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cnvpytor track update: improve y axis labels (#1712)
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* cnvpytor track update: improve y axis labels

* update scale and bug fix for default cnv caller
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@arpanda
arpanda authored Oct 19, 2023
1 parent 2a96b2f commit fc2c8e2
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Showing 4 changed files with 108 additions and 26 deletions.
6 changes: 3 additions & 3 deletions js/cnvpytor/CombinedCaller.js
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Original file line number Diff line number Diff line change
Expand Up @@ -352,7 +352,7 @@ class CombinedCaller{
return results
}

formatDataStructure_BAF(feature_column, scaling_factor = 2) {
formatDataStructure_BAF(feature_column, scaling_factor = -1) {
const baf1 = []
const baf2 = []
for (const [chr, wig] of Object.entries(this.wigFeatures)) {
Expand All @@ -364,10 +364,10 @@ class CombinedCaller{

let value = sample[feature_column]
if (value != 0.5){
baf2_value.value = -2 * (1 - value)
baf2_value.value = scaling_factor * (1 - value)
baf2.push(baf2_value)
}
baf1_value.value = -2 * value
baf1_value.value = scaling_factor * value
baf1.push(baf1_value)

})
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12 changes: 6 additions & 6 deletions js/cnvpytor/HDF5IndexedReader.js
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Original file line number Diff line number Diff line change
Expand Up @@ -232,7 +232,7 @@ class HDF5Reader {
return chr_wig
}

async get_baf_signals(chrom, bin_size, signal_name){
async get_baf_signals(chrom, bin_size, signal_name, scaling_factor = -1){
/* return two list of dictionary*/
let chr_wig_1 = [];
let chr_wig_2 = [];
Expand All @@ -243,16 +243,16 @@ class HDF5Reader {
let max_value = Math.max(...bin_value);
const res = bin_value.indexOf(max_value);
let lh = Math.max(res / 200, 1 - res / 200);
chr_wig_1.push({chr:chrom, start: bin_idx*bin_size, end: (bin_idx+1) * bin_size, value: -2 * lh})
chr_wig_1.push({chr:chrom, start: bin_idx*bin_size, end: (bin_idx+1) * bin_size, value: scaling_factor * lh})
if(lh != 0.5){
chr_wig_2.push({chr:chrom, start: bin_idx*bin_size, end: (bin_idx+1) * bin_size, value: -2 *(1-lh)})
chr_wig_2.push({chr:chrom, start: bin_idx*bin_size, end: (bin_idx+1) * bin_size, value: scaling_factor *(1-lh)})
}
});
}
return [chr_wig_1, chr_wig_2]
}

async get_baf_signals_v2(chrom, bin_size, signal_name){
async get_baf_signals_v2(chrom, bin_size, signal_name, scaling_factor = -1){

/* return two list of dictionary*/
let chr_wig_1 = [];
Expand All @@ -262,9 +262,9 @@ class HDF5Reader {
let chrom_data = await chrom_dataset.to_array() //create_nested_array(value, shape)
chrom_data.forEach((lh, bin_idx) => {
if (!isNaN(lh)){
chr_wig_1.push({chr:chrom, start: bin_idx*bin_size, end: (bin_idx+1) * bin_size, value: -2 * ( 0.5 - lh )})
chr_wig_1.push({chr:chrom, start: bin_idx*bin_size, end: (bin_idx+1) * bin_size, value: scaling_factor * ( 0.5 - lh )})
if(lh != 0.5){
chr_wig_2.push({chr:chrom, start: bin_idx*bin_size, end: (bin_idx+1) * bin_size, value: -2 * ( 0.5 + lh )})
chr_wig_2.push({chr:chrom, start: bin_idx*bin_size, end: (bin_idx+1) * bin_size, value: scaling_factor * ( 0.5 + lh )})
}
}
});
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101 changes: 94 additions & 7 deletions js/cnvpytor/cnvpytorTrack.js
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Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,6 @@
*/

import TrackBase from "../trackBase.js"
import paintAxis from "../util/paintAxis.js"
import MenuUtils from "../ui/menuUtils.js"
import HDF5IndexedReader from "./HDF5IndexedReader.js"
import {CNVpytorVCF} from "./cnvpytorVCF.js"
Expand All @@ -47,7 +46,6 @@ class CNVPytorTrack extends TrackBase {
constructor(config, browser) {
super(config, browser)
this.featureType = 'numeric'
this.paintAxis = paintAxis

if (!config.max) {
this.defaultScale = true
Expand Down Expand Up @@ -118,8 +116,9 @@ class CNVPytorTrack extends TrackBase {
this.wigFeatures_obj[this.bin_size] = {}

let dataWigs;
if(this.config.cnv_caller == '2D'){

if(this.cnv_caller == '2D'){

dataWigs = await cnvpytor_obj.read_rd_baf('2D')

wigFeatures = dataWigs[0]
Expand Down Expand Up @@ -409,17 +408,17 @@ class CNVPytorTrack extends TrackBase {
if (this.defaultScale) {
if (this.signal_name == 'rd_snp') {
this.dataRange = {
min: this.config.min || this.dataRange.min || -2,
max: this.config.max || this.dataRange.max || 6
min: this.config.min || this.dataRange.min || -1,
max: this.config.max || this.dataRange.max || 5
}
} else if (this.signal_name == 'rd') {
this.dataRange = {
min: this.config.min || this.dataRange.min || 0,
max: this.config.max || this.dataRange.max || 6
max: this.config.max || this.dataRange.max || 5
}
} else if (this.signal_name == 'snp') {
this.dataRange = {
min: this.config.min || this.dataRange.min || -2,
min: this.config.min || this.dataRange.min || -1,
max: this.config.max || this.dataRange.max || 0
}
}
Expand Down Expand Up @@ -463,8 +462,96 @@ class CNVPytorTrack extends TrackBase {
}
}
}

let props = {
'strokeStyle': 'lightgray',
'strokeWidth': 0.5
}
let y = yScale(2);
IGVGraphics.dashedLine(options.context, 0, y, options.pixelWidth, y, 5, props)

