons: Exon[] | ||
| } | ||
|
|
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| const constraintColor = '#fd8d3c' | ||
|
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| const Legend = () => ( | ||
| <> | ||
| <span>Constrained region</span> | ||
| <svg width={50} height={25}> | ||
| <rect x={10} y={3} width={30} height={10} stroke="#000" fill={constraintColor} /> | ||
| </svg> | ||
| </> | ||
| ) | ||
|
|
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| type TooltipProps = { | ||
| region: MitochondrialConstraintRegion | ||
| } | ||
|
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| const Tooltip = ({ region }: TooltipProps) => { | ||
| return ( | ||
| <RegionAttributeList> | ||
| <div> | ||
| <dt>Coordinates:</dt> | ||
| <dd>{`M:${region.start}-${region.stop}`}</dd> | ||
| </div> | ||
| <div> | ||
| <dt>Missense observed/expected:</dt> | ||
| <dd> | ||
| {region.oe.toFixed(3)} ({region.oe_lower.toFixed(3)}-{region.oe_upper.toFixed(3)}) | ||
| </dd> | ||
| </div> | ||
| </RegionAttributeList> | ||
| ) | ||
| } | ||
|
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| const formattedOE = (region: MitochondrialConstraintRegion) => region.oe.toFixed(3) | ||
|
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| const MitochondrialConstraintRegionTrack = ({ constraintRegions, exons }: Props) => { | ||
| if (constraintRegions === null) { | ||
| return null | ||
| } | ||
|
|
||
| return ( | ||
| <ConstraintTrack | ||
| trackTitle="Regional constraint" | ||
| infobuttonTopic="TK-mitochondrial-gene-constraint" | ||
| legend={<Legend />} | ||
| valueFn={formattedOE} | ||
| colorFn={() => constraintColor} | ||
| tooltipComponent={Tooltip} | ||
| allRegions={null} | ||
| constrainedRegions={regionsInExons( | ||
| constraintRegions, | ||
| exons.filter((exon) => exon.feature_type === 'CDS') | ||
| )} | ||
| /> | ||
| ) | ||
| } | ||
|
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| export default MitochondrialConstraintRegionTrack |
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