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Generalize RegionalMissenseConstraintTrack
Here we extract a generic `ConstraintTrack` component from `RegionalMissenseConstraintTrack` so that we can build a mitochondrial constraint track on the new generic component.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,87 @@ | ||
| import { regionsInExons, GenericRegion } from './ConstraintTrack' | ||
| import { exonFactory } from './__factories__/Gene' | ||
| import { Exon } from './TranscriptPage/TranscriptPage' | ||
|
|
||
| test('regionsInExons', () => { | ||
| const testCases = [ | ||
| { | ||
| regions: [ | ||
| { start: 2, stop: 4, i: 1 }, | ||
| { start: 6, stop: 8, i: 2 }, | ||
| ], | ||
| exons: [exonFactory.build({ start: 2, stop: 6 }), exonFactory.build({ start: 6, stop: 9 })], | ||
| expected: [ | ||
| { start: 2, stop: 4, i: 1, unclamped_start: 2, unclamped_stop: 4 }, | ||
| { start: 6, stop: 8, i: 2, unclamped_start: 6, unclamped_stop: 8 }, | ||
| ], | ||
| }, | ||
| { | ||
| regions: [ | ||
| { start: 2, stop: 4, i: 1 }, | ||
| { start: 6, stop: 8, i: 2 }, | ||
| ], | ||
| exons: [exonFactory.build({ start: 1, stop: 8 })], | ||
| expected: [ | ||
| { start: 2, stop: 4, i: 1, unclamped_start: 2, unclamped_stop: 4 }, | ||
| { start: 6, stop: 8, i: 2, unclamped_start: 6, unclamped_stop: 8 }, | ||
| ], | ||
| }, | ||
| { | ||
| regions: [ | ||
| { start: 2, stop: 4, i: 1 }, | ||
| { start: 6, stop: 8, i: 2 }, | ||
| ], | ||
| exons: [ | ||
| exonFactory.build({ start: 1, stop: 3 }), | ||
| exonFactory.build({ start: 3, stop: 5 }), | ||
| exonFactory.build({ start: 5, stop: 9 }), | ||
| ], | ||
| expected: [ | ||
| { start: 2, stop: 3, i: 1, unclamped_start: 2, unclamped_stop: 4 }, | ||
| { start: 3, stop: 4, i: 1, unclamped_start: 2, unclamped_stop: 4 }, | ||
| { start: 6, stop: 8, i: 2, unclamped_start: 6, unclamped_stop: 8 }, | ||
| ], | ||
| }, | ||
| { | ||
| regions: [ | ||
| { start: 2, stop: 4, misc_field_1: 2, misc_field_2: 4 }, | ||
| { start: 6, stop: 8, misc_field_1: 6, misc_field_2: 8 }, | ||
| ], | ||
| exons: [ | ||
| exonFactory.build({ start: 1, stop: 3 }), | ||
| exonFactory.build({ start: 3, stop: 5 }), | ||
| exonFactory.build({ start: 5, stop: 9 }), | ||
| ], | ||
| expected: [ | ||
| { | ||
| start: 2, | ||
| stop: 3, | ||
| misc_field_1: 2, | ||
| misc_field_2: 4, | ||
| unclamped_start: 2, | ||
| unclamped_stop: 4, | ||
| }, | ||
| { | ||
| start: 3, | ||
| stop: 4, | ||
| misc_field_1: 2, | ||
| misc_field_2: 4, | ||
| unclamped_start: 2, | ||
| unclamped_stop: 4, | ||
| }, | ||
| { | ||
| start: 6, | ||
| stop: 8, | ||
| misc_field_1: 6, | ||
| misc_field_2: 8, | ||
| unclamped_start: 6, | ||
| unclamped_stop: 8, | ||
| }, | ||
| ], | ||
| }, | ||
| ] | ||
|
|
||
| testCases.forEach(({ regions, exons, expected }) => { | ||
| expect(regionsInExons(regions as GenericRegion[], exons as Exon[])).toEqual(expected) | ||
| }) | ||
| }) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,210 @@ | ||
| import React, { ReactNode } from 'react' | ||
| import styled from 'styled-components' | ||
| // @ts-expect-error TS(7016) FIXME: Could not find a declaration file for module '@gno... Remove this comment to see the full error message | ||
| import { Track } from '@gnomad/region-viewer' | ||
| import InfoButton from './help/InfoButton' | ||
| import { TooltipAnchor } from '@gnomad/ui' | ||
| import { Exon } from './TranscriptPage/TranscriptPage' | ||
|
|
||
| export const PlotWrapper = styled.div` | ||
| display: flex; | ||
| flex-direction: column; | ||
| justify-content: center; | ||
| height: 100%; | ||
| ` | ||
|
|
||
| type TrackProps = { | ||
| scalePosition: (input: number) => number | ||
| width: number | ||
| } | ||
|
|
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| const Wrapper = styled.div` | ||
| display: flex; | ||
| flex-direction: column; | ||
| margin-bottom: 1em; | ||
| ` | ||
|
|
||
| export const SidePanel = styled.div` | ||
| display: flex; | ||
| align-items: center; | ||
| height: 100%; | ||
| ` | ||
|
|
||
| const TopPanel = styled.div` | ||
| display: flex; | ||
| justify-content: flex-end; | ||
| width: 100%; | ||
| margin-bottom: 5px; | ||
| ` | ||
|
|
||
| export interface GenericRegion { | ||
| start: number | ||
| stop: number | ||
| } | ||
|
|
||
| // When clamping constrained regions to exons, we remember the original | ||
| // boundaries of the region for display in the region tooltip | ||
| export type RegionWithUnclamped<R extends GenericRegion> = R & { | ||
