@sjcrh/proteinpaint-shared 2.87.1 → 2.95.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-shared",
-  "version": "2.87.1",
+  "version": "2.95.0",
   "description": "ProteinPaint code that is shared between server and client-side workspaces",
   "type": "module",
   "main": "src/index.js",

package/src/common.js

@@ -282,6 +282,9 @@ mclass[mclasssv] = {
 	key: mclasssv
 }
 
+// "CNV_amp" represents "CNV Gain" and is used in both 2-category and 5-category CNV data representation
+// "CNV_amplification" represents CNV amplification and is used in 5-category CNV
+// "CNV_amp" have to stay as-is since it may be hardcoded in lots of data beyond portal code.
 export const mclasscnvgain = 'CNV_amp'
 mclass[mclasscnvgain] = {
 	label: 'Copy number gain',
@@ -300,6 +303,25 @@ mclass[mclasscnvloss] = {
 	key: mclasscnvloss
 }
 
+// mclasscnvAmp is next level above mclasscnvgain and is used in 5-category CNV data
+export const mclasscnvAmp = 'CNV_amplification'
+mclass[mclasscnvAmp] = {
+	label: 'Copy number amplification',
+	color: '#900000',
+	dt: dtcnv,
+	desc: 'Copy number amplification',
+	key: mclasscnvAmp
+}
+
+export const mclasscnvHomozygousDel = 'CNV_homozygous_deletion'
+mclass[mclasscnvHomozygousDel] = {
+	label: 'Copy number homozygous deletion',
+	color: '#00457C',
+	dt: dtcnv,
+	desc: 'Copy number homozygous deletion',
+	key: mclasscnvHomozygousDel
+}
+
 export const mclasscnvloh = 'CNV_loh'
 mclass[mclasscnvloh] = { label: 'LOH', color: '#12EDFC', dt: dtcnv, desc: 'Loss of heterozygosity', key: mclasscnvloh }
 

package/src/descriptive.stats.js

@@ -42,15 +42,15 @@ export default function summaryStats(array) {
 	return {
 		values: [
 			{ id: 'total', label: 'Total', value: n },
-			{ id: 'min', label: 'Minimum', value: roundValueAuto(min) },
-			{ id: 'p25', label: '1st quartile', value: roundValueAuto(p25) },
-			{ id: 'median', label: 'Median', value: roundValueAuto(median) },
-			{ id: 'mean', label: 'Mean', value: roundValueAuto(mean(arr)) },
-			{ id: 'p75', label: '3rd quartile', value: roundValueAuto(p75) },
-			{ id: 'max', label: 'Maximum', value: roundValueAuto(max) },
-			{ id: 'SD', label: 'Standard deviation', value: roundValueAuto(stdDev) },
-			{ id: 'variance', label: 'Variance', value: roundValueAuto(variance) },
-			{ id: 'IQR', label: 'Inter-quartile range', value: roundValueAuto(IQR) }
+			{ id: 'min', label: 'Minimum', value: roundValueAuto(min, true) },
+			{ id: 'p25', label: '1st quartile', value: roundValueAuto(p25, true) },
+			{ id: 'median', label: 'Median', value: roundValueAuto(median, true) },
+			{ id: 'mean', label: 'Mean', value: roundValueAuto(mean(arr), true) },
+			{ id: 'p75', label: '3rd quartile', value: roundValueAuto(p75, true) },
+			{ id: 'max', label: 'Maximum', value: roundValueAuto(max, true) },
+			{ id: 'SD', label: 'Standard deviation', value: roundValueAuto(stdDev, true) },
+			{ id: 'variance', label: 'Variance', value: roundValueAuto(variance, true) },
+			{ id: 'IQR', label: 'Inter-quartile range', value: roundValueAuto(IQR, true) }
 		]
 	}
 }

package/src/roundValue.js

@@ -11,19 +11,22 @@ digits: number of digits to round to
 export function roundValue(value, digits) {
 	const v = Number(value)
 	if (Number.isInteger(v)) return v
-	const abs = Math.abs(v)
-	if (abs < 1 || abs > 9999) {
-		//Number() reverts positive values less than 10^21 to a whole number
-		return abs > 9999 ? v.toPrecision(digits) : Number(v.toPrecision(digits))
-	}
+	if (Math.abs(v) < 1) return Number(v.toPrecision(digits))
 	return Number(v.toFixed(digits))
 }
 
-export function roundValueAuto(value) {
+/** Rounds numbers to the appropriate decimal point
+ * if format is true, returns either a number or string in
+ * scientific notation.
+ *
+ * TODO: Review digit logic.
+ */
+
+export function roundValueAuto(value, format = false) {
 	if (!value && value != 0) return value
 	const dp = decimalPlacesUntilFirstNonZero(value)
 	const digits = Math.abs(value) > 1 ? 2 : dp > 0 ? dp + 1 : 2
-
+	if (format) return formatValue(value, digits)
 	return roundValue(value, digits)
 }
 
@@ -52,3 +55,39 @@ export function decimalPlacesUntilFirstNonZero(number) {
 
 	return decimalPlaces
 }
+
+/* 
+simple logic to return a number close to original while rounding up decimals.
+supplements roundValueAuto which rounds 12345 to 1.2e4 which is only suitable for human quick glance but not subsequent computing
+
+TODO:
+10000 and 10001 to 1e4
+0.00001 to 1e-5
+1.00001 to 1
+*/
+export function roundValue2(value) {
+	if (!Number.isFinite(value)) return value // not a number
+	if (Number.isInteger(value)) return value // is integer, do not convert
+	const abs = Math.abs(value)
+	if (abs > 100) return Math.round(value) // 12345.1234 to 12345 (compared to 1.2e4 from roundValueAuto)
+	if (abs > 10) return Number(value.toFixed(1)) // 99.1234 to 99.1
+	if (abs > 1) return Number(value.toFixed(2)) // 9.1234 to 9.12
+	if (abs > 0.1) return Number(value.toFixed(3)) // 0.12345 to 0.123
+	if (abs > 0.01) return Number(value.toFixed(4)) // 0.012345 to 0.0123
+	return value // as is
+}
+
+/** Use to return displayed values in scientific notation
+ * Do not use for values intended for calculation later.
+ */
+export function formatValue(value, digits) {
+	const v = Number(value)
+	if (Number.isInteger(v)) return v
+	const abs = Math.abs(v)
+	if (abs < 1 || abs > 9999) {
+		//Number() reverts positive values less than 10^21 to a whole number
+		//To return the value in scientific notation, use toPrecision without Number()
+		return abs > 9999 ? v.toPrecision(digits) : Number(v.toPrecision(digits))
+	}
+	return Number(v.toFixed(digits))
+}