Most frequent alt

plugins/variants/src/MultiLinearVariantMatrixRenderer/makeImageData.ts

@@ -40,7 +40,7 @@ export async function makeImageData({
   await updateStatus('Drawing variant matrix', statusCallback, () => {
     for (let i = 0; i < m; i++) {
       const arr2 = [] as string[]
-      const { feature } = mafs[i]!
+      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>
@@ -66,7 +66,7 @@ export async function makeImageData({
                 }
               } else {
                 const alleles = genotype.split(/[/|]/)
-                drawColorAlleleCount(alleles, ctx, x, y, w, h)
+                drawColorAlleleCount(alleles, ctx, x, y, w, h, mostFrequentAlt)
               }
             }
           }
@@ -92,7 +92,7 @@ export async function makeImageData({
               }
             } else {
               const alleles = genotype.split(/[/|]/)
-              drawColorAlleleCount(alleles, ctx, x, y, w, h)
+              drawColorAlleleCount(alleles, ctx, x, y, w, h, mostFrequentAlt)
             }
           }
         }

plugins/variants/src/MultiLinearVariantRenderer/makeImageData.ts

@@ -28,7 +28,7 @@ export async function makeImageData(
     minorAlleleFrequencyFilter,
   )
   const rbush = new RBush()
-  for (const { feature } of mafs) {
+  for (const { mostFrequentAlt, feature } of mafs) {
     const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx)
     const w = Math.max(Math.round(rightPx - leftPx), 2)
     const samp = feature.get('genotypes') as Record<string, string>
@@ -59,7 +59,7 @@ export async function makeImageData(
           }
         } else {
           const alleles = genotype.split(/[/|]/)
-          drawColorAlleleCount(alleles, ctx, x, y, w, h)
+          drawColorAlleleCount(alleles, ctx, x, y, w, h, mostFrequentAlt)
         }
       }
       y += rowHeight

plugins/variants/src/shared/drawAlleleCount.ts

@@ -1,5 +1,40 @@
+import { colord } from '@jbrowse/core/util/colord'
+
 import { f2 } from './constants'
-import { getColorAlleleCount } from './multiVariantColor'
+
+function getColorAlleleCount(alleles: string[], mostFrequentAlt: string) {
+  const total = alleles.length
+  let alt = 0
+  let uncalled = 0
+  let alt2 = 0
+  let ref = 0
+  for (const allele of alleles) {
+    if (allele === mostFrequentAlt) {
+      alt++
+    } else if (allele === '0') {
+      ref++
+    } else if (allele === '.') {
+      uncalled++
+    } else {
+      alt2++
+    }
+  }
+
+  if (ref === total) {
+    return `#ccc`
+  } else {
+    let a1 = colord(`hsl(200,50%,${80 - (alt / total) * 50}%)`)
+    if (alt2) {
+      // @ts-ignore
+      a1 = a1.mix(`hsla(0,100%,20%,${alt2 / total})`)
+    }
+    if (uncalled) {
+      // @ts-ignore
+      a1 = a1.mix(`hsla(50,50%,50%,${uncalled / total / 2})`)
+    }
+    return a1.toHex()
+  }
+}
 
 export function drawColorAlleleCount(
   alleles: string[],
@@ -8,7 +43,8 @@ export function drawColorAlleleCount(
   y: number,
   w: number,
   h: number,
+  mostFrequentAlt: string,
 ) {
-  ctx.fillStyle = getColorAlleleCount(alleles)
+  ctx.fillStyle = getColorAlleleCount(alleles, mostFrequentAlt)
   ctx.fillRect(x - f2, y - f2, w + f2, h + f2)
 }

plugins/variants/src/shared/drawPhased.ts

@@ -1,5 +1,17 @@
+import { set1 } from '@jbrowse/core/ui/colors'
+
 import { f2 } from './constants'
-import { getColorPhased, getColorPhasedWithPhaseSet } from './multiVariantColor'
+import { colorify } from './util'
+
+function getColorPhased(alleles: string[], HP: number) {
+  const c = +alleles[HP]!
+  return c ? set1[c - 1] || 'black' : '#ccc'
+}
+
+function getColorPhasedWithPhaseSet(alleles: string[], HP: number, PS: string) {
+  const c = +alleles[HP]!
+  return c ? colorify(+PS) || 'black' : '#ccc'
+}
 
 export function drawPhased(
   alleles: string[],

plugins/variants/src/shared/findSecondLargestNumber.ts

@@ -1 +0,0 @@
-

plugins/variants/src/shared/minorAlleleFrequencyUtils.ts

@@ -1,6 +1,6 @@
 import { sum } from '@jbrowse/core/util'
 
-import type { Feature} from '@jbrowse/core/util'
+import type { Feature } from '@jbrowse/core/util'
 
 export function findSecondLargestNumber(arr: Iterable<number>) {
   let firstMax = 0
@@ -27,8 +27,18 @@ export function calculateAlleleCounts(feat: Feature) {
       alleleCounts.set(allele, (alleleCounts.get(allele) || 0) + 1)
     }
   }
+  let mostFrequentAlt
+  let max = 0
+  for (const [alt, altCount] of alleleCounts.entries()) {
+    if (alt !== '.' && alt !== '0') {
+      if (altCount > max) {
+        mostFrequentAlt = alt
+        max = altCount
+      }
+    }
+  }
 
-  return alleleCounts
+  return { alleleCounts, mostFrequentAlt }
 }
 
 export function calculateMinorAlleleFrequency(
@@ -46,16 +56,19 @@ export function getFeaturesThatPassMinorAlleleFrequencyFilter(
 ) {
   const results = [] as {
     feature: Feature
-    alleleCounts: Map<string, number>
+    mostFrequentAlt: string
   }[]
-  for (const feat of feats) {
-    if (feat.get('end') - feat.get('start') <= 10) {
-      const alleleCounts = calculateAlleleCounts(feat)
+  for (const feature of feats) {
+    if (feature.get('end') - feature.get('start') <= 10) {
+      const { mostFrequentAlt, alleleCounts } = calculateAlleleCounts(feature)
       if (
         calculateMinorAlleleFrequency(alleleCounts) >=
         minorAlleleFrequencyFilter
       ) {
-        results.push({ feature: feat, alleleCounts })
+        results.push({
+          feature,
+          mostFrequentAlt,
+        })
       }
     }
   }

plugins/variants/src/util.ts

@@ -1 +0,0 @@
-