Calculate most frequent non-ref allele for multi-variant renderer (#4826)

* Intermediate

* Small types

* Misc

* Move files around

* Misc

* wow

* Mov

* Async

* Most frequent alt

Author: cmdcolin

plugins/hic/src/HicRenderer/HicRenderer.tsx

@@ -42,6 +42,7 @@ export interface RenderArgsDeserialized
 export interface RenderArgsDeserializedWithFeatures
   extends RenderArgsDeserialized {
   features: HicFeature[]
+  statusCallback?: (arg: string) => void
 }
 
 export type ResultsSerialized = ServerSideResultsSerialized
@@ -95,10 +96,9 @@ export default class HicRenderer extends ServerSideRendererType {
         .getFeatures(regions[0]!, args)
         .pipe(toArray()),
     )
-    // cast to any to avoid return-type conflict, because the
-    // types of features returned by our getFeatures are quite
-    // different from the base interface
 
+    // cast to any to avoid return-type conflict, because the types of features
+    // returned by our getFeatures are quite different from the base interface
     return features as any
   }
 }

plugins/hic/src/HicRenderer/makeImageData.ts

@@ -43,7 +43,6 @@ export async function makeImageData(
   } = props
 
   const { statusCallback = () => {} } = props
-  // @ts-expect-error
   statusCallback('Drawing Hi-C matrix')
   const region = regions[0]!
   const { dataAdapter } = await getAdapter(

plugins/variants/src/MultiLinearVariantDisplay/components/Crosshair.tsx

@@ -2,7 +2,7 @@ import { getContainingView } from '@jbrowse/core/util'
 import { observer } from 'mobx-react'
 import { makeStyles } from 'tss-react/mui'
 
-import MultiVariantTooltip from '../../shared/MultiVariantTooltip'
+import MultiVariantTooltip from '../../shared/components/MultiVariantTooltip'
 
 import type { MultiLinearVariantDisplayModel } from '../model'
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'

plugins/variants/src/MultiLinearVariantDisplay/components/VariantDisplayComponent.tsx

@@ -4,7 +4,7 @@ import { BaseLinearDisplayComponent } from '@jbrowse/plugin-linear-genome-view'
 import { observer } from 'mobx-react'
 
 import Crosshair from './Crosshair'
-import LegendBar from '../../shared/LegendBar'
+import LegendBar from '../../shared/components/LegendBar'
 
 import type { MultiLinearVariantDisplayModel } from '../model'
 

plugins/variants/src/MultiLinearVariantDisplay/renderSvg.tsx

@@ -2,7 +2,7 @@ import { getContainingView } from '@jbrowse/core/util'
 import { when } from 'mobx'
 
 // locals
-import LegendBar from '../shared/LegendBar'
+import LegendBar from '../shared/components/LegendBar'
 
 import type { MultiLinearVariantDisplayModel } from './model'
 import type {

plugins/variants/src/MultiLinearVariantMatrixDisplay/components/Crosshair.tsx

@@ -2,7 +2,7 @@ import { getContainingView } from '@jbrowse/core/util'
 import { observer } from 'mobx-react'
 import { makeStyles } from 'tss-react/mui'
 
-import MultiVariantTooltip from '../../shared/MultiVariantTooltip'
+import MultiVariantTooltip from '../../shared/components/MultiVariantTooltip'
 
 import type { MultiLinearVariantMatrixDisplayModel } from '../model'
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'

plugins/variants/src/MultiLinearVariantMatrixDisplay/components/VariantDisplayComponent.tsx

@@ -5,7 +5,7 @@ import { observer } from 'mobx-react'
 
 import Crosshair from './Crosshair'
 import LinesConnectingMatrixToGenomicPosition from './LinesConnectingMatrixToGenomicPosition'
-import LegendBar from '../../shared/LegendBar'
+import LegendBar from '../../shared/components/LegendBar'
 
 import type { MultiLinearVariantMatrixDisplayModel } from '../model'
 

plugins/variants/src/MultiLinearVariantMatrixDisplay/renderSvg.tsx

@@ -1,9 +1,8 @@
 import { getContainingView } from '@jbrowse/core/util'
 import { when } from 'mobx'
 
-// locals
-import LegendBar from '../shared/LegendBar'
 import LinesConnectingMatrixToGenomicPosition from './components/LinesConnectingMatrixToGenomicPosition'
+import LegendBar from '../shared/components/LegendBar'
 
 import type { MultiLinearVariantMatrixDisplayModel } from './model'
 import type {

plugins/variants/src/MultiLinearVariantMatrixRenderer/LinearVariantMatrixRenderer.ts

@@ -45,13 +45,13 @@ export default class LinearVariantMatrixRenderer extends BoxRendererType {
       ...res,
       features: new Map(),
       simplifiedFeatures: mafs.map(
-        (s: Feature) =>
+        ({ feature }: { feature: Feature }) =>
           new SimpleFeature({
-            id: s.id(),
+            id: feature.id(),
             data: {
-              start: s.get('start'),
-              end: s.get('end'),
-              refName: s.get('refName'),
+              start: feature.get('start'),
+              end: feature.get('end'),
+              refName: feature.get('refName'),
             },
           }),
       ),

plugins/variants/src/MultiLinearVariantMatrixRenderer/makeImageData.ts

@@ -1,45 +1,15 @@
-import {
-  getColorAlleleCount,
-  getColorPhased,
-  getColorPhasedWithPhaseSet,
-} from '../shared/multiVariantColor'
-import { getFeaturesThatPassMinorAlleleFrequencyFilter } from '../util'
+import { updateStatus } from '@jbrowse/core/util'
 
-import type { RenderArgsDeserializedWithFeaturesAndLayout } from './types'
-
-const fudgeFactor = 0.6
-const f2 = fudgeFactor / 2
+import { f2 } from '../shared/constants'
+import { drawColorAlleleCount } from '../shared/drawAlleleCount'
+import { drawPhased } from '../shared/drawPhased'
+import { getFeaturesThatPassMinorAlleleFrequencyFilter } from '../shared/minorAlleleFrequencyUtils'
 
-function drawColorAlleleCount(
-  alleles: string[],
-  ctx: CanvasRenderingContext2D,
-  x: number,
-  y: number,
-  w: number,
-  h: number,
-) {
-  ctx.fillStyle = getColorAlleleCount(alleles)
-  ctx.fillRect(x - f2, y - f2, w + f2, h + f2)
-}
+import type { RenderArgsDeserializedWithFeaturesAndLayout } from './types'
 
-function drawPhased(
-  alleles: string[],
-  ctx: CanvasRenderingContext2D,
-  x: number,
-  y: number,
-  w: number,
-  h: number,
-  HP: number,
-  PS?: string,
-) {
-  ctx.fillStyle =
-    PS !== undefined
-      ? getColorPhasedWithPhaseSet(alleles, HP, PS)
-      : getColorPhased(alleles, HP)
-  ctx.fillRect(x - f2, y - f2, w + f2, h + f2)
-}
+type SampleGenotype = Record<string, string[]>
 
-export function makeImageData({
+export async function makeImageData({
   ctx,
   canvasWidth,
   canvasHeight,
@@ -58,78 +28,78 @@ export function makeImageData({
   } = renderArgs
 