| unclamped_start: number | ||
| unclamped_stop: number | ||
| } | ||
|
|
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| type Props<R extends GenericRegion> = { | ||
| trackTitle: string | ||
| allRegions: R[] | null | ||
| constrainedRegions: RegionWithUnclamped<R>[] | ||
| infobuttonTopic: string | ||
| legend: ReactNode | ||
| tooltipComponent: any // TK any | ||
| colorFn: (region: R) => string | ||
| valueFn: (region: R) => string | ||
| } | ||
|
|
||
| export const regionsInExons = <R extends GenericRegion>( | ||
| regions: R[], | ||
| exons: Exon[] | ||
| ): RegionWithUnclamped<R>[] => { | ||
| const sortedRegions = regions.sort((a, b) => a.start - b.start) | ||
| const sortedExons = exons.sort((a, b) => a.start - b.start) | ||
|
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| const intersections = [] | ||
|
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| let regionIndex = 0 | ||
| let exonIndex = 0 | ||
|
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| while (regionIndex < regions.length && exonIndex < exons.length) { | ||
| const region = sortedRegions[regionIndex] | ||
| const exon = sortedExons[exonIndex] | ||
| const maxStart = Math.max(region.start, exon.start) | ||
| const minStop = Math.min(region.stop, exon.stop) | ||
|
|
||
| if (maxStart < minStop) { | ||
| const next: RegionWithUnclamped<R> = { | ||
| ...region, | ||
| start: maxStart, | ||
| stop: minStop, | ||
| unclamped_start: region.start, | ||
| unclamped_stop: region.stop, | ||
| } | ||
| intersections.push(next) | ||
| } | ||
|
|
||
| if (region.stop === minStop) { | ||
| regionIndex += 1 | ||
| } | ||
| if (exon.stop === minStop) { | ||
| exonIndex += 1 | ||
| } | ||
| } | ||
| return intersections | ||
| } | ||
|
|
||
| const ConstraintTrack = <R extends GenericRegion>({ | ||
| trackTitle, | ||
| allRegions, | ||
| constrainedRegions, | ||
| infobuttonTopic, | ||
| legend, | ||
| tooltipComponent, | ||
| colorFn, | ||
| valueFn, | ||
| }: Props<R>) => ( | ||
| <Wrapper> | ||
| <Track | ||
| renderLeftPanel={() => ( | ||
| <SidePanel> | ||
| <span>{trackTitle}</span> | ||
| <InfoButton topic={infobuttonTopic} /> | ||
| </SidePanel> | ||
| )} | ||
| > | ||
| {({ scalePosition, width }: TrackProps) => ( | ||
| <> | ||
| <TopPanel>{legend}</TopPanel> | ||
| <PlotWrapper> | ||
| <svg height={55} width={width}> | ||
| {constrainedRegions.map((region: RegionWithUnclamped<R>) => { | ||
| const startX = scalePosition(region.start) | ||
| const stopX = scalePosition(region.stop) | ||
| const regionWidth = stopX - startX | ||
|
|
||
| return ( | ||
| <TooltipAnchor | ||
| key={`${region.start}-${region.stop}`} | ||
| // @ts-expect-error need to redefine TooltipAnchor to allow arbitrary props for the children type-safely | ||
| region={region} | ||
| isTranscript={allRegions && allRegions.length === 1} | ||
| tooltipComponent={tooltipComponent} | ||
| > | ||
| <g> | ||
| <rect | ||
| x={startX} | ||
| y={0} | ||
| width={regionWidth} | ||
| height={15} | ||
| fill={colorFn(region)} | ||
| stroke="black" | ||
| /> | ||
| </g> | ||
| </TooltipAnchor> | ||
| ) | ||
| })} | ||
| <g transform="translate(0,20)"> | ||
| {allRegions && | ||
| allRegions.map((region: R, index: number) => { | ||
| const startX = scalePosition(region.start) | ||
| const stopX = scalePosition(region.stop) | ||
| const regionWidth = stopX - startX | ||
| const midX = (startX + stopX) / 2 | ||
| const offset = index * 0 | ||
|
|
||
| return ( | ||
| <g key={`${region.start}-${region.stop}`}> | ||
| <line | ||
| x1={startX} | ||
| y1={2 + offset} | ||
| x2={startX} | ||
| y2={11 + offset} | ||
| stroke="#424242" | ||
| /> | ||
| <line | ||
| x1={startX} | ||
| y1={7 + offset} | ||
| x2={stopX} | ||
| y2={7 + offset} | ||
| stroke="#424242" | ||
| /> | ||
| <line | ||
| x1={stopX} | ||
| y1={2 + offset} | ||
| x2={stopX} | ||
| y2={11 + offset} | ||
| stroke="#424242" | ||
| /> | ||
| {regionWidth > 40 && ( | ||
| <> | ||
| <rect | ||
| x={midX - 15} | ||
| y={3 + offset} | ||
| width={30} | ||
| height={5} | ||
| fill="#fafafa" | ||
| /> | ||
| <text x={midX} y={8 + offset} dy="0.33em" textAnchor="middle"> | ||
| {valueFn(region)} | ||
| </text> | ||
| </> | ||
| )} | ||
| </g> | ||
| ) | ||
| })} | ||
| </g> | ||
| </svg> | ||
| </PlotWrapper> | ||
| </> | ||
| )} | ||
| </Track> | ||
| </Wrapper> | ||
| ) | ||
|
|
||
| export default ConstraintTrack |
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