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Draw SNPs in modifications/methylation views #3001

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merged 1 commit into from
Jun 29, 2022
Merged

Draw SNPs in modifications/methylation views #3001

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56 changes: 30 additions & 26 deletions plugins/alignments/src/PileupRenderer/PileupRenderer.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -138,8 +138,8 @@ interface LayoutFeature {
feature: Feature
}

function shouldDrawSNPs(type?: string) {
return !['methylation', 'modifications'].includes(type || '')
function shouldDrawSNPsMuted(type?: string) {
return ['methylation', 'modifications'].includes(type || '')
}

function shouldDrawIndels(type?: string) {
Expand Down Expand Up @@ -830,7 +830,7 @@ export default class PileupRenderer extends BoxRendererType {
colorForBase,
contrastForBase,
canvasWidth,
drawSNPs = true,
drawSNPsMuted,
drawIndels = true,
}: {
ctx: CanvasRenderingContext2D
Expand All @@ -839,8 +839,8 @@ export default class PileupRenderer extends BoxRendererType {
colorForBase: { [key: string]: string }
contrastForBase: { [key: string]: string }
mismatchAlpha?: boolean
drawSNPs?: boolean
drawIndels?: boolean
drawSNPsMuted?: boolean
minSubfeatureWidth: number
largeInsertionIndicatorScale: number
charWidth: number
Expand Down Expand Up @@ -872,30 +872,34 @@ export default class PileupRenderer extends BoxRendererType {
const mbase = mismatch.base
const [leftPx, rightPx] = bpSpanPx(mstart, mstart + mlen, region, bpPerPx)
const widthPx = Math.max(minSubfeatureWidth, Math.abs(leftPx - rightPx))
if (mismatch.type === 'mismatch' && drawSNPs) {
const baseColor = colorForBase[mismatch.base] || '#888'
if (mismatch.type === 'mismatch') {
if (!drawSNPsMuted) {
const baseColor = colorForBase[mismatch.base] || '#888'

fillRect(
ctx,
leftPx,
topPx,
widthPx,
heightPx,
canvasWidth,
!mismatchAlpha
? baseColor
: mismatch.qual !== undefined
? // @ts-ignore
Color(baseColor)
.alpha(Math.min(1, mismatch.qual / 50))
.hsl()
.string()
: baseColor,
)
fillRect(
ctx,
leftPx,
topPx,
widthPx,
heightPx,
canvasWidth,
!mismatchAlpha
? baseColor
: mismatch.qual !== undefined
? // @ts-ignore
Color(baseColor)
.alpha(Math.min(1, mismatch.qual / 50))
.hsl()
.string()
: baseColor,
)
}

if (widthPx >= charWidth && heightPx >= heightLim) {
// normal SNP coloring
const contrastColor = contrastForBase[mismatch.base] || 'black'
const contrastColor = drawSNPsMuted
? 'black'
: contrastForBase[mismatch.base] || 'black'
ctx.fillStyle = !mismatchAlpha
? contrastColor
: mismatch.qual !== undefined
Expand Down Expand Up @@ -1160,7 +1164,7 @@ export default class PileupRenderer extends BoxRendererType {
ctx.font = 'bold 10px Courier New,monospace'

const { charWidth, charHeight } = this.getCharWidthHeight(ctx)
const drawSNPs = shouldDrawSNPs(colorBy?.type)
const drawSNPsMuted = shouldDrawSNPsMuted(colorBy?.type)
const drawIndels = shouldDrawIndels(colorBy?.type)
for (let i = 0; i < layoutRecords.length; i++) {
const feat = layoutRecords[i]
Expand All @@ -1184,7 +1188,7 @@ export default class PileupRenderer extends BoxRendererType {
feat,
renderArgs,
mismatchAlpha,
drawSNPs,
drawSNPsMuted,
drawIndels,
largeInsertionIndicatorScale,
minSubfeatureWidth,
Expand Down