@milaboratories/graph-maker 1.1.132 → 1.1.133

package/dist/node_modules/@milaboratories/miplots4/dist/discrete/layers/logo.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"logo.js","sources":["../../../../../../../node_modules/@milaboratories/miplots4/src/discrete/layers/logo.ts"],"sourcesContent":["import type {GroupKey} from '../../DataFrame';\nimport type {DataFrame} from '../../DataFrame';\nimport type {LogoPlotLayer} from '../DiscreteSettingsImpl';\nimport type {LogoPlotData} from './types';\nimport {getFacetStringKey} from '../utils/getFacetStringKey';\nimport type {ColumnName, Row} from '../../types';\nimport {sum} from 'd3-array';\n\ntype LetterPart = {\n    height: number,\n    key: string\n}\n\nexport type LogoStack = {\n    key: string;\n    valuesMap: Record<string, LetterPart>;\n    primaryGrouping: string;\n    boundsY: {\n        min: number;\n        max: number;\n    };\n};\n\nexport function getLogoData(\n    layer: LogoPlotLayer,\n    groupingKeys: {\n        facet: GroupKey[][],\n        primary: GroupKey[],\n        secondary: GroupKey[]\n    },\n    data: DataFrame,\n    y: ColumnName,\n): LogoPlotData {\n    let maxY = -Infinity;\n\n    return {\n        type: 'logo',\n        geoms: groupingKeys.facet.reduce((res: Record<string, LogoStack[]>, facetKey) => {\n            const strFacetKey = getFacetStringKey(facetKey);\n            res[strFacetKey] = [];\n            groupingKeys.primary.forEach(primaryKey => {\n                let currentHeight = 0;\n                const letterParts:Record<string, LetterPart> = {};\n                groupingKeys.secondary.forEach(secondaryKey => {\n                    const rows = data.getRowsByGrouping([...facetKey, primaryKey, secondaryKey]);\n                    if (!rows.length) {\n                        return;\n                    }\n                    const height = sum(rows, (row:Row) => Number(row[y.value]));\n                    letterParts[String(secondaryKey)] = {\n                        height,\n                        key: String(secondaryKey),\n                    };\n                    currentHeight += height;\n                });\n                const maxStackHeight = currentHeight;\n                if (layer.normalize) { // show in percents of every stack\n                    groupingKeys.secondary.forEach(secondaryKey => {\n                        if (!letterParts[String(secondaryKey)]) {\n                            return;\n                        }\n                        letterParts[String(secondaryKey)].height = letterParts[String(secondaryKey)].height /  maxStackHeight * 100;\n                    });\n                }\n                maxY = Math.max(maxY, currentHeight);\n                res[strFacetKey].push({\n                    key: `logo_${String(primaryKey)}`,\n                    valuesMap: letterParts,\n                    primaryGrouping: primaryKey,\n                    boundsY: {min: 0, max: layer.normalize ? maxStackHeight : 100},\n                } as LogoStack);\n            });\n            return res;\n        }, {}),\n        meta: {minY: 0, maxY: layer.normalize ? 100 : maxY, normalize: layer.normalize},\n        aes: layer.aes,\n    };\n}\n"],"names":["getLogoData","layer","groupingKeys","data","y","maxY","res","facetKey","strFacetKey","getFacetStringKey","primaryKey","currentHeight","letterParts","secondaryKey","rows","height","sum","row","maxStackHeight"],"mappings":";;AAuBO,SAASA,EACZC,GACAC,GAKAC,GACAC,GACY;AACZ,MAAIC,IAAO;AAEX,SAAO;AAAA,IACH,MAAM;AAAA,IACN,OAAOH,EAAa,MAAM,OAAO,CAACI,GAAkCC,MAAa;AAC7E,YAAMC,IAAcC,EAAkBF,CAAQ;AAC9C,aAAAD,EAAIE,CAAW,IAAI,CAAA,GACnBN,EAAa,QAAQ,QAAQ,CAAAQ,MAAc;AACvC,YAAIC,IAAgB;AACpB,cAAMC,IAAyC,CAAA;AAC/CV,QAAAA,EAAa,UAAU,QAAQ,CAAAW,MAAgB;AAC3C,gBAAMC,IAAOX,EAAK,kBAAkB,CAAC,GAAGI,GAAUG,GAAYG,CAAY,CAAC;AAC3E,cAAI,CAACC,EAAK;AACN;AAEJ,gBAAMC,IAASC,EAAIF,GAAM,CAACG,MAAY,OAAOA,EAAIb,EAAE,KAAK,CAAC,CAAC;AAC1DQ,UAAAA,EAAY,OAAOC,CAAY,CAAC,IAAI;AAAA,YAChC,QAAAE;AAAAA,YACA,KAAK,OAAOF,CAAY;AAAA,UAAA,GAE5BF,KAAiBI;AAAAA,QACrB,CAAC;AACD,cAAMG,IAAiBP;AACnBV,QAAAA,EAAM,aACNC,EAAa,UAAU,QAAQ,CAAAW,MAAgB;AACtCD,UAAAA,EAAY,OAAOC,CAAY,CAAC,MAGrCD,EAAY,OAAOC,CAAY,CAAC,EAAE,SAASD,EAAY,OAAOC,CAAY,CAAC,EAAE,SAAUK,IAAiB;AAAA,QAC5G,CAAC,GAELb,IAAO,KAAK,IAAIA,GAAMM,CAAa,GACnCL,EAAIE,CAAW,EAAE,KAAK;AAAA,UAClB,KAAK,QAAQ,OAAOE,CAAU,CAAC;AAAA,UAC/B,WAAWE;AAAAA,UACX,iBAAiBF;AAAAA,UACjB,SAAS,EAAC,KAAK,GAAG,KAAKT,EAAM,YAAYiB,IAAiB,IAAA;AAAA,QAAA,CAChD;AAAA,MAClB,CAAC,GACMZ;AAAAA,IACX,GAAG,CAAA,CAAE;AAAA,IACL,MAAM,EAAC,MAAM,GAAG,MAAML,EAAM,YAAY,MAAMI,GAAM,WAAWJ,EAAM,UAAA;AAAA,IACrE,KAAKA,EAAM;AAAA,EAAA;AAEnB;","x_google_ignoreList":[0]}

package/dist/node_modules/@milaboratories/miplots4/dist/discrete/layers/pairedPoints.js

@@ -0,0 +1,89 @@
+import { getOutliersBounds as Y } from "../utils/getOutliersBounds.js";
+import { getFacetStringKey as G } from "../utils/getFacetStringKey.js";
+import w from "../../node_modules/lodash/lodash.js";
+function O(n, a) {
+  if (a.length === 2)
+    return "secondary";
+  if (n.length === 2 && a.length < 2)
+    return "primary";
+  throw Error("Too many groups for paired points layer");
+}
+function b(n, a, p, S, $, v, h, c, l) {
+  const y = w.groupBy(p, (e) => e[$.value]), d = w.groupBy(S, (e) => e[$.value]), u = Object.keys(y), s = Object.keys(d);
+  if (w.uniq(u).length !== u.length || w.uniq(s).length !== s.length)
+    throw Error(`Non unique keys in groups ${String(n)}, ${String(a)} for paired points layer`);
+  if (u.length !== s.length || w.intersection(u, s).length !== u.length)
+    throw Error(`Keys in groups ${String(n)}, ${String(a)} not match for paired points layer`);
+  const i = (e) => Number(e[v.value]);
+  let t = 1 / 0, r = -1 / 0, k = !1;
+  const g = l === "log";
+  let M = u.map((e) => {
+    const x = y[e][0], B = d[e][0], m = i(x), o = i(B);
+    return (m === 0 || o === 0) && (k = !0), t = Math.min(t, g && m === 0 ? 1 / 0 : m, g && o === 0 ? 1 / 0 : o), r = Math.max(r, g && m === 0 ? -1 / 0 : m, g && o === 0 ? -1 / 0 : o), {
+      id: e,
+      key1: { id: `${e}_${String(n)}`, value: m, data: x },
+      key2: { id: `${e}_${String(a)}`, value: o, data: B }
+    };
+  });
+  if (!c) {
+    t = 1 / 0, r = -1 / 0;
+    const [e, x] = Y(p, l, i), [B, m] = Y(S, l, i);
+    M = M.filter(({ key1: o, key2: f }) => o.value < e || o.value > x || f.value < B || f.value > m ? !1 : (t = Math.min(t, g && o.value === 0 ? 1 / 0 : o.value, g && f.value === 0 ? 1 / 0 : f.value), r = Math.max(r, g && o.value === 0 ? -1 / 0 : o.value, g && f.value === 0 ? -1 / 0 : f.value), !0));
+  }
+  return t = k ? t / 10 : t, r = Math.max(r, t), {
+    id: `${String(n)}_${String(a)}`,
+    key1: String(n),
+    key2: String(a),
+    pairs: M.map((e) => ({
+      ...e,
+      key1: { ...e.key1, value: e.key1.value === 0 ? t : e.key1.value },
+      key2: { ...e.key2, value: e.key2.value === 0 ? t : e.key2.value }
+    })),
+    grouping: h,
+    boundsY: { min: t, max: r }
+  };
+}
+function R(n, a, p, S, $) {
+  const v = O(a.primary, a.secondary);
+  let h = 1 / 0, c = -1 / 0;
+  return {
+    type: "pairedPoints",
+    geoms: a.facet.reduce((l, y) => {
+      const d = G(y);
+      if (l[d] = [], v === "primary") {
+        const [u, s] = a.primary, i = p.getRowsByGrouping([...y, u]), t = p.getRowsByGrouping([...y, s]), r = b(
+          u,
+          s,
+          i,
+          t,
+          n.linkColumn,
+          S,
+          v,
+          n.aes.showOutliers,
+          $.scale
+        );
+        h = Math.min(h, r.boundsY.min), c = Math.max(c, r.boundsY.max), l[d].push(r);
+      } else v === "secondary" && a.primary.forEach((u) => {
+        const [s, i] = a.secondary, t = p.getRowsByGrouping([...y, u, s]), r = p.getRowsByGrouping([...y, u, i]), k = b(
+          s,
+          i,
+          t,
+          r,
+          n.linkColumn,
+          S,
+          v,
+          n.aes.showOutliers,
+          $.scale
+        );
+        h = Math.min(h, k.boundsY.min), c = Math.max(c, k.boundsY.max), l[d].push(k);
+      });
+      return l;
+    }, {}),
+    meta: { minY: h, maxY: c },
+    aes: n.aes
+  };
+}
+export {
+  R as getPairedPointsData
+};
+//# sourceMappingURL=pairedPoints.js.map

package/dist/node_modules/@milaboratories/miplots4/dist/discrete/layers/pairedPoints.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"pairedPoints.js","sources":["../../../../../../../node_modules/@milaboratories/miplots4/src/discrete/layers/pairedPoints.ts"],"sourcesContent":["import type {GroupKey} from '../../DataFrame';\nimport type {DataFrame} from '../../DataFrame';\nimport type {DiscreteSettingsImpl} from '../DiscreteSettingsImpl';\nimport type {PairedPointsLayer} from '../DiscreteSettingsImpl';\nimport type {PairedPointsData} from './types';\nimport {getOutliersBounds} from '../utils';\nimport {getFacetStringKey} from '../utils/getFacetStringKey';\nimport type {ColumnName, Row} from '../../types';\nimport lodash from 'lodash';\n\ntype Point = {\n    id: string;\n    value: number;\n    data: Row;\n};\n\nexport type PairedPoints = {\n    id: string;\n    key1: string;\n    key2: string;\n    grouping: 'primary' | 'secondary';\n    pairs: {key1: Point; key2: Point; id: string}[];\n    boundsY: {\n        min: number;\n        max: number;\n    };\n};\n\nfunction getGroupingType(primaryKeys: GroupKey[], secondaryKeys: GroupKey[]) {\n    if (secondaryKeys.length === 2) {\n        return 'secondary';\n    }\n    if (primaryKeys.length === 2 && secondaryKeys.length < 2) {\n        return 'primary';\n    }\n    throw Error('Too many groups for paired points layer');\n}\n\nfunction getPairedGroup(\n    key1: GroupKey,\n    key2: GroupKey,\n    rowsGroup1: Row[],\n    rowsGroup2: Row[],\n    linkColumn: ColumnName,\n    yColumn: ColumnName,\n    grouping: 'primary' | 'secondary',\n    showOutliers: boolean,\n    scale: 'linear' | 'log'\n): PairedPoints {\n    const group1 = lodash.groupBy(rowsGroup1, row => row[linkColumn.value]);\n    const group2 = lodash.groupBy(rowsGroup2, row => row[linkColumn.value]);\n    const pointKeys1 = Object.keys(group1);\n    const pointKeys2 = Object.keys(group2);\n    // Sets of point ids from group 1 and group 2 must be the same and must contain unique ids\n    if (lodash.uniq(pointKeys1).length !== pointKeys1.length || lodash.uniq(pointKeys2).length !== pointKeys2.length) {\n        throw Error(`Non unique keys in groups ${String(key1)}, ${String(key2)} for paired points layer`);\n    }\n    if (\n        pointKeys1.length !== pointKeys2.length ||\n        lodash.intersection(pointKeys1, pointKeys2).length !== pointKeys1.length\n    ) {\n        throw Error(`Keys in groups ${String(key1)}, ${String(key2)} not match for paired points layer`);\n    }\n\n    const yGetter = (row: Row) => Number(row[yColumn.value]);\n    let min = Infinity;\n    let max = -Infinity;\n    let hasZero = false;\n    const isLog = scale === 'log';\n    let pairs = pointKeys1.map(pairKey => {\n        const p1 = group1[pairKey][0];\n        const p2 = group2[pairKey][0];\n        const v1 = yGetter(p1);\n        const v2 = yGetter(p2);\n        if (v1 === 0 || v2 === 0) {\n            hasZero = true;\n        }\n        min = Math.min(min, isLog && v1 === 0 ? Infinity : v1, isLog && v2 === 0 ? Infinity : v2);\n        max = Math.max(max, isLog && v1 === 0 ? -Infinity : v1, isLog && v2 === 0 ? -Infinity : v2);\n        return {\n            id: pairKey,\n            key1: {id: `${pairKey}_${String(key1)}`, value: v1, data: p1},\n            key2: {id: `${pairKey}_${String(key2)}`, value: v2, data: p2},\n        };\n    });\n    if (!showOutliers) {\n        min = Infinity;\n        max = -Infinity;\n        const [boundsMin1, boundMax1] = getOutliersBounds(rowsGroup1, scale, yGetter);\n        const [boundsMin2, boundMax2] = getOutliersBounds(rowsGroup2, scale, yGetter);\n        pairs = pairs.filter(({key1, key2}) => {\n            const outlier =\n                key1.value < boundsMin1 || key1.value > boundMax1 || key2.value < boundsMin2 || key2.value > boundMax2;\n            if (outlier) {\n                return false;\n            }\n            min = Math.min(min, isLog && key1.value === 0 ? Infinity : key1.value, isLog && key2.value === 0 ? Infinity : key2.value);\n            max = Math.max(max, isLog && key1.value === 0 ? -Infinity : key1.value, isLog && key2.value === 0 ? -Infinity : key2.value);\n            return true;\n        });\n    }\n    min = hasZero ? min / 10 : min;\n    max = Math.max(max, min);\n    return {\n        id: `${String(key1)}_${String(key2)}`,\n        key1: String(key1),\n        key2: String(key2),\n        pairs: pairs.map(pair => ({\n            ...pair,\n            key1: {...pair.key1, value: pair.key1.value === 0 ? min : pair.key1.value},\n            key2: {...pair.key2, value: pair.key2.value === 0 ? min : pair.key2.value},\n        })),\n        grouping,\n        boundsY: {min, max},\n    };\n}\n\nexport function getPairedPointsData(\n    layer: PairedPointsLayer,\n    groupingKeys: {\n        facet: GroupKey[][],\n        primary: GroupKey[],\n        secondary: GroupKey[]\n    },\n    data: DataFrame,\n    y: ColumnName,\n    yAxis: DiscreteSettingsImpl['chartSettings']['yAxis']\n): PairedPointsData {\n    const grouping = getGroupingType(groupingKeys.primary, groupingKeys.secondary);\n    let minY = Infinity;\n    let maxY = -Infinity;\n\n    return {\n        type: 'pairedPoints',\n        geoms: groupingKeys.facet.reduce((res: Record<string, PairedPoints[]>, facetKey) => {\n            const strFacetKey = getFacetStringKey(facetKey);\n            res[strFacetKey] = [];\n            if (grouping === 'primary') {\n                const [key1, key2] = groupingKeys.primary;\n                const group1 = data.getRowsByGrouping([...facetKey, key1]);\n                const group2 = data.getRowsByGrouping([...facetKey, key2]);\n                const pairedPointsGroup = getPairedGroup(\n                    key1,\n                    key2,\n                    group1,\n                    group2,\n                    layer.linkColumn,\n                    y,\n                    grouping,\n                    layer.aes.showOutliers,\n                    yAxis.scale\n                );\n                minY = Math.min(minY, pairedPointsGroup.boundsY.min);\n                maxY = Math.max(maxY, pairedPointsGroup.boundsY.max);\n                res[strFacetKey].push(pairedPointsGroup);\n            } else if (grouping === 'secondary') {\n                groupingKeys.primary.forEach(primaryKey => {\n                    const [key1, key2] = groupingKeys.secondary;\n                    const group1 = data.getRowsByGrouping([...facetKey, primaryKey, key1]);\n                    const group2 = data.getRowsByGrouping([...facetKey, primaryKey, key2]);\n                    const pairedPointsGroup = getPairedGroup(\n                        key1,\n                        key2,\n                        group1,\n                        group2,\n                        layer.linkColumn,\n                        y,\n                        grouping,\n                        layer.aes.showOutliers,\n                        yAxis.scale\n                    );\n                    minY = Math.min(minY, pairedPointsGroup.boundsY.min);\n                    maxY = Math.max(maxY, pairedPointsGroup.boundsY.max);\n                    res[strFacetKey].push(pairedPointsGroup);\n                });\n            }\n            return res;\n        }, {}),\n        meta: {minY, maxY},\n        aes: layer.aes,\n    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package/dist/node_modules/@milaboratories/miplots4/dist/discrete/layers/sina.js

