@sjcrh/proteinpaint-client 2.166.0 → 2.167.1

package/dist/chunk-FN5XPUPH.js

@@ -0,0 +1,83 @@
+// plots/bars.settings.js
+var plotLength = 300;
+var rendererSettings = JSON.stringify({
+  plotLength,
+  // maximum bar length
+  barwidth: 20,
+  // bar thickness
+  barspace: 2,
+  // space between two bars
+  orientation: "horizontal",
+  // vertical | horizontal
+  h: {},
+  relayTiles: false,
+  svgw: 600,
+  svgh: 400,
+  unit: "abs",
+  // abs | pct
+  scale: "byChart",
+  // byGroup | byChart
+  currAge: 20,
+  rowkey: "dataId",
+  rowgrpkey: "rowgrp",
+  colkey: "seriesId",
+  colgrpkey: "colgrp",
+  rowh: 22,
+  colw: 36,
+  rowspace: 1,
+  colspace: 1,
+  rowtick: 8,
+  coltick: 5,
+  rowlabtickspace: 0,
+  collabtickspace: 0,
+  collabelh: 100,
+  rowlabelw: 100,
+  rowheadleft: true,
+  colheadtop: false,
+  legendontop: false,
+  legendh: 0,
+  legendpadleft: 170,
+  hidelegend: false,
+  showgrid: true,
+  gridstroke: "#fff",
+  showEmptyCells: false,
+  cellbg: "#eeeeee",
+  fontsizeratio: 0.9,
+  rowlabelfontsizemax: 16,
+  collabelfontsizemax: 12,
+  crudefill: true,
+  duration: 1e3,
+  delay: 0,
+  cellfontsize: 11,
+  colgspace: 4,
+  rowgspace: 4,
+  rowglabspace: 5,
+  colglabspace: 5,
+  colgrplabelh: 25,
+  rowgrplabelw: 25,
+  rowglabfontsize: 15,
+  rowglabfontsizemax: 25,
+  colglabfontsize: 15,
+  colglabfontsizemax: 25,
+  borderwidth: 2,
+  svgPadding: {
+    top: 10,
+    left: 30,
+    right: 10,
+    bottom: 30
+  },
+  exclude: {
+    rows: [],
+    cols: [],
+    colgrps: [],
+    // used when expanding a column group
+    rowgrps: []
+  },
+  axisTitleFontSize: 16
+});
+
+export {
+  plotLength,
+  rendererSettings
+};
+//# sourceMappingURL=chunk-FN5XPUPH.js.map

package/dist/chunk-FN5XPUPH.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/bars.settings.js"],
+  "sourcesContent": ["export const plotLength = 300\n\n// Example barchart renderer settings\nexport const rendererSettings = JSON.stringify({\n\tplotLength: plotLength, // maximum bar length\n\tbarwidth: 20, // bar thickness\n\tbarspace: 2, // space between two bars\n\n\torientation: 'horizontal', // vertical | horizontal\n\th: {},\n\trelayTiles: false,\n\tsvgw: 600,\n\tsvgh: 400,\n\tunit: 'abs', // abs | pct\n\tscale: 'byChart', // byGroup | byChart\n\tcurrAge: 20,\n\n\trowkey: 'dataId',\n\trowgrpkey: 'rowgrp',\n\tcolkey: 'seriesId',\n\tcolgrpkey: 'colgrp',\n\n\trowh: 22,\n\tcolw: 36,\n\n\trowspace: 1,\n\tcolspace: 1,\n\n\trowtick: 8,\n\tcoltick: 5,\n\trowlabtickspace: 0,\n\tcollabtickspace: 0,\n\n\tcollabelh: 100,\n\trowlabelw: 100,\n\trowheadleft: true,\n\tcolheadtop: false,\n\n\tlegendontop: false,\n\tlegendh: 0,\n\tlegendpadleft: 170,\n\thidelegend: false,\n\n\tshowgrid: true,\n\tgridstroke: '#fff',\n\tshowEmptyCells: false,\n\n\tcellbg: '#eeeeee',\n\n\tfontsizeratio: 0.9,\n\trowlabelfontsizemax: 16,\n\tcollabelfontsizemax: 12,\n\tcrudefill: true,\n\tduration: 1000,\n\tdelay: 0,\n\n\tcellfontsize: 11,\n\n\tcolgspace: 4,\n\trowgspace: 4,\n\trowglabspace: 5,\n\n\tcolglabspace: 5,\n\tcolgrplabelh: 25,\n\trowgrplabelw: 25,\n\n\trowglabfontsize: 15,\n\trowglabfontsizemax: 25,\n\tcolglabfontsize: 15,\n\tcolglabfontsizemax: 25,\n\tborderwidth: 2,\n\n\tsvgPadding: {\n\t\ttop: 10,\n\t\tleft: 30,\n\t\tright: 10,\n\t\tbottom: 30\n\t},\n\n\texclude: {\n\t\trows: [],\n\t\tcols: [],\n\t\tcolgrps: [], // used when expanding a column group\n\t\trowgrps: []\n\t},\n\taxisTitleFontSize: 16\n})\n"],
+  "mappings": ";AAAO,IAAM,aAAa;AAGnB,IAAM,mBAAmB,KAAK,UAAU;AAAA,EAC9C;AAAA;AAAA,EACA,UAAU;AAAA;AAAA,EACV,UAAU;AAAA;AAAA,EAEV,aAAa;AAAA;AAAA,EACb,GAAG,CAAC;AAAA,EACJ,YAAY;AAAA,EACZ,MAAM;AAAA,EACN,MAAM;AAAA,EACN,MAAM;AAAA;AAAA,EACN,OAAO;AAAA;AAAA,EACP,SAAS;AAAA,EAET,QAAQ;AAAA,EACR,WAAW;AAAA,EACX,QAAQ;AAAA,EACR,WAAW;AAAA,EAEX,MAAM;AAAA,EACN,MAAM;AAAA,EAEN,UAAU;AAAA,EACV,UAAU;AAAA,EAEV,SAAS;AAAA,EACT,SAAS;AAAA,EACT,iBAAiB;AAAA,EACjB,iBAAiB;AAAA,EAEjB,WAAW;AAAA,EACX,WAAW;AAAA,EACX,aAAa;AAAA,EACb,YAAY;AAAA,EAEZ,aAAa;AAAA,EACb,SAAS;AAAA,EACT,eAAe;AAAA,EACf,YAAY;AAAA,EAEZ,UAAU;AAAA,EACV,YAAY;AAAA,EACZ,gBAAgB;AAAA,EAEhB,QAAQ;AAAA,EAER,eAAe;AAAA,EACf,qBAAqB;AAAA,EACrB,qBAAqB;AAAA,EACrB,WAAW;AAAA,EACX,UAAU;AAAA,EACV,OAAO;AAAA,EAEP,cAAc;AAAA,EAEd,WAAW;AAAA,EACX,WAAW;AAAA,EACX,cAAc;AAAA,EAEd,cAAc;AAAA,EACd,cAAc;AAAA,EACd,cAAc;AAAA,EAEd,iBAAiB;AAAA,EACjB,oBAAoB;AAAA,EACpB,iBAAiB;AAAA,EACjB,oBAAoB;AAAA,EACpB,aAAa;AAAA,EAEb,YAAY;AAAA,IACX,KAAK;AAAA,IACL,MAAM;AAAA,IACN,OAAO;AAAA,IACP,QAAQ;AAAA,EACT;AAAA,EAEA,SAAS;AAAA,IACR,MAAM,CAAC;AAAA,IACP,MAAM,CAAC;AAAA,IACP,SAAS,CAAC;AAAA;AAAA,IACV,SAAS,CAAC;AAAA,EACX;AAAA,EACA,mBAAmB;AACpB,CAAC;",
+  "names": []
+}

package/dist/chunk-GLSDMBHR.js

@@ -0,0 +1,55 @@
+import {
+  TwRouter,
+  routedTermTypes
+} from "./chunk-W5EG334J.js";
+
+// plots/PlotBase.ts
+var PlotBase = class {
+  constructor(opts, plotApi) {
+    this.dom = {};
+    this.components = {};
+    if (plotApi) this.api = plotApi;
+    this.opts = opts;
+    this.id = opts?.id;
+    this.app = opts?.app;
+    this.parentId = opts?.parentId;
+  }
+  async getMutableConfig() {
+    const config = structuredClone(this.state.config);
+    if (!config || !this.configTermKeys?.length) return structuredClone(config);
+    const opts = {
+      vocabApi: this.app.vocabApi
+    };
+    for (const key of this.configTermKeys) {
+      const value = config[key];
+      if (!value) continue;
+      if (Array.isArray(value)) {
+        for (const [i, tw] of value.entries()) {
+          if (routedTermTypes.has(tw.term?.type)) config[key][i] = TwRouter.init(tw, opts);
+        }