   const { statusCallback = () => {} } = renderArgs
-  // @ts-expect-error
-  statusCallback('Drawing variant matrix')
   const h = canvasHeight / sources.length
   const mafs = getFeaturesThatPassMinorAlleleFrequencyFilter(
     features.values(),
     minorAlleleFrequencyFilter,
   )
-
   const arr = [] as string[][]
   const m = mafs.length
   const w = canvasWidth / m
-  for (let i = 0; i < m; i++) {
-    const arr2 = [] as string[]
-    const f = mafs[i]!
-    const hasPhaseSet = (f.get('format') as string).includes('PS')
-    if (hasPhaseSet) {
-      const samp = f.get('samples') as Record<string, Record<string, string[]>>
-      const x = (i / mafs.length) * canvasWidth
-      const sln = sources.length
-      for (let j = 0; j < sln; j++) {
-        const y = (j / sln) * canvasHeight
-        const { name, HP } = sources[j]!
-        const s = samp[name]
-        if (s) {
-          const genotype = s.GT?.[0]
+
+  await updateStatus('Drawing variant matrix', statusCallback, () => {
+    for (let i = 0; i < m; i++) {
+      const arr2 = [] as string[]
+      const { feature, mostFrequentAlt } = mafs[i]!
+      const hasPhaseSet = (feature.get('format') as string).includes('PS')
+      if (hasPhaseSet) {
+        const samp = feature.get('samples') as Record<string, SampleGenotype>
+        const x = (i / mafs.length) * canvasWidth
+        const sln = sources.length
+        for (let j = 0; j < sln; j++) {
+          const y = (j / sln) * canvasHeight
+          const { name, HP } = sources[j]!
+          const s = samp[name]
+          if (s) {
+            const genotype = s.GT?.[0]
+            if (genotype) {
+              arr2.push(genotype)
+              const isPhased = genotype.includes('|')
+              if (renderingMode === 'phased') {
+                if (isPhased) {
+                  const PS = s.PS?.[0]
+                  const alleles = genotype.split('|')
+                  drawPhased(alleles, ctx, x, y, w, h, HP!, PS)
+                } else {
+                  ctx.fillStyle = 'black'
+                  ctx.fillRect(x - f2, y - f2, w + f2, h + f2)
+                }
+              } else {
+                const alleles = genotype.split(/[/|]/)
+                drawColorAlleleCount(alleles, ctx, x, y, w, h, mostFrequentAlt)
+              }
+            }
+          }
+        }
+      } else {
+        const samp = feature.get('genotypes') as Record<string, string>
+        const x = (i / mafs.length) * canvasWidth
+        const sln = sources.length
+        for (let j = 0; j < sln; j++) {
+          const y = (j / sln) * canvasHeight
+          const { name, HP } = sources[j]!
+          const genotype = samp[name]
           if (genotype) {
             arr2.push(genotype)
             const isPhased = genotype.includes('|')
             if (renderingMode === 'phased') {
               if (isPhased) {
-                const PS = s.PS?.[0]
                 const alleles = genotype.split('|')
-                drawPhased(alleles, ctx, x, y, w, h, HP!, PS)
+                drawPhased(alleles, ctx, x, y, w, h, HP!)
               } else {
                 ctx.fillStyle = 'black'
                 ctx.fillRect(x - f2, y - f2, w + f2, h + f2)
               }
             } else {
               const alleles = genotype.split(/[/|]/)
-              drawColorAlleleCount(alleles, ctx, x, y, w, h)
+              drawColorAlleleCount(alleles, ctx, x, y, w, h, mostFrequentAlt)
             }
           }
         }
       }
-    } else {
-      const samp = f.get('genotypes') as Record<string, string>
-      const x = (i / mafs.length) * canvasWidth
-      const sln = sources.length
-      for (let j = 0; j < sln; j++) {
-        const y = (j / sln) * canvasHeight
-        const { name, HP } = sources[j]!
-        const genotype = samp[name]
-        if (genotype) {
-          arr2.push(genotype)
-          const isPhased = genotype.includes('|')
-          if (renderingMode === 'phased') {
-            if (isPhased) {
-              const alleles = genotype.split('|')
-              drawPhased(alleles, ctx, x, y, w, h, HP!)
-            } else {
-              ctx.fillStyle = 'black'
-              ctx.fillRect(x - f2, y - f2, w + f2, h + f2)
-            }
-          } else {
-            const alleles = genotype.split(/[/|]/)
-            drawColorAlleleCount(alleles, ctx, x, y, w, h)
-          }
-        }
-      }
+      arr.push(arr2)
     }
-    arr.push(arr2)
-  }
+  })
   return {
     mafs,
     arr,

plugins/variants/src/MultiLinearVariantMatrixRenderer/types.ts

@@ -1,4 +1,4 @@
-import type { Source } from '../types'
+import type { Source } from '../shared/types'
 import type { RenderArgsDeserialized as BoxRenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType'
 import type { Feature } from '@jbrowse/core/util'
 