}
paintAxis(ctx, pixelWidth, pixelHeight) {

var x1,
x2,
y1,
y2,
a,
b,
reference,
shim,
font = {
'font': 'normal 10px Arial',
'textAlign': 'right',
'strokeStyle': "black"
}

if (undefined === this.dataRange || undefined === this.dataRange.max || undefined === this.dataRange.min) {
return
}

let flipAxis = (undefined === this.flipAxis) ? false : this.flipAxis

IGVGraphics.fillRect(ctx, 0, 0, pixelWidth, pixelHeight, {'fillStyle': "rgb(255, 255, 255)"})

reference = 0.95 * pixelWidth
x1 = reference - 8
x2 = reference

//shim = 0.5 * 0.125;
shim = .01
y1 = y2 = shim * pixelHeight

a = {x: x2, y: y1}

// tick
IGVGraphics.strokeLine(ctx, x1, y1, x2, y2, font)
IGVGraphics.fillText(ctx, prettyPrint(flipAxis ? this.dataRange.min : this.dataRange.max), x1 + 4, y1 + 12, font)

//shim = 0.25 * 0.125;
y1 = y2 = (1.0 - shim) * pixelHeight

b = {x: x2, y: y1}

// tick
IGVGraphics.strokeLine(ctx, x1, y1, x2, y2, font)
IGVGraphics.fillText(ctx, prettyPrint(flipAxis ? this.dataRange.max : this.dataRange.min), x1 + 4, y1 - 4, font)

IGVGraphics.strokeLine(ctx, a.x, a.y, b.x, b.y, font)

function prettyPrint(number) {
// if number >= 100, show whole number
// if >= 1 show 1 significant digits
// if < 1 show 2 significant digits

if (number === 0) {
return "0"
} else if (Math.abs(number) >= 10) {
return number.toFixed()
} else if (number %1 == 0){
return number.toFixed()
}
else if (Math.abs(number) >= 1) {
return number.toFixed(1)
} else {
return number.toFixed(2)
}
}
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)

const n = Math.ceil((this.dataRange.max - this.dataRange.min) /10)
for (let p = Math.ceil(this.dataRange.min+1); p < Math.round(this.dataRange.max - 0.4 ); p += n) {
const yp = yScale(p)
IGVGraphics.strokeLine(ctx, 45, yp, 50, yp, font) // Offset dashes up by 2 pixel
IGVGraphics.fillText(ctx, prettyPrint(flipAxis ? this.dataRange.max-p: p), 44, yp+4, font)

}

}
popupData(clickState, features) {

const featuresArray = features || clickState.viewport.cachedFeatures
Expand Down
15 changes: 5 additions & 10 deletions js/cnvpytor/cnvpytorVCF.js
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Original file line number Diff line number Diff line change
Expand Up @@ -78,16 +78,13 @@ class CNVpytorVCF {
// finalFeatureSet = this.readDepthMeanshift(avgbin)
var baf = this.formatDataStructure_BAF(avgbin, 'max_likelihood')
}else if(caller=='2D'){

let caller_obj = new combined_caller.CombinedCaller(avgbin, this.binSize)
let processed_bins = await caller_obj.call_2d()

finalFeatureSet = [processed_bins.binScore, [], processed_bins.segment_score]

var baf = caller_obj.formatDataStructure_BAF('max_likelihood')
var baf = caller_obj.formatDataStructure_BAF('max_likelihood', -1)
}


return [finalFeatureSet, baf]
}

Expand All @@ -108,8 +105,6 @@ class CNVpytorVCF {
return results
}



format_BAF_likelihood(wigFeatures) {
const results = []

Expand Down Expand Up @@ -155,8 +150,8 @@ class CNVpytorVCF {



formatDataStructure_BAF(wigFeatures, feature_column, scaling_factor = 2) {
/* Rescale the BAF level from 0:1 to -2:0*/
formatDataStructure_BAF(wigFeatures, feature_column, scaling_factor=-1) {
/* Rescale the BAF level from 0:1 to scaling_factpr:0*/
const baf1 = []
const baf2 = []
for (const [chr, wig] of Object.entries(wigFeatures)) {
Expand All @@ -168,10 +163,10 @@ class CNVpytorVCF {

let value = sample[feature_column]
if (value != 0.5){
baf2_value.value = -2 * (1 - value)
baf2_value.value = scaling_factor * (1 - value)
baf2.push(baf2_value)
}
baf1_value.value = -2 * value
baf1_value.value = scaling_factor * value
baf1.push(baf1_value)

}
Expand Down

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