+      } else if (routedTermTypes.has(value.term?.type)) {
+        config[key] = await TwRouter.initRaw(value, opts);
+      }
+    }
+    return config;
+  }
+};
+var defaultUiLabels = {
+  Samples: "Samples",
+  samples: "samples",
+  Sample: "Sample",
+  sample: "sample",
+  Terms: "Variables",
+  terms: "variables",
+  Term: "Variable",
+  term: "Variable",
+  Mutations: "Mutations",
+  term2: { label: "Overlay", title: "Overlay data" },
+  term0: { label: "Divide by", title: "Divide by data" }
+};
+
+export {
+  PlotBase,
+  defaultUiLabels
+};
+//# sourceMappingURL=chunk-GLSDMBHR.js.map

package/dist/chunk-GLSDMBHR.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/PlotBase.ts"],
+  "sourcesContent": ["import type { AppApi, ComponentApi } from '#rx'\nimport { TwRouter, routedTermTypes } from '#tw'\n\nexport class PlotBase {\n\t//type: string\n\t//id: string\n\tapi?: ComponentApi\n\topts: any\n\tapp: AppApi\n\tid: string\n\tstate: any\n\tparentId?: string\n\n\tdom: {\n\t\t[name: string]: any\n\t} = {}\n\n\tcomponents: {\n\t\t[name: string]: ComponentApi | { [name: string]: ComponentApi }\n\t} = {}\n\n\t// dom: any\n\t// config: any\n\tconfigTermKeys?: string[]\n\n\tconstructor(opts, plotApi?: ComponentApi) {\n\t\tif (plotApi) this.api = plotApi\n\t\tthis.opts = opts\n\t\tthis.id = opts?.id\n\t\tthis.app = opts?.app\n\t\tthis.parentId = opts?.parentId\n\t}\n\n\tasync getMutableConfig() {\n\t\t// TODO: may improve to not require a full copy??\n\t\tconst config = structuredClone(this.state.config)\n\t\tif (!config || !this.configTermKeys?.length) return structuredClone(config)\n\n\t\tconst opts = {\n\t\t\tvocabApi: this.app.vocabApi\n\t\t}\n\n\t\tfor (const key of this.configTermKeys) {\n\t\t\tconst value = config[key]\n\t\t\t// const orig = this.state.config[key] // TODO: may reuse the original copy if there's a better way to mutate\n\t\t\tif (!value) continue\n\t\t\tif (Array.isArray(value)) {\n\t\t\t\tfor (const [i, tw] of value.entries()) {\n\t\t\t\t\t/*const xtw = orig[i]\n\t\t\t\t\tif (xtw.type && xtw.contructor?.name != 'Object') config[key][i] = xtw\n\t\t\t\t\telse*/ if (routedTermTypes.has(tw.term?.type)) config[key][i] = TwRouter.init(tw, opts)\n\t\t\t\t}\n\t\t\t} /*else if (typeof orig == 'object' && orig.contructor?.name != 'Object') {\n\t\t\t\tconfig[key] = orig\n\t\t\t}*/ else if (routedTermTypes.has(value.term?.type)) {\n\t\t\t\tconfig[key] = await TwRouter.initRaw(value, opts)\n\t\t\t}\n\t\t}\n\n\t\treturn config\n\t}\n}\n\n// default UI labels\n// used by plot controls and tooltips\nexport const defaultUiLabels = {\n\tSamples: 'Samples',\n\tsamples: 'samples',\n\tSample: 'Sample',\n\tsample: 'sample',\n\tTerms: 'Variables',\n\tterms: 'variables',\n\tTerm: 'Variable',\n\tterm: 'Variable',\n\tMutations: 'Mutations',\n\tterm2: { label: 'Overlay', title: 'Overlay data' },\n\tterm0: { label: 'Divide by', title: 'Divide by data' }\n}\n"],