@@ -15,4 +15,5 @@ export interface RenderArgsDeserializedWithFeaturesAndLayout
   sources: Source[]
   features: Map<string, Feature>
   renderingMode: string
+  statusCallback?: (arg: string) => void
 }

plugins/variants/src/MultiLinearVariantRenderer/MultiVariantRendering.tsx

@@ -4,7 +4,7 @@ import { PrerenderedCanvas } from '@jbrowse/core/ui'
 import { observer } from 'mobx-react'
 import RBush from 'rbush'
 
-import type { Source } from '../types'
+import type { Source } from '../shared/types'
 import type { Feature } from '@jbrowse/core/util'
 import type { Region } from '@jbrowse/core/util/types'
 

plugins/variants/src/MultiLinearVariantRenderer/components/MultiVariantRendering.tsx

@@ -0,0 +1,83 @@
+import { useMemo, useRef } from 'react'
+
+import { PrerenderedCanvas } from '@jbrowse/core/ui'
+import { observer } from 'mobx-react'
+import RBush from 'rbush'
+
+import type { Source } from '../../shared/types'
+import type { Feature } from '@jbrowse/core/util'
+import type { Region } from '@jbrowse/core/util/types'
+
+const MultiVariantRendering = observer(function (props: {
+  regions: Region[]
+  features: Map<string, Feature>
+  bpPerPx: number
+  width: number
+  height: number
+  sources: Source[]
+  scrollTop: number
+  totalHeight: number
+  rbush: RBush<{ genotype: string }>
+  displayModel: any
+  onMouseLeave?: (event: React.MouseEvent) => void
+  onMouseMove?: (event: React.MouseEvent, arg?: Feature) => void
+  onFeatureClick?: (event: React.MouseEvent, arg?: Feature) => void
+}) {
+  const { totalHeight, scrollTop } = props
+  const { rbush, displayModel } = props
+  const ref = useRef<HTMLDivElement>(null)
+  const rbush2 = useMemo(
+    () => new RBush<{ genotype: string }>().fromJSON(rbush),
+    [rbush],
+  )
+
+  function getFeatureUnderMouse(eventClientX: number, eventClientY: number) {
+    let offsetX = 0
+    let offsetY = 0
+    if (ref.current) {
+      const r = ref.current.getBoundingClientRect()
+      offsetX = eventClientX - r.left
+      offsetY = eventClientY - r.top
+    }
+    const ret = rbush2.search({
+      minX: offsetX,
+      maxX: offsetX + 3,
+      minY: offsetY,
+      maxY: offsetY + 3,
+    })
+    return ret[0]?.genotype
+  }
+
+  return (
+    <div
+      ref={ref}
+      onMouseMove={e =>
+        displayModel.setHoveredGenotype?.(
+          getFeatureUnderMouse(e.clientX, e.clientY),
+        )
+      }
+      onMouseLeave={() => {
+        displayModel.setHoveredGenotype?.(undefined)
+      }}
+      onMouseOut={() => {
+        displayModel.setHoveredGenotype?.(undefined)
+      }}
+      style={{
+        overflow: 'visible',
+        position: 'relative',
+        height: totalHeight,
+      }}
+    >
+      <PrerenderedCanvas
+        {...props}
+        style={{
+          position: 'absolute',
+          left: 0,
+          top: scrollTop,
+        }}
+      />
+    </div>
+  )
+})
+
+export default MultiVariantRendering

plugins/variants/src/MultiLinearVariantRenderer/index.ts

@@ -1,5 +1,5 @@
 import MultiVariantRenderer from './MultiVariantRenderer'
-import ReactComponent from './MultiVariantRendering'
+import ReactComponent from './components/MultiVariantRendering'
 import configSchema from './configSchema'
 
 import type PluginManager from '@jbrowse/core/PluginManager'