@sjcrh/proteinpaint-shared 2.109.1-0 → 2.109.1

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-shared",
-  "version": "2.109.1-0",
+  "version": "2.109.1",
   "description": "ProteinPaint code that is shared between server and client-side workspaces",
   "type": "module",
   "main": "src/index.js",

package/src/termdb.initbinconfig.js

@@ -7,6 +7,7 @@ Initialize a bin configuration for a numeric dataset
 */
 export default function initBinConfig(data, opts = {}) {
 	if (data.find(d => !Number.isFinite(d))) throw 'non-numeric values found'
+
 	let binConfig
 	const s = new Set(data)
 	if (s.size === 1) {

package/src/violin.bins.js

@@ -32,7 +32,7 @@ output:
 import { bin } from 'd3-array'
 import * as d3 from 'd3'
 
-export function getBinsDensity(scale, plot, isKDE = false, ticks = 20) {
+export function getBinsDensity(plot, isKDE = false, ticks = 20) {
 	const [valuesMin, valuesMax] = d3.extent(plot.values) //Min and max on plot
 	//Commented out as it seems to be handled by kde with automatic bandwidth
 	//if (valuesMin == valuesMax) return { bins: [{ x0: valuesMin, density: 1 }], densityMax: valuesMax, densityMin: 0}
@@ -48,12 +48,12 @@ export function getBinsDensity(scale, plot, isKDE = false, ticks = 20) {
 	//Divided thresholds(or bins) into 3 parts, below p2nd, between p2nd and p98, above p98. This allows to handle outliers better.
 	//When there are no outliers, p2nd and p98 will be the same or very close to valuesMin and valuesMax respectively
 	if (p2nd > valuesMin) thresholds = [...getThresholds(valuesMin, p2nd, ticks)]
-	if (p98 > p2nd) thresholds.push(...getThresholds(p2nd, p98, ticks))
+	if (p98 >= p2nd) thresholds.push(...getThresholds(p2nd, p98, ticks))
 	if (p98 < valuesMax) thresholds.push(...getThresholds(p98, valuesMax, ticks))
 
 	const result = isKDE
 		? kde(gaussianKernel, thresholds, plot.values, valuesMin, valuesMax)
-		: getBinsHist(scale, plot.values, thresholds, valuesMin, valuesMax)
+		: getBinsHist(plot.values, thresholds, valuesMin, valuesMax)
 
 	result.bins.unshift({ x0: valuesMin, density: result.densityMin }) //This allows to start the plot from min prob, avoids rendering issues
 
@@ -157,9 +157,9 @@ function silvermanBandwidth(data) {
 	return h
 }
 
-function getBinsHist(scale, values, thresholds, valuesMin, valuesMax) {
+function getBinsHist(values, thresholds, valuesMin, valuesMax) {
 	const binBuilder = bin()
-		.domain(scale.domain()) /* extent of the data that is lowest to highest*/
+		.domain([valuesMin, valuesMax]) /* extent of the data that is lowest to highest*/
 		.thresholds(thresholds) /* buckets are created which are separated by the threshold*/
 		.value(d => d) /* bin the data points into this bucket*/
 	const bins0 = binBuilder(values)