+  "mappings": ";;;;;;AAGO,IAAM,WAAN,MAAe;AAAA,EAsBrB,YAAY,MAAM,SAAwB;AAZ1C,eAEI,CAAC;AAEL,sBAEI,CAAC;AAOJ,QAAI,QAAS,MAAK,MAAM;AACxB,SAAK,OAAO;AACZ,SAAK,KAAK,MAAM;AAChB,SAAK,MAAM,MAAM;AACjB,SAAK,WAAW,MAAM;AAAA,EACvB;AAAA,EAEA,MAAM,mBAAmB;AAExB,UAAM,SAAS,gBAAgB,KAAK,MAAM,MAAM;AAChD,QAAI,CAAC,UAAU,CAAC,KAAK,gBAAgB,OAAQ,QAAO,gBAAgB,MAAM;AAE1E,UAAM,OAAO;AAAA,MACZ,UAAU,KAAK,IAAI;AAAA,IACpB;AAEA,eAAW,OAAO,KAAK,gBAAgB;AACtC,YAAM,QAAQ,OAAO,GAAG;AAExB,UAAI,CAAC,MAAO;AACZ,UAAI,MAAM,QAAQ,KAAK,GAAG;AACzB,mBAAW,CAAC,GAAG,EAAE,KAAK,MAAM,QAAQ,GAAG;AAG/B,cAAI,gBAAgB,IAAI,GAAG,MAAM,IAAI,EAAG,QAAO,GAAG,EAAE,CAAC,IAAI,SAAS,KAAK,IAAI,IAAI;AAAA,QACvF;AAAA,MACD,WAEa,gBAAgB,IAAI,MAAM,MAAM,IAAI,GAAG;AACnD,eAAO,GAAG,IAAI,MAAM,SAAS,QAAQ,OAAO,IAAI;AAAA,MACjD;AAAA,IACD;AAEA,WAAO;AAAA,EACR;AACD;AAIO,IAAM,kBAAkB;AAAA,EAC9B,SAAS;AAAA,EACT,SAAS;AAAA,EACT,QAAQ;AAAA,EACR,QAAQ;AAAA,EACR,OAAO;AAAA,EACP,OAAO;AAAA,EACP,MAAM;AAAA,EACN,MAAM;AAAA,EACN,WAAW;AAAA,EACX,OAAO,EAAE,OAAO,WAAW,OAAO,eAAe;AAAA,EACjD,OAAO,EAAE,OAAO,aAAa,OAAO,iBAAiB;AACtD;",
+  "names": []
+}

package/dist/chunk-H3BSKMND.js

@@ -0,0 +1,487 @@
+import {
+  matrix_groups_exports
+} from "./chunk-2HJ7OD7H.js";
+import {
+  setComputedConfig
+} from "./chunk-W4SEWZF2.js";
+import {
+  MatrixCluster
+} from "./chunk-A5TSPTYC.js";
+import {
+  MatrixControls
+} from "./chunk-CCB5KYFQ.js";
+import {
+  matrix_data_exports
+} from "./chunk-CWHBWY3B.js";
+import {
+  matrix_layout_exports
+} from "./chunk-CKLYFA7H.js";
+import {
+  matrix_serieses_exports
+} from "./chunk-DNU4IPD2.js";
+import {
+  matrix_legend_exports
+} from "./chunk-56IFQMJK.js";
+import {
+  setMatrixDom
+} from "./chunk-3JFEWVHR.js";
+import {
+  setInteractivity
+} from "./chunk-ZGQ3BMLW.js";
+import {
+  setRenderers
+} from "./chunk-RL7RU2V7.js";
+import {
+  rebaseGroupFilter
+} from "./chunk-LMELY5Z2.js";
+import {
+  PlotBase
+} from "./chunk-GLSDMBHR.js";
+import {
+  TwRouter,
+  getCombinedTermFilter,
+  sayerror,
+  svgLegend
+} from "./chunk-W5EG334J.js";
+import {
+  dt2label,
+  mclass,
+  morigin
+} from "./chunk-6VQ4C735.js";
+import {
+  copyMerge,
+  deepEqual,
+  getCompInit
+} from "./chunk-DDOM4XYV.js";
+import {
+  convertUnits
+} from "./chunk-RA5EXEHB.js";
+import {
+  select_default
+} from "./chunk-NDWTN4U5.js";
+
+// plots/matrix/matrix.xtw.ts
+var addons;
+function getTermGroups(termgroups, app) {
+  const termGroups = structuredClone(termgroups);
+  if (!addons)
+    addons = {
+      QualTWValues: discreteAddons,
+      QualTWPredefinedGS: discreteAddons,
+      QualTWCustomGS: discreteAddons,
+      NumTWRegularBin: discreteAddons,
+      NumTWCustomBin: discreteAddons,
+      NumTWCont: continuousAddons
+    };
+  const opts = {
+    vocabApi: app.vocabApi,
+    addons
+  };
+  for (const [origIndex, tG] of termGroups.entries()) {
+    tG.origIndex = origIndex;
+    if (tG.type == "hierCluster") continue;
+    const xtwlst = [];
+    for (const tw of tG.lst) {
+      xtwlst.push(tw.type in opts.addons ? TwRouter.init(tw, opts) : tw);
+    }
+    tG.lst = xtwlst;
+  }
+  return termGroups;
+}
+var discreteAddons = {
+  setCellProps: {
+    value: function(cell, anno, value, s, t, self2, width, height, dx, dy, i) {
+      const tw = this.getTw();
+      const key = anno.key;
+      const values = tw.term.values || {};
+      cell.label = "label" in anno ? anno.label : values[key]?.label ? values[key].label : key;
+      const tw$id = tw.$id;
+      cell.fill = self2.config.settings.matrix.twSpecificSettings?.[tw$id]?.[key]?.color || anno.color || values[anno.key]?.color || self2.data.refs.byTermId?.[tw$id]?.bins?.find((b) => anno.key == b.name)?.color;
+      cell.order = t.ref.bins ? t.ref.bins.findIndex((bin) => bin.name == key) : 0;
+      cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
+      cell.y = height * i;
+      const group = tw.legend?.group || tw$id;
+      return { ref: t.ref, group, value: key, entry: { key, label: cell.label, fill: cell.fill } };
+    }
+  }
+};
+var continuousAddons = {
+  setCellProps: {
+    value: function(cell, anno, value, s, t, self2, width, height, dx, dy, i) {
+      const tw = this.getTw();
+      const key = anno.key;
+      const values = tw.term.values || {};
+      cell.label = "label" in anno ? anno.label : values[key]?.label ? values[key].label : key;
+      cell.fill = anno.color || values[anno.key]?.color;
+      const tw$id = tw.$id;
+      const twSpecificSettings = self2.config.settings.matrix.twSpecificSettings;
+      if (!twSpecificSettings[tw$id]) twSpecificSettings[tw$id] = {};
+      const twSettings = twSpecificSettings[tw$id];
+      if (!twSettings.contBarH) twSettings.contBarH = s.barh;
+      if (!("gap" in twSettings)) twSettings.contBarGap = 4;
+      const specialValue = tw.term.values?.[cell.key];
+      if (specialValue?.uncomputable) {
+        cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
+        cell.y = height * i;
+        cell.height = twSettings.contBarH;
+        cell.fill = "transparent";
+        cell.label = specialValue.label;
+        const group = tw.legend?.group || tw.$id;
+        return {
+          ref: t.ref,
+          group,
+          value: specialValue.label || specialValue.key,
+          entry: { key, label: cell.label, fill: cell.fill }
+        };
+      }
+      cell.fill = self2.config.settings.matrix.twSpecificSettings?.[tw$id]?.contBarColor || "#555";
+      if (s.transpose) {
+        cell.height = t.scale(cell.key);
+        cell.x = twSettings.contBarGap;
+      } else {
+        const vc = cell.term.valueConversion;
+        let renderV = vc ? cell.key * vc.scaleFactor : cell.key;
+        if (this.q.convert2ZScore) {
+          renderV = (renderV - t.mean) / t.std;
+          cell.fill = renderV > 0 ? "#FF6666" : "#6666FF";
+          cell.zscoreLabel = ` (Z-score: ${renderV.toFixed(2)})`;
+        }
+        cell.label = "label" in anno ? anno.label : values[key]?.label ? values[key].label : this.term.unit ? `${cell.key.toFixed(2)} ${this.term.unit}` : cell.key.toFixed(2);
+        cell.height = renderV >= 0 ? t.scales.pos(renderV) : t.scales.neg(renderV);
+        cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
+        cell.y = renderV >= 0 ? t.counts.posMaxHt + twSettings.contBarGap - cell.height : t.counts.posMaxHt + twSettings.contBarGap;
+        cell.convertedValueLabel = !vc ? "" : convertUnits(cell.key, vc.fromUnit, vc.toUnit, vc.scaleFactor);
+      }
+    }
+  }
+};
+
+// plots/matrix/matrix.js
+var Matrix = class extends PlotBase {
+  constructor(opts) {
+    super(opts);
+    this.type = "matrix";
+    this.holderTitle = "Sample Matrix";
+    this.optionalFeatures = JSON.parse(sessionStorage.getItem("optionalFeatures") || `{}`)?.matrix || [];
+    setInteractivity(this);
+    setRenderers(this);
+  }
+  async init(appState) {
+    const opts = this.opts;
+    if (opts.reactsTo) this.reactsTo = opts.reactsTo;
+    this.setDom = setMatrixDom;
+    this.setDom(opts);
+    this.config = appState.plots.find((p) => p.id === this.id);
+    this.settings = Object.assign({}, this.config.settings.matrix);
+    this.computed = {};
+    if (this.dom.header) this.dom.header.html(this.config.preBuiltPlotTitle || this.holderTitle);
+    this.setControls(appState);
+    this.clusterRenderer = new MatrixCluster({ holder: this.dom.cluster, app: this.app, parent: this });
+    this.legendRenderer = svgLegend({
+      holder: this.dom.legendG,
+      rectFillFxn: (d) => d.color,
+      iconStroke: "#aaa",
+      handlers: {
+        legend: {
+          click: this.legendClick
+        }
+      },
+      settings: {
+        isExcludedAttr: "isExcluded"
+      },
+      note: "CLICK A ROW LABEL OR ITEM TO APPLY FILTERING"
+    });
+    this.customTipApi = this.dom.tip.getCustomApi({
+      d: this.dom.menubody,
+      clear: (event) => {
+        if (event?.target) this.dom.menutop.style("display", "none");
+        this.dom.menubody.selectAll("*").remove();
+        return this.customTipApi;
+      },
+      show: () => {
+        this.dom.menubody.style("display", "block");
+      },
+      hide: () => {
+      }
+    });
+    this.setPill(appState);
+    const commonKeys = { mