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Add log scale feature to negative values in WIG track #1873

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merged 4 commits into from
Aug 20, 2024
Merged

Add log scale feature to negative values in WIG track #1873

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557f5fe
Accounted for y coordinates being 0 based in wigtrack
milandomazet Aug 9, 2024
05203c0
Added logscale to negative values in wigtrack
milandomazet Aug 9, 2024
91bdded
Fixed scenario in which max and min are < 0
milandomazet Aug 9, 2024
a292d07
Fixed flipAxis for negative log scale
milandomazet Aug 9, 2024
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33 changes: 18 additions & 15 deletions js/feature/wigTrack.js
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Original file line number Diff line number Diff line change
Expand Up @@ -158,7 +158,9 @@ class WigTrack extends TrackBase {

// TODO: refactor to igvUtils.js
getScaleFactor(min, max, height, logScale) {
const scale = logScale ? height / (Math.log10(max + 1) - (min <= 0 ? 0 : Math.log10(min + 1))) : height / (max - min)
const minValue = (logScale === true) ? ((min < 0) ? -Math.log10(Math.abs(min) + 1) : Math.log10(Math.abs(min) + 1)) : min
const maxValue = (logScale === true) ? Math.log10(Math.abs(max) + 1) : max
const scale = height / (maxValue - minValue)
return scale
}

Expand All @@ -168,12 +170,11 @@ class WigTrack extends TrackBase {

computeYPixelValueInLogScale(yValue, yScaleFactor) {
let maxValue = this.dataRange.max
let minValue = this.dataRange.min
if (maxValue <= 0) return 0 // TODO:
if (minValue <= -1) minValue = 0
minValue = (minValue <= 0) ? 0 : Math.log10(minValue + 1)
maxValue = Math.log10(maxValue + 1)
yValue = Math.log10(yValue + 1)
let minValue = this.dataRange.min
minValue = (minValue < 0) ? -Math.log10(Math.abs(minValue) + 1) : Math.log10(Math.abs(minValue) + 1)
maxValue = (maxValue < 0) ? -Math.log10(Math.abs(maxValue) + 1) : Math.log10(Math.abs(maxValue) + 1)

yValue = (yValue < 0) ? -Math.log10(Math.abs(yValue) +1) : Math.log10(yValue + 1)
return ((this.flipAxis ? (yValue - minValue) : (maxValue - yValue)) * yScaleFactor)
}

Expand All @@ -184,12 +185,10 @@ class WigTrack extends TrackBase {
const bpPerPixel = options.bpPerPixel
const bpStart = options.bpStart
const pixelWidth = options.pixelWidth
const pixelHeight = options.pixelHeight
const pixelHeight = options.pixelHeight - 1
const bpEnd = bpStart + pixelWidth * bpPerPixel + 1
const posColor = this.color || DEFAULT_COLOR

let lastNegValue = 1
const scaleFactor = this.getScaleFactor(this.dataRange.min, this.dataRange.max, options.pixelHeight, this.logScale)

const scaleFactor = this.getScaleFactor(this.dataRange.min, this.dataRange.max, pixelHeight, this.logScale)
const yScale = (yValue) => this.logScale
? this.computeYPixelValueInLogScale(yValue, scaleFactor)
: this.computeYPixelValue(yValue, scaleFactor)
Expand Down Expand Up @@ -247,7 +246,7 @@ class WigTrack extends TrackBase {
if (f.value > this.dataRange.max) {
IGVGraphics.fillRect(ctx, x, 0, width, 3, {fillStyle: this.overflowColor})
} else if (f.value < this.dataRange.min) {
IGVGraphics.fillRect(ctx, x, pixelHeight - 3, width, 3, {fillStyle: this.overflowColor})
IGVGraphics.fillRect(ctx, x, pixelHeight - 2, width, 3, {fillStyle: this.overflowColor})
}

}
Expand All @@ -257,8 +256,12 @@ class WigTrack extends TrackBase {

// If the track includes negative values draw a baseline
if (this.dataRange.min < 0) {
const ratio = this.dataRange.max / (this.dataRange.max - this.dataRange.min)
const basepx = this.flipAxis ? (1 - ratio) * options.pixelHeight : ratio * options.pixelHeight
let maxValue = this.dataRange.max
let minValue = this.dataRange.min
minValue = (this.logScale === true) ? ((minValue < 0) ? -Math.log10(Math.abs(minValue) + 1) : Math.log10(Math.abs(minValue) + 1)) : minValue
maxValue = (this.logScale === true) ? ((maxValue < 0) ? -Math.log10(Math.abs(maxValue) + 1) : Math.log10(Math.abs(maxValue) + 1)) : maxValue
const ratio = maxValue / (maxValue - minValue)
const basepx = this.flipAxis ? (1 - ratio) * pixelHeight : ratio * pixelHeight
IGVGraphics.strokeLine(ctx, 0, basepx, options.pixelWidth, basepx, {strokeStyle: this.baselineColor})
}
}
Expand Down
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