@@ -0,0 +1,96 @@
+import { getOutliersBounds as D } from "../utils/getOutliersBounds.js";
+import { getFacetStringKey as G } from "../utils/getFacetStringKey.js";
+import E from "../../node_modules/lodash/lodash.js";
+import O from "../../node_modules/d3-random/src/lcg.js";
+import q from "../../node_modules/d3-scale/src/linear.js";
+import N from "../../node_modules/d3-array/src/max.js";
+import { quantileSorted as v } from "../../node_modules/d3-array/src/quantile.js";
+import Y from "../../node_modules/d3-array/src/mean.js";
+var P = Object.defineProperty, j = (t, r, o) => r in t ? P(t, r, { enumerable: !0, configurable: !0, writable: !0, value: o }) : t[r] = o, g = (t, r, o) => j(t, typeof r != "symbol" ? r + "" : r, o);
+const k = 30;
+function B(t, r) {
+  return function(o) {
+    return r.map(function(e) {
+      return Y(o, (m) => t(e - m));
+    });
+  };
+}
+function I(t) {
+  return function(r) {
+    return 1 / Math.sqrt(2 * Math.PI) * Math.pow(Math.E, -0.5 * Math.pow(r / t, 2));
+  };
+}
+function R(t) {
+  const r = Y(t);
+  return Y(t.map((o) => Math.pow(o - r, 2)));
+}
+function U(t) {
+  return Math.sqrt(R(t));
+}
+function _(t) {
+  const r = v(t, 0.25), o = (v(t, 0.75) - r) / 1.34, e = U(t);
+  return 1.06 * Math.min(e, o) * Math.pow(t.length, -1 / 5);
+}
+class $ {
+  constructor(r, o, e, m, y, d) {
+    g(this, "key"), g(this, "maxDensity"), g(this, "primaryGrouping"), g(this, "secondaryGrouping"), g(this, "points"), g(this, "boundsY");
+    const b = k;
+    if (r.length === 0)
+      throw Error("Unable to calculate sina on empty data");
+    this.primaryGrouping = String(m), this.secondaryGrouping = String(y), this.key = `sina_${this.primaryGrouping}_${this.secondaryGrouping}`;
+    const c = (n) => e === "log" ? Math.log10(n) : n, l = (n) => e === "log" ? Math.pow(10, n) : n, a = (n) => Number(n[o.value]), p = r.filter((n) => e === "log" && a(n) === 0 ? (console.warn("Value = 0 on chart with log scale, it was removed from calculation"), !1) : !0).sort((n, f) => c(a(n)) - c(a(f))), u = p.map((n) => c(a(n))), h = u[0], s = u[p.length - 1], x = (s - h) / b, i = _(u), w = E.range(h + x, s, x);
+    this.boundsY = {
+      min: l(h),
+      max: l(s)
+    };
+    const M = B(I(i), w)(u), S = q().domain(w).range(M).clamp(!0);
+    this.maxDensity = N(M), this.points = p.map((n, f) => ({
+      x: a(n),
+      y: S(c(a(n))) / this.maxDensity,
+      id: String(f),
+      jitter: d(),
+      data: n
+    }));
+  }
+}
+function J(t, r, o, e, m) {
+  let y = 0, d = 1 / 0, b = -1 / 0;
+  const c = O(1);
+  return {
+    type: "sina",
+    geoms: r.facet.reduce((l, a) => {
+      const p = G(a);
+      return l[p] = [], r.primary.forEach((u) => {
+        r.secondary.forEach((h) => {
+          const s = o.getRowsByGrouping([...a, u, h]);
+          if (!s.length)
+            return;
+          let x = s;
+          if (!t.aes.showOutliers) {
+            const w = (n) => Number(n[e.value]), [M, S] = D(s, m.scale, w);
+            x = s.filter((n) => {
+              const f = w(n);
+              return f >= M && f <= S;
+            });
+          }
+          const i = new $(
+            x,
+            e,
+            m.scale,
+            u,
+            h,
+            c
+          );
+          i.maxDensity > y && (y = i.maxDensity), i.boundsY.min < d && (d = i.boundsY.min), i.boundsY.max > b && (b = i.boundsY.max), l[p].push(i);
+        });
+      }), l;
+    }, {}),
+    meta: { maxDensity: y, minY: d, maxY: b },
+    aes: t.aes
+  };
+}
+export {
+  $ as Sina,
+  J as getSinaData
+};
+//# sourceMappingURL=sina.js.map

package/dist/node_modules/@milaboratories/miplots4/dist/discrete/layers/sina.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"sina.js","sources":["../../../../../../../node_modules/@milaboratories/miplots4/src/discrete/layers/sina.ts"],"sourcesContent":["import type {GroupKey, NO_GROUPED} from '../../DataFrame';\nimport type {DataFrame} from '../../DataFrame';\nimport type {DiscreteSettingsImpl, SinaLayer} from '../DiscreteSettingsImpl';\nimport type {SinaData} from './types';\nimport {getOutliersBounds} from '../utils';\nimport {getFacetStringKey} from '../utils/getFacetStringKey';\nimport type {ColumnName, DataValue, Row} from '../../types';\nimport {max, mean, quantileSorted} from 'd3-array';\nimport {randomLcg} from 'd3-random';\nimport {scaleLinear} from 'd3-scale';\nimport lodash from 'lodash';\n\nconst DEFAULT_STEPS_COUNT = 30;\n\nfunction kernelDensityEstimator(kernel: (v: number) => number, thresholds: number[]) {\n    return function (arr: number[]) {\n        return thresholds.map(function (x):number {\n            return mean(arr, v => kernel(x - v)) as number;\n        });\n    };\n}\n\nfunction kernelGaussian(bandwidth: number) {\n    return function (v: number) {\n        return (1 / Math.sqrt(2 * Math.PI)) * Math.pow(Math.E, -0.5 * Math.pow(v / bandwidth, 2));\n    };\n}\n\nfunction getVariance(arr: number[]) {\n    const vMean = mean(arr) as number;\n\n    return mean(arr.map(v => Math.pow(v - vMean, 2))) as number;\n}\nfunction getStandardDeviation(arr: number[]) {\n    return Math.sqrt(getVariance(arr));\n}\nfunction nrdBandwidth(arr: number[]) {\n    const q1 = quantileSorted(arr, 0.25) as number;\n    const q3 = quantileSorted(arr, 0.75) as number;\n    const iqr = q3 - q1;\n    const h = iqr / 1.34;\n    const sigma = getStandardDeviation(arr);\n\n    return 1.06 * Math.min(sigma, h) * Math.pow(arr.length, -1 / 5);\n}\n\nexport class Sina {\n    key: string;\n    maxDensity: number;\n    primaryGrouping: string;\n    secondaryGrouping: string;\n\n    points: {x: number, y: number, jitter: number, id: string, data: Row}[];\n\n    boundsY: {\n        min: number;\n        max: number;\n    };\n\n    constructor(\n        rowValues: Row[],\n        y:ColumnName,\n        scale: 'linear' | 'log',\n        primaryGrouping: DataValue | typeof NO_GROUPED,\n        secondaryGrouping: DataValue | typeof NO_GROUPED,\n        getJitter: () => number\n    ) {\n        const stepsCount = DEFAULT_STEPS_COUNT;\n        if (rowValues.length === 0) {\n            throw Error('Unable to calculate sina on empty data');\n        }\n\n        this.primaryGrouping = String(primaryGrouping);\n        this.secondaryGrouping = String(secondaryGrouping);\n        this.key = `sina_${this.primaryGrouping}_${this.secondaryGrouping}`;\n\n        const convertToScale = (v: number) => (scale === 'log' ? Math.log10(v) : v);\n        const convertFromScale = (v: number) => (scale === 'log' ? Math.pow(10, v) : v);\n        const getterY = (r:Row) => Number(r[y.value]);\n\n        const sortedGroup = rowValues\n            .filter((r:Row) => {\n                if (scale === 'log' && getterY(r) === 0) {\n                    console.warn('Value = 0 on chart with log scale, it was removed from calculation');\n                    return false;\n                }\n                return true;\n            })\n            .sort((a, b) => convertToScale(getterY(a)) - convertToScale(getterY(b)));\n        const sortedValues = sortedGroup.map((r) => convertToScale(getterY(r)));\n        const minV = sortedValues[0];\n        const maxV = sortedValues[sortedGroup.length - 1];\n        const xRange = maxV - minV;\n        const step = xRange / stepsCount;\n        const bandwidth = nrdBandwidth(sortedValues);\n        const thresholds = lodash.range(minV + step, maxV, step);\n\n        this.boundsY = {\n            min: convertFromScale(minV),\n            max: convertFromScale(maxV),\n        };\n\n        const kde = kernelDensityEstimator(kernelGaussian(bandwidth), thresholds);\n        const density = kde(sortedValues);\n        const scaleY = scaleLinear().domain(thresholds).range(density).clamp(true);\n\n        this.maxDensity = max(density) as number;\n\n        this.points = sortedGroup.map((row:Row, idx) => {\n            return {\n                x: getterY(row),\n                y: scaleY(convertToScale(getterY(row))) / this.maxDensity,\n                id: String(idx),\n                jitter: getJitter(),\n                data: row\n            };\n        });\n    }\n}\n\nexport function getSinaData(\n    layer: SinaLayer,\n    groupingKeys: {\n        facet: GroupKey[][],\n        primary: GroupKey[],\n        secondary: GroupKey[]\n    },\n    data: DataFrame,\n    y: DiscreteSettingsImpl['y'],\n    yAxis: DiscreteSettingsImpl['chartSettings']['yAxis']\n): SinaData {\n    let maxDensity = 0;\n    let minY = Infinity;\n    let maxY = -Infinity;\n    const getJitter = randomLcg(1);\n\n    const geoms = groupingKeys.facet.reduce((res: Record<string, Sina[]>, facetKey) => {\n        const strFacetKey = getFacetStringKey(facetKey);\n        res[strFacetKey] = [];\n        groupingKeys.primary.forEach(primaryKey => {\n            groupingKeys.secondary.forEach(secondaryKey => {\n                const values = data.getRowsByGrouping([...facetKey, primaryKey, secondaryKey]);\n                if (!values.length) {\n                    return;\n                }\n                let valuesFiltered = values;\n                if (!layer.aes.showOutliers) {\n                    const yGetter = (r:Row) => Number(r[y.value]);\n                    const [boundsMin, boundMax] = getOutliersBounds(values, yAxis.scale, yGetter);\n                    valuesFiltered = values.filter((row: Row) => {\n                        const value = yGetter(row);\n                        return value >= boundsMin && value <= boundMax;\n                    });\n                }\n                const sina = new Sina(\n                    valuesFiltered,\n                    y,\n                    yAxis.scale,\n                    primaryKey,\n                    secondaryKey,\n                    getJitter\n                );\n\n                if (sina.maxDensity > maxDensity) {\n                    maxDensity = sina.maxDensity;\n                }\n                if (sina.boundsY.min < minY) {\n                    minY = sina.boundsY.min;\n                }\n                if (sina.boundsY.max > maxY) {\n                    maxY = sina.boundsY.max;\n                }\n                res[strFacetKey].push(sina);\n            });\n        });\n        return res;\n    }, {});\n\n    return {\n        type: 'sina',\n        geoms,\n        meta: {maxDensity, minY, maxY},\n        aes: layer.aes,\n    };\n}\n"],"names":["DEFAULT_STEPS_COUNT","kernelDensityEstimator","kernel","thresholds","arr","x","mean","v","kernelGaussian","bandwidth","getVariance","vMean","getStandardDeviation","nrdBandwidth","q1","quantileSorted","h","sigma","Sina","rowValues","y","scale","primaryGrouping","secondaryGrouping","getJitter","__publicField","stepsCount","convertToScale","convertFromScale","getterY","r","sortedGroup","a","b","sortedValues","minV","maxV","step","lodash","density","scaleY","scaleLinear","max","row","idx","getSinaData","layer","groupingKeys","data","yAxis","maxDensity","minY","maxY","randomLcg","res","facetKey","strFacetKey","getFacetStringKey","primaryKey","secondaryKey","values","valuesFiltered","yGetter","boundsMin","boundMax","getOutliersBounds","value","sina"],"mappings":";;;;;;;;;AAYA,MAAMA,IAAsB;AAE5B,SAASC,EAAuBC,GAA+BC,GAAsB;AACjF,SAAO,SAAUC,GAAe;AAC5B,WAAOD,EAAW,IAAI,SAAUE,GAAU;AACtC,aAAOC,EAAKF,GAAK,CAAAG,MAAKL,EAAOG,IAAIE,CAAC,CAAC;AAAA,IACvC,CAAC;AAAA,EACL;AACJ;AAEA,SAASC,EAAeC,GAAmB;AACvC,SAAO,SAAUF,GAAW;AACxB,WAAQ,IAAI,KAAK,KAAK,IAAI,KAAK,EAAE,IAAK,KAAK,IAAI,KAAK,GAAG,OAAO,KAAK,IAAIA,IAAIE,GAAW,CAAC,CAAC;AAAA,EAC5F;AACJ;AAEA,SAASC,EAAYN,GAAe;AAChC,QAAMO,IAAQL,EAAKF,CAAG;AAEtB,SAAOE,EAAKF,EAAI,IAAI,CAAAG,MAAK,KAAK,IAAIA,IAAII,GAAO,CAAC,CAAC,CAAC;AACpD;AACA,SAASC,EAAqBR,GAAe;AACzC,SAAO,KAAK,KAAKM,EAAYN,CAAG,CAAC;AACrC;AACA,SAASS,EAAaT,GAAe;AACjC,QAAMU,IAAKC,EAAeX,GAAK,IAAI,GAG7BY,KAFKD,EAAeX,GAAK,IAAI,IAClBU,KACD,MACVG,IAAQL,EAAqBR,CAAG;AAEtC,SAAO,OAAO,KAAK,IAAIa,GAAOD,CAAC,IAAI,KAAK,IAAIZ,EAAI,QAAQ,KAAK,CAAC;AAClE;AAEO,MAAMc,EAAK;AAAA,EAad,YACIC,GACAC,GACAC,GACAC,GACAC,GACAC,GACF;AAnBFC,IAAAA,EAAA,MAAA,KAAA,GACAA,EAAA,MAAA,YAAA,GACAA,EAAA,MAAA,iBAAA,GACAA,EAAA,MAAA,mBAAA,GAEAA,EAAA,MAAA,QAAA,GAEAA,EAAA,MAAA,SAAA;AAaI,UAAMC,IAAa1B;AACnB,QAAImB,EAAU,WAAW;AACrB,YAAM,MAAM,wCAAwC;AAGxD,SAAK,kBAAkB,OAAOG,CAAe,GAC7C,KAAK,oBAAoB,OAAOC,CAAiB,GACjD,KAAK,MAAM,QAAQ,KAAK,eAAe,IAAI,KAAK,iBAAiB;AAEjE,UAAMI,IAAiB,CAACpB,MAAec,MAAU,QAAQ,KAAK,MAAMd,CAAC,IAAIA,GACnEqB,IAAmB,CAACrB,MAAec,MAAU,QAAQ,KAAK,IAAI,IAAId,CAAC,IAAIA,GACvEsB,IAAU,CAACC,MAAU,OAAOA,EAAEV,EAAE,KAAK,CAAC,GAEtCW,IAAcZ,EACf,OAAO,CAACW,MACDT,MAAU,SAASQ,EAAQC,CAAC,MAAM,KAClC,QAAQ,KAAK,oEAAoE,GAC1E,MAEJ,EACV,EACA,KAAK,CAACE,GAAGC,MAAMN,EAAeE,EAAQG,CAAC,CAAC,IAAIL,EAAeE,EAAQI,CAAC,CAAC,CAAC,GACrEC,IAAeH,EAAY,IAAI,CAACD,MAAMH,EAAeE,EAAQC,CAAC,CAAC,CAAC,GAChEK,IAAOD,EAAa,CAAC,GACrBE,IAAOF,EAAaH,EAAY,SAAS,CAAC,GAE1CM,KADSD,IAAOD,KACAT,GAChBjB,IAAYI,EAAaqB,CAAY,GACrC/B,IAAamC,EAAO,MAAMH,IAAOE,GAAMD,GAAMC,CAAI;AAEvD,SAAK,UAAU;AAAA,MACX,KAAKT,EAAiBO,CAAI;AAAA,MAC1B,KAAKP,EAAiBQ,CAAI;AAAA,IAAA;AAI9B,UAAMG,IADMtC,EAAuBO,EAAeC,CAAS,GAAGN,CAAU,EACpD+B,CAAY,GAC1BM,IAASC,EAAAA,EAAc,OAAOtC,CAAU,EAAE,MAAMoC,CAAO,EAAE,MAAM,EAAI;AAEzE,SAAK,aAAaG,EAAIH,CAAO,GAE7B,KAAK,SAASR,EAAY,IAAI,CAACY,GAASC,OAC7B;AAAA,MACH,GAAGf,EAAQc,CAAG;AAAA,MACd,GAAGH,EAAOb,EAAeE,EAAQc,CAAG,CAAC,CAAC,IAAI,KAAK;AAAA,MAC/C,IAAI,OAAOC,CAAG;AAAA,MACd,QAAQpB,EAAAA;AAAAA,MACR,MAAMmB;AAAAA,IAAA,EAEb;AAAA,EACL;AACJ;AAEO,SAASE,EACZC,GACAC,GAKAC,GACA5B,GACA6B,GACQ;AACR,MAAIC,IAAa,GACbC,IAAO,OACPC,IAAO;AACX,QAAM5B,IAAY6B,EAAU,CAAC;AA4C7B,SAAO;AAAA,IACH,MAAM;AAAA,IACN,OA5CUN,EAAa,MAAM,OAAO,CAACO,GAA6BC,MAAa;AAC/E,YAAMC,IAAcC,EAAkBF,CAAQ;AAC9C,aAAAD,EAAIE,CAAW,IAAI,CAAA,GACnBT,EAAa,QAAQ,QAAQ,CAAAW,MAAc;AACvCX,QAAAA,EAAa,UAAU,QAAQ,CAAAY,MAAgB;AAC3C,gBAAMC,IAASZ,EAAK,kBAAkB,CAAC,GAAGO,GAAUG,GAAYC,CAAY,CAAC;AAC7E,cAAI,CAACC,EAAO;AACR;AAEJ,cAAIC,IAAiBD;AACrB,cAAI,CAACd,EAAM,IAAI,cAAc;AACzB,kBAAMgB,IAAU,CAAChC,MAAU,OAAOA,EAAEV,EAAE,KAAK,CAAC,GACtC,CAAC2C,GAAWC,CAAQ,IAAIC,EAAkBL,GAAQX,EAAM,OAAOa,CAAO;AAC5ED,gBAAiBD,EAAO,OAAO,CAACjB,MAAa;AACzC,oBAAMuB,IAAQJ,EAAQnB,CAAG;AACzB,qBAAOuB,KAASH,KAAaG,KAASF;AAAAA,YAC1C,CAAC;AAAA,UACL;AACA,gBAAMG,IAAO,IAAIjD;AAAAA,YACb2C;AAAAA,YACAzC;AAAAA,YACA6B,EAAM;AAAA,YACNS;AAAAA,YACAC;AAAAA,YACAnC;AAAAA,UAAA;AAGA2C,UAAAA,EAAK,aAAajB,MAClBA,IAAaiB,EAAK,aAElBA,EAAK,QAAQ,MAAMhB,MACnBA,IAAOgB,EAAK,QAAQ,MAEpBA,EAAK,QAAQ,MAAMf,MACnBA,IAAOe,EAAK,QAAQ,MAExBb,EAAIE,CAAW,EAAE,KAAKW,CAAI;AAAA,QAC9B,CAAC;AAAA,MACL,CAAC,GACMb;AAAAA,IACX,GAAG,CAAA,CAAE;AAAA,IAKD,MAAM,EAAC,YAAAJ,GAAY,MAAAC,GAAM,MAAAC,EAAAA;AAAAA,IACzB,KAAKN,EAAM;AAAA,EAAA;AAEnB;","x_google_ignoreList":[0]}

package/dist/node_modules/@milaboratories/miplots4/dist/discrete/layers/stackedBar.js

@@ -0,0 +1,44 @@
+import { NO_GROUPED as y } from "../../DataFrame.js";
+import { getFacetStringKey as x } from "../utils/getFacetStringKey.js";
+import E from "../../node_modules/d3-array/src/sum.js";
+function G(a, o, d, z) {
+  let m = -1 / 0, i = 1 / 0;
+  return {
+    type: "stackedBar",
+    geoms: o.facet.reduce((s, l) => {
+      const u = x(l);
+      return s[u] = [], o.primary.forEach((c) => {
+        let n = 0;
+        const t = {};
+        o.secondary.forEach((r) => {
+          const e = r === y ? "null" : r, p = d.getRowsByGrouping([...l, c, r]);
+          if (!p.length)
+            return;
+          const f = E(p, (k) => Number(k[z.value]));
+          t[e] = {
+            height: f,
+            key: String(e)
+          }, n += f;
+        });
+        const g = n;
+        a.normalize && o.secondary.forEach((r) => {
+          const e = r === y ? "null" : r;
+          t[e] && (t[e].height = t[e].height / g * 100);
+        }), m = Math.max(m, 0, n), i = Math.min(i, 0, n);
+        const h = a.normalize ? 100 : g;
+        s[u].push({
+          key: `stackedBar_${String(c)}`,
+          valuesMap: t,
+          primaryGrouping: c,
+          boundsY: { min: Math.min(h, 0), max: Math.max(h, 0) }
+        });
+      }), s;
+    }, {}),
+    meta: { minY: a.normalize ? 0 : i, maxY: a.normalize ? 100 : m, normalize: a.normalize },
+    aes: a.aes
+  };
+}
+export {
+  G as getStackedBarsData
+};
+//# sourceMappingURL=stackedBar.js.map

package/dist/node_modules/@milaboratories/miplots4/dist/discrete/layers/stackedBar.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"stackedBar.js","sources":["../../../../../../../node_modules/@milaboratories/miplots4/src/discrete/layers/stackedBar.ts"],"sourcesContent":["import type {DataFrame, GroupKey} from '../../DataFrame';\nimport {NO_GROUPED} from '../../DataFrame';\nimport type {StackedBarLayer} from '../DiscreteSettingsImpl';\nimport type {StackedBarsData} from './types';\nimport {getFacetStringKey} from '../utils/getFacetStringKey';\nimport type {ColumnName, Row} from '../../types';\nimport {sum} from 'd3-array';\n\ntype BarPart = {\n    height: number;\n    key: string;\n};\n\nexport type StackedBar = {\n    key: string;\n    valuesMap: Record<string, BarPart>;\n    primaryGrouping: string;\n    boundsY: {\n        min: number;\n        max: number;\n    };\n};\n\nexport function getStackedBarsData(\n    layer: StackedBarLayer,\n    groupingKeys: {\n        facet: GroupKey[][],\n        primary: GroupKey[],\n        secondary: GroupKey[]\n    },\n    data: DataFrame,\n    y: ColumnName,\n): StackedBarsData {\n    let maxY = -Infinity;\n    let minY = Infinity;\n\n    return {\n        type: 'stackedBar',\n        geoms: groupingKeys.facet.reduce((res: Record<string, StackedBar[]>, facetKey) => {\n            const strFacetKey = getFacetStringKey(facetKey);\n            res[strFacetKey] = [];\n            groupingKeys.primary.forEach(primaryKey => {\n                let currentHeight = 0;\n                const barParts:Record<string, BarPart> = {};\n                groupingKeys.secondary.forEach(secondaryKey => {\n                    const secondaryKeyStr = secondaryKey === NO_GROUPED ? 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package/dist/node_modules/@milaboratories/miplots4/dist/discrete/layers/stats/MannWhitneyU.js

@@ -0,0 +1,147 @@
+import f from "../../../node_modules/lodash/lodash.js";
+var m = Object.defineProperty, y = (h, t, n) => t in h ? m(h, t, { enumerable: !0, configurable: !0, writable: !0, value: n }) : h[t] = n, P = (h, t, n) => y(h, t + "", n);
+function b(h) {
+  const t = Math.abs(h), n = 1 / (1 + t / 2), e = n * Math.exp(-t * t - 1.26551223 + n * (1.00002368 + n * (0.37409196 + n * (0.09678418 + n * (-0.18628806 + n * (0.27886807 + n * (-1.13520398 + n * (1.48851587 + n * (-0.82215223 + n * 0.17087277)))))))));
+  return h >= 0 ? e : 2 - e;
+}
+function w(h) {
+  return 0.5 * b(-h / Math.sqrt(2));
+}
+class v {
+  constructor(t, n) {
+    this.value = t, this.position = n;
+  }
+  getValue() {
+    return this.value;
+  }
+  getPosition() {
+    return this.position;
+  }
+}
+function A(h) {
+  const t = new Array(h.length);
+  for (let s = 0; s < h.length; s++)
+    t[s] = new v(h[s], s);
+  const n = U(t);
+  t.sort((s, l) => s.getValue() - l.getValue());
+  const e = new Array(t.length);
+  let r = 1;
+  e[t[0].getPosition()] = r;
+  let o = [];
+  o.push(t[0].getPosition());
+  for (let s = 1; s < t.length; s++)
+    t[s].getValue() > t[s - 1].getValue() && (r = s + 1, o.length > 1 && p(e, o), o = []), o.push(t[s].getPosition()), e[t[s].getPosition()] = r;
+  return o.length > 1 && p(e, o), E(e, n), e;
+}
+function p(h, t) {
+  const n = (2 * h[t[0]] + t.length - 1) / 2;
+  t.forEach((e) => {
+    h[e] = n;
+  });
+}
+function E(h, t) {
+  t.forEach((n) => {
+    h[n] = NaN;
+  });
+}
+function U(h) {
+  const t = [];
+  for (let n = 0; n < h.length; n++)
+    isNaN(h[n].getValue()) && t.push(n);
+  return t;
+}
+class L {
+  constructor() {
+    P(this, "SMALL_SAMPLE_SIZE", 50);
+  }
+  mannWhitneyU(t, n) {
+    const e = [...t, ...n], r = A(e);
+    let o = 0;
+    for (let i = 0; i < t.length; i++)
+      o += r[i];
+    const s = o - t.length * (t.length + 1) / 2, l = t.length * n.length - s;
+    return Math.min(s, l);
+  }
+  mannWhitneyUTest(t, n, e) {
+    if (typeof e > "u")
+      return t.length + n.length <= this.SMALL_SAMPLE_SIZE && Object.keys(this.tiesMap(t, n)).length === 0 ? this.mannWhitneyUTest(t, n, !0) : this.mannWhitneyUTest(t, n, !1);
+    const r = this.tiesMap(t, n), o = this.mannWhitneyU(t, n);
+    if (e) {
+      if (Object.keys(r).length !== 0)
+        throw new Error();
+      return this.exactP(t.length, n.length, o);
+    }
+    return this.approximateP(
+      o,
+      t.length,
+      n.length,
+      this.varU(t.length, n.length, r)
+    );
+  }
+  approximateP(t, n, e, r) {
+    const o = n * e / 2;
+    if (o == t)
+      return 1;
+    const s = -Math.abs(t - o + 0.5) / Math.sqrt(r);
+    return 2 * w(s);
+  }
+  exactP(t, n, e) {
+    const r = n * t;
+    if (e > r)
+      return 1;
+    const o = e < r / 2 ? e : r / 2 - e;
+    let s = 0, l = 0;
+    for (; l <= o; )
+      s += this.uDensity(t, n, l), l++;
+    return 2 * s;
+  }
+  uDensity(t, n, e) {
+    if (e < 0 || e > n * t)
+      return 0;
+    const r = this.uFrequencies(t, n);
+    return r[Math.round(e + 1)] / f.sum(r);
+  }
+  uFrequencies(t, n) {
+    const e = Math.max(n, t);
+    if (e > 100)
+      throw Error("n or m > 100");
+    const r = Math.min(n, t), o = new Array(t * n + 2), s = new Array(t * n + 2);
+    for (let i = 1; i < o.length; i++)
+      o[i] = i <= e + 1 ? 1 : 0;
+    s[1] = 0;
+    let l = e;
+    for (let i = 2; i <= r; i++) {
+      s[i] = 0, l = l + e;
+      let u = l + 2;
+      const M = 1 + l / 2;
+      let g = i;
+      for (let a = 1; a <= M; a++) {
+        g++, u = u - 1;
+        const c = o[a] + s[a];
+        o[a] = c, s[g] = c - o[u], o[u] = c;
+      }
+    }
+    return o;
+  }
+  varU(t, n, e) {
+    const r = t * n;
+    if (Object.keys(e).length === 0)
+      return r * (t + n + 1) / 12;
+    const o = f.sum(Object.values(e).map((l) => l * l * l - l)), s = t + n;
+    return r / 12 * (s + 1 - o / (s * (s - 1)));
+  }
+  tiesMap(t, n) {
+    const e = {};
+    for (let r = 0; r < t.length; r++)
+      e[t[r]] = e[t[r]] ? e[t[r]] + 1 : 1;
+    for (let r = 0; r < n.length; r++)
+      e[n[r]] = e[n[r]] ? e[n[r]] + 1 : 1;
+    for (const r in e)
+      e[r] === 1 && delete e[r];
+    return e;
+  }
+}
+export {
+  L as MannWhitneyU
+};
+//# sourceMappingURL=MannWhitneyU.js.map

package/dist/node_modules/@milaboratories/miplots4/dist/discrete/layers/stats/MannWhitneyU.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"MannWhitneyU.js","sources":["../../../../../../../../node_modules/@milaboratories/miplots4/src/discrete/layers/stats/MannWhitneyU.ts"],"sourcesContent":["import lodash from 'lodash';\n\n// Normal distribution - complementary error function\n// https://en.wikipedia.org/wiki/Error_function#Complementary_error_function\n// https://github.com/errcw/gaussian/blob/master/lib/gaussian.js#L5\nfunction erfc(x:number):number {\n    const z = Math.abs(x);\n    const t = 1 / (1 + z / 2);\n    const r = t * Math.exp(-z * z - 1.26551223 + t * (1.00002368 +\n        t * (0.37409196 + t * (0.09678418 + t * (-0.18628806 +\n            t * (0.27886807 + t * (-1.13520398 + t * (1.48851587 +\n                t * (-0.82215223 + t * 0.17087277)))))))));\n    return x >= 0 ? r : 2 - r;\n}\n// Normal distribution - cumulative probability, for mean = 0, standardDeviation = 1\n// https://github.com/errcw/gaussian/blob/master/lib/gaussian.js#L54\nfunction standardNormalCumulativeProbability (x:number):number {\n    return 0.5 * erfc(-x / (Math.sqrt(2)));\n}\n\n// Natural ranking\n// https://github.com/apache/commons-math/blob/ece74cff78ae7858827f1913bb63854601d88c06/commons-math-legacy/src/main/java/org/apache/commons/math4/legacy/stat/ranking/NaturalRanking.java#L195\nclass IntDoublePair {\n    constructor(private value:number, private position:number) {}\n    public getValue() {\n        return this.value;\n    }\n    public getPosition() {\n        return this.position;\n    }\n}\n// with NaNStrategy.FIXED, TiesStrategy.AVERAGE https://github.com/milaboratory/miplots/blob/559b13065f17dfc7c4dd332247dd1ce0183affcc/src/main/kotlin/com/milaboratory/miplots/stat/util/MannWhitneyU.kt#L36\nfunction rank(data:number[]) {\n    // Array recording initial positions of data to be ranked\n    const ranks:IntDoublePair[] = new Array(data.length);\n    for (let i = 0; i < data.length; i++) {\n        ranks[i] = new IntDoublePair(data[i], i);\n    }\n\n    // Recode, remove or record positions of NaNs\n    const nanPositions = getNanPositions(ranks);\n    // Sort the IntDoublePairs\n    ranks.sort((a, b) => a.getValue() - b.getValue());\n\n    // Walk the sorted array, filling output array using sorted positions,\n    // resolving ties as we go\n    const out:number[] = new Array(ranks.length);\n    let pos = 1;  // position in sorted array\n    out[ranks[0].getPosition()] = pos;\n    let tiesTrace = [];\n    tiesTrace.push(ranks[0].getPosition());\n\n    for (let i = 1; i < ranks.length; i++) {\n        if (ranks[i].getValue() > ranks[i - 1].getValue()) {\n            // tie sequence has ended (or had length 1)\n            pos = i + 1;\n            if (tiesTrace.length > 1) {  // if seq is nontrivial, resolve\n                resolveTie(out, tiesTrace);\n            }\n            tiesTrace = [];\n            tiesTrace.push(ranks[i].getPosition());\n        } else {\n            // tie sequence continues\n            tiesTrace.push(ranks[i].getPosition());\n        }\n        out[ranks[i].getPosition()] = pos;\n    }\n\n    if (tiesTrace.length > 1) {  // handle tie sequence at end\n        resolveTie(out, tiesTrace);\n    }\n    restoreNaNs(out, nanPositions);\n    return out;\n}\n\nfunction resolveTie(ranks:number[], tiesTrace:number[]) {\n    // constant value of ranks over tiesTrace\n    const c = ranks[tiesTrace[0]];\n    const value = (2 * c + tiesTrace.length - 1) / 2;\n\n    tiesTrace.forEach((trace) => {\n        ranks[trace] = value;\n    });\n}\n\nfunction restoreNaNs(ranks:number[], nanPositions:number[]) {\n    nanPositions.forEach((position) => {\n        ranks[position] = NaN;\n    });\n}\n\nfunction getNanPositions(ranks:IntDoublePair[] ) {\n    const out = [];\n    for (let i = 0; i < ranks.length; i++) {\n        if (isNaN(ranks[i].getValue())){\n            out.push(i);\n        }\n    }\n    return out;\n}\n\n// https://github.com/milaboratory/miplots/blob/559b13065f17dfc7c4dd332247dd1ce0183affcc/src/main/kotlin/com/milaboratory/miplots/stat/util/MannWhitneyU.kt#L36\nexport class MannWhitneyU {\n    SMALL_SAMPLE_SIZE = 50;\n\n    mannWhitneyU (x: number[], y: number[]): number {\n        const z = [...x, ...y];\n        const ranks = rank(z);\n        let sumRankX = 0;\n\n        /*\n         * The ranks for x is in the first x.length entries in ranks because x\n         * is in the first x.length entries in z\n         */for (let i = 0; i < x.length; i++) {\n            sumRankX += ranks[i];\n        }\n\n        /*\n         * U1 = R1 - (n1 * (n1 + 1)) / 2 where R1 is sum of ranks for sample 1,\n         * e.g. x, n1 is the number of observations in sample 1.\n         */\n        const U1 = sumRankX - x.length * (x.length + 1) / 2;\n\n        /*\n         * U1 + U2 = n1 * n2\n         */\n        const U2 = x.length * y.length - U1;\n        return Math.min(U1, U2);\n    }\n\n    mannWhitneyUTest(x: number[], y: number[], exact?:boolean): number {\n        if (typeof exact === 'undefined') {\n            // If samples are both small and there are no ties, perform exact test\n            if (x.length + y.length <= this.SMALL_SAMPLE_SIZE && Object.keys(this.tiesMap(x, y)).length === 0) {\n                return this.mannWhitneyUTest(x, y, true);\n            }\n            // Normal approximation\n            return this.mannWhitneyUTest(x, y, false);\n        }\n\n        const tiesMap = this.tiesMap(x, y);\n        const u = this.mannWhitneyU(x, y);\n        if (exact) {\n            if (Object.keys(tiesMap).length !== 0) {\n                throw new Error();\n            }\n            return this.exactP(x.length, y.length, u);\n        }\n        return this.approximateP(\n            u, x.length, y.length,\n            this.varU(x.length, y.length, tiesMap)\n        );\n    }\n\n    approximateP(u: number, n1: number, n2: number, varU: number): number {\n        const mu = n1 * n2 / 2;\n\n        // If u == mu, return 1\n        if (mu == u) {\n            return 1.0;\n        }\n\n        // Force z <= 0 so we get tail probability. Also apply continuity\n        // correction\n        const z = -Math.abs(u - mu + 0.5) / Math.sqrt(varU);\n        return 2 * standardNormalCumulativeProbability(z);\n    }\n\n    exactP(n: number, m: number, u: number): number {\n        const nm = m * n;\n        if (u > nm) { // Quick exit if u is out of range\n            return 1.0;\n        }\n        // Need to convert u to a mean deviation, so cumulative probability is\n        // tail probability\n        const crit = (u < nm / 2) ? u : nm / 2 - u;\n        let cum = 0;\n        let ct = 0;\n        while (ct <= crit) {\n            cum += this.uDensity(n, m, ct);\n            ct++;\n        }\n        return 2 * cum;\n    }\n\n    uDensity(n: number, m: number, u: number): number {\n        if (u < 0 || u > m * n) {\n            return 0;\n        }\n        const freq = this.uFrequencies(n, m);\n        return freq[Math.round(u + 1)] / lodash.sum(freq);\n    }\n\n    uFrequencies(n: number, m: number): number[] {\n        const max = Math.max(m, n);\n        if (max > 100) {\n            throw Error('n or m > 100');\n        }\n        const min = Math.min(m, n);\n        const out = new Array(n * m + 2);\n        const work = new Array(n * m + 2);\n        for (let i = 1; i < out.length; i++) {\n            out[i] = (i <= max + 1) ? 1 : 0;\n        }\n        work[1] = 0;\n        let in_ = max;\n        for (let i = 2; i <= min; i++) {\n            work[i] = 0;\n            in_ = in_ + max;\n            let n1 = in_ + 2;\n            const l = (1 + in_ / 2);\n            let k = i;\n            for (let j = 1; j <= l; j++) {\n                k++;\n                n1 = n1 - 1;\n                const sum_ = out[j] + work[j];\n                out[j] = sum_;\n                work[k] = sum_ - out[n1];\n                out[n1] = sum_;\n            }\n        }\n        return out;\n    }\n\n    varU(n: number, m: number, tiesMap: Record<number, number>): number {\n        const nm = n * m;\n        if (Object.keys(tiesMap).length === 0) {\n            return nm * (n + m + 1) / 12.0;\n        }\n        const tSum = lodash.sum(Object.values(tiesMap).map(( value) => value * value * value - value));\n        const totalN = n + m;\n        return nm / 12 * (totalN + 1 - tSum / (totalN * (totalN - 1)));\n    }\n\n    tiesMap(x: number[], y: number[]): Record<number, number> {\n        const tiesMap: Record<number, number> = {};\n        for (let i = 0; i < x.length; i++) {\n            tiesMap[x[i]] = tiesMap[x[i]] ? tiesMap[x[i]] + 1 : 1;\n        }\n        for (let i = 0; i < y.length; i++) {\n            tiesMap[y[i]] = tiesMap[y[i]] ? tiesMap[y[i]] + 1 : 1;\n        }\n        for (const key in tiesMap) {\n            if (tiesMap[key] === 1) {\n                delete tiesMap[key];\n            }\n        }\n        return tiesMap;\n    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package/dist/node_modules/@milaboratories/miplots4/dist/discrete/layers/stats/index.js

@@ -0,0 +1,84 @@
+import { NO_GROUPED as m } from "../../../DataFrame.js";
+import { calculatePValue as p } from "./pValueCalculation.js";
+import { adjustPValues as h } from "./pValueCorrection.js";
+import { getFacetStringKey as v } from "../../utils/getFacetStringKey.js";
+function y(t) {
+  return t.slice(0, -1).reduce(
+    (g, l, a) => g.concat(t.slice(a + 1).map((s) => [l, s])),
+    []
+  );
+}
+function w(t, g, l, a, s) {
+  return {
+    type: "stats",
+    values: g.reduce((f, i) => {
+      let u = [];
+      switch (t.statType) {
+        case "overall": {
+          const r = l.map((e) => s.getColumnByGrouping([...i, e], a.value)).filter((e) => e.length > 0);
+          if (r.length < 2)
+            break;
+          const c = p(r, t.testMethod, t.paired);
+          u = [[["overall"], c]];
+          break;
+        }
+        case "referenceGroup": {
+          const r = t.referenceGroup === null ? m : String(t.referenceGroup);
+          if (r !== m && !l.includes(r))
+            throw new Error(`Reference group ${String(r)} for ${t.testMethod} test is not in available groups`);
+          const c = s.getColumnByGrouping([...i, r], a.value);
+          if (c.length === 0) {
+            u = [];
+            break;
+          }
+          const e = l.filter((n) => n !== r).map((n) => [n, s.getColumnByGrouping([...i, n], a.value)]).filter(([, n]) => n.length > 0);
+          if (e.length < 2 && t.correctionMethod !== null)
+            break;
+          const o = h(
+            e.map(
+              ([, n]) => p(
+                [c, n],
+                t.testMethod,
+                t.paired
+              )
+            ),
+            t.correctionMethod
+          );
+          u = e.map(([n], d) => [[n], o[d]]);
+          break;
+        }
+        case "pairwise": {
+          const r = y(l).map(([e, o]) => [
+            [e, o],
+            [
+              s.getColumnByGrouping([...i, e], a.value),
+              s.getColumnByGrouping([...i, o], a.value)
+            ]
+          ]).filter(([, [e, o]]) => e.length && o.length);
+          if (r.length < 1)
+            break;
+          const c = h(
+            r.map(([, e]) => p(e, t.testMethod, t.paired)),
+            t.correctionMethod
+          );
+          u = r.map(([e], o) => [e, c[o]]);
+          break;
+        }
+        default:
+          throw new Error("Unknown statType");
+      }
+      return f[v(i)] = u, f;
+    }, {}),
+    meta: {
+      statType: t.statType,
+      testMethod: t.testMethod,
+      format: t.format,
+      ns: t.ns,
+      significanceLevels: t.significanceLevels
+    }
+  };
+}
+export {
+  w as getStatsData
+};
+//# sourceMappingURL=index.js.map

package/dist/node_modules/@milaboratories/miplots4/dist/discrete/layers/stats/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sources":["../../../../../../../../node_modules/@milaboratories/miplots4/src/discrete/layers/stats/index.ts"],"sourcesContent":["import type {DataFrame, GroupKey} from '../../../DataFrame';\nimport {NO_GROUPED} from '../../../DataFrame';\nimport type {DiscreteSettingsImpl, StatLayer} from '../../DiscreteSettingsImpl';\nimport {calculatePValue} from './pValueCalculation';\nimport {adjustPValues} from './pValueCorrection';\nimport type {StatsData} from '../types';\nimport {getFacetStringKey} from '../../utils/getFacetStringKey';\n\n// all available pairs of unequal keys from array of keys\nfunction getAllKeyPairs (keys:GroupKey[]) {\n    return keys\n        .slice(0,-1)\n        .reduce(\n            (res: [GroupKey, GroupKey][], key1, index) =>\n                res.concat(keys.slice(index + 1).map(key2 => [key1, key2])),\n            []\n        );\n}\n\nexport function getStatsData(\n    layer: StatLayer,\n    facetKeys: GroupKey[][],\n    primaryKeys: GroupKey[],\n    y: DiscreteSettingsImpl['y'],\n    data: DataFrame\n): StatsData {\n    return {\n        type: 'stats',\n        values: facetKeys.reduce((res: StatsData['values'], facetKey) => {\n            let values: [string[], number][] = [];\n            switch (layer.statType) {\n                case 'overall': {\n                    const groups = primaryKeys\n                        .map(primaryKey => data.getColumnByGrouping([...facetKey, primaryKey], y.value))\n                        .filter((group) => group.length > 0);\n                    if (groups.length < 2) {\n                        break;\n                    }\n                    const pValue = calculatePValue(groups, layer.testMethod, layer.paired);\n                    values = [[['overall'], pValue]];\n                    break;\n                }\n                case 'referenceGroup': {\n                    const referenceKey = layer.referenceGroup === null ? NO_GROUPED : String(layer.referenceGroup);\n                    if (referenceKey !== NO_GROUPED && !primaryKeys.includes(referenceKey)) {\n                        throw new Error(`Reference group ${String(referenceKey)} for ${layer.testMethod} test is not in available groups`);\n                    }\n                    const referenceGroup = data.getColumnByGrouping([...facetKey, referenceKey], y.value);\n                    if (referenceGroup.length === 0) {\n                        values = [];\n                        break;\n                    }\n\n                    const keys = primaryKeys.filter(key => key !== referenceKey);\n                    const keysAndGroupsNonEmpty:[string, number[]][] = keys\n                        .map(primaryKey => [primaryKey, data.getColumnByGrouping([...facetKey, primaryKey], y.value)] as [string, number[]])\n                        .filter(([, group]) => group.length > 0);\n                    if (keysAndGroupsNonEmpty.length < 2 && layer.correctionMethod !== null) {\n                        break;\n                    }\n                    const pValues = adjustPValues(\n                        keysAndGroupsNonEmpty.map(([,group]) =>\n                            calculatePValue(\n                                [referenceGroup, group],\n                                layer.testMethod,\n                                layer.paired\n                            )\n                        ),\n                        layer.correctionMethod\n                    );\n                    values = keysAndGroupsNonEmpty.map(([primaryKey], index) => [[primaryKey], pValues[index]]);\n                    break;\n                }\n                case 'pairwise': {\n                    const keysPairs = getAllKeyPairs(primaryKeys);\n                    const keysAndGroupsNonEmpty:[string[], number[][]][] = keysPairs\n                        .map(([key1, key2]) => [\n                            [key1, key2],\n                            [\n                                data.getColumnByGrouping([...facetKey, key1], y.value),\n                                data.getColumnByGrouping([...facetKey, key2], y.value)\n                            ]\n                        ] as [string[], number[][]])\n                        .filter(([,[gr1, gr2]]) => gr1.length && gr2.length);\n\n                    if (keysAndGroupsNonEmpty.length < 1) {\n                        break;\n                    }\n                    const pValues = adjustPValues(\n                        keysAndGroupsNonEmpty.map(([,groups]) => calculatePValue(groups, layer.testMethod, layer.paired)),\n                        layer.correctionMethod\n                    );\n                    values = keysAndGroupsNonEmpty.map(([keysPair], index) => [keysPair, pValues[index]]);\n                    break;\n                }\n                default: {\n                    throw new Error('Unknown statType');\n                }\n            }\n            res[getFacetStringKey(facetKey)] = values;\n            return res;\n        }, {}),\n        meta: {\n            statType: layer.statType,\n            testMethod: layer.testMethod,\n            format: layer.format,\n            ns: layer.ns,\n            significanceLevels: layer.significanceLevels\n        },\n    };\n}\n"],"names":["getAllKeyPairs","keys","res","key1","index","key2","getStatsData","layer","facetKeys","primaryKeys","y","data","facetKey","values","groups","primaryKey","group","pValue","calculatePValue","referenceKey","NO_GROUPED","referenceGroup","keysAndGroupsNonEmpty","key","pValues","adjustPValues","gr1","gr2","keysPair","getFacetStringKey"],"mappings":";;;;AASA,SAASA,EAAgBC,GAAiB;AACtC,SAAOA,EACF,MAAM,GAAE,EAAE,EACV;AAAA,IACG,CAACC,GAA6BC,GAAMC,MAChCF,EAAI,OAAOD,EAAK,MAAMG,IAAQ,CAAC,EAAE,IAAI,CAAAC,MAAQ,CAACF,GAAME,CAAI,CAAC,CAAC;AAAA,IAC9D,CAAA;AAAA,EAAA;AAEZ;AAEO,SAASC,EACZC,GACAC,GACAC,GACAC,GACAC,GACS;AACT,SAAO;AAAA,IACH,MAAM;AAAA,IACN,QAAQH,EAAU,OAAO,CAACN,GAA0BU,MAAa;AAC7D,UAAIC,IAA+B,CAAA;AACnC,cAAQN,EAAM,UAAA;AAAA,QACV,KAAK,WAAW;AACZ,gBAAMO,IAASL,EACV,IAAI,CAAAM,MAAcJ,EAAK,oBAAoB,CAAC,GAAGC,GAAUG,CAAU,GAAGL,EAAE,KAAK,CAAC,EAC9E,OAAO,CAACM,MAAUA,EAAM,SAAS,CAAC;AACvC,cAAIF,EAAO,SAAS;AAChB;AAEJ,gBAAMG,IAASC,EAAgBJ,GAAQP,EAAM,YAAYA,EAAM,MAAM;AACrEM,UAAAA,IAAS,CAAC,CAAC,CAAC,SAAS,GAAGI,CAAM,CAAC;AAC/B;AAAA,QACJ;AAAA,QACA,KAAK,kBAAkB;AACnB,gBAAME,IAAeZ,EAAM,mBAAmB,OAAOa,IAAa,OAAOb,EAAM,cAAc;AAC7F,cAAIY,MAAiBC,KAAc,CAACX,EAAY,SAASU,CAAY;AACjE,kBAAM,IAAI,MAAM,mBAAmB,OAAOA,CAAY,CAAC,QAAQZ,EAAM,UAAU,kCAAkC;AAErH,gBAAMc,IAAiBV,EAAK,oBAAoB,CAAC,GAAGC,GAAUO,CAAY,GAAGT,EAAE,KAAK;AACpF,cAAIW,EAAe,WAAW,GAAG;AAC7BR,YAAAA,IAAS,CAAA;AACT;AAAA,UACJ;AAGA,gBAAMS,IADOb,EAAY,OAAO,CAAAc,MAAOA,MAAQJ,CAAY,EAEtD,IAAI,CAAAJ,MAAc,CAACA,GAAYJ,EAAK,oBAAoB,CAAC,GAAGC,GAAUG,CAAU,GAAGL,EAAE,KAAK,CAAC,CAAuB,EAClH,OAAO,CAAC,CAAA,EAAGM,CAAK,MAAMA,EAAM,SAAS,CAAC;AAC3C,cAAIM,EAAsB,SAAS,KAAKf,EAAM,qBAAqB;AAC/D;AAEJ,gBAAMiB,IAAUC;AAAAA,YACZH,EAAsB;AAAA,cAAI,CAAC,CAAA,EAAEN,CAAK,MAC9BE;AAAAA,gBACI,CAACG,GAAgBL,CAAK;AAAA,gBACtBT,EAAM;AAAA,gBACNA,EAAM;AAAA,cAAA;AAAA,YAAA;AAAA,YAGdA,EAAM;AAAA,UAAA;AAEVM,UAAAA,IAASS,EAAsB,IAAI,CAAC,CAACP,CAAU,GAAGX,MAAU,CAAC,CAACW,CAAU,GAAGS,EAAQpB,CAAK,CAAC,CAAC;AAC1F;AAAA,QACJ;AAAA,QACA,KAAK,YAAY;AAEb,gBAAMkB,IADYtB,EAAeS,CAAW,EAEvC,IAAI,CAAC,CAACN,GAAME,CAAI,MAAM;AAAA,YACnB,CAACF,GAAME,CAAI;AAAA,YACX;AAAA,cACIM,EAAK,oBAAoB,CAAC,GAAGC,GAAUT,CAAI,GAAGO,EAAE,KAAK;AAAA,cACrDC,EAAK,oBAAoB,CAAC,GAAGC,GAAUP,CAAI,GAAGK,EAAE,KAAK;AAAA,YAAA;AAAA,UAAA,CAElC,EAC1B,OAAO,CAAC,CAAA,EAAE,CAACgB,GAAKC,CAAG,CAAC,MAAMD,EAAI,UAAUC,EAAI,MAAM;AAEvD,cAAIL,EAAsB,SAAS;AAC/B;AAEJ,gBAAME,IAAUC;AAAAA,YACZH,EAAsB,IAAI,CAAC,CAAA,EAAER,CAAM,MAAMI,EAAgBJ,GAAQP,EAAM,YAAYA,EAAM,MAAM,CAAC;AAAA,YAChGA,EAAM;AAAA,UAAA;AAEVM,UAAAA,IAASS,EAAsB,IAAI,CAAC,CAACM,CAAQ,GAAGxB,MAAU,CAACwB,GAAUJ,EAAQpB,CAAK,CAAC,CAAC;AACpF;AAAA,QACJ;AAAA,QACA;AACI,gBAAM,IAAI,MAAM,kBAAkB;AAAA,MAAA;AAG1C,aAAAF,EAAI2B,EAAkBjB,CAAQ,CAAC,IAAIC,GAC5BX;AAAAA,IACX,GAAG,CAAA,CAAE;AAAA,IACL,MAAM;AAAA,MACF,UAAUK,EAAM;AAAA,MAChB,YAAYA,EAAM;AAAA,MAClB,QAAQA,EAAM;AAAA,MACd,IAAIA,EAAM;AAAA,MACV,oBAAoBA,EAAM;AAAA,IAAA;AAAA,EAAA;AAGtC;","x_google_ignoreList":[0]}

package/dist/node_modules/@milaboratories/miplots4/dist/discrete/layers/stats/pValueCalculation.js

@@ -0,0 +1,50 @@
+import i from "../../../node_modules/@stdlib/stats-anova1/lib/index.js";
+import f from "../../../node_modules/@stdlib/stats-ttest/lib/index.js";
+import l from "../../../node_modules/@stdlib/stats-ttest2/lib/index.js";
+import p from "../../../node_modules/@stdlib/stats-kruskal-test/lib/index.js";
+import m from "../../../node_modules/@stdlib/stats-wilcoxon/lib/index.js";
+import { MannWhitneyU as u } from "./MannWhitneyU.js";
+import n from "../../../node_modules/lodash/lodash.js";
+function E(e, a, t) {
+  switch (a) {
+    case "ttest": {
+      if (e.length > 2)
+        throw new Error("more than 2 datasets passed");
+      if (t) {
+        if (e[0].length !== e[1].length)
+          throw Error("Different size groups in paired test");
+        return f(e[0], e[1]).pValue;
+      }
+      const r = l(e[0], e[1]).pValue;
+      return isNaN(r) ? 1 : r;
+    }
+    case "anova": {
+      const r = i(
+        n.flatten(e),
+        n.flatten(e.map((o, s) => o.map(() => String(s))))
+      ).pValue;
+      return isNaN(r) ? 1 : r;
+    }
+    case "wilcoxon": {
+      if (e.length > 2)
+        throw new Error("more than 2 datasets passed");
+      if (t) {
+        if (e[0].length !== e[1].length)
+          throw Error("Different size groups in paired test");
+        return m(e[0], e[1]).pValue;
+      }
+      const r = new u().mannWhitneyUTest(e[0], e[1]);
+      return isNaN(r) ? 1 : r;
+    }
+    case "kruskalWallis": {
+      const r = p(...e).pValue;
+      return isNaN(r) ? 1 : r;
+    }
+    default:
+      throw new Error("Unknown test method");
+  }
+}
+export {
+  E as calculatePValue
+};
+//# sourceMappingURL=pValueCalculation.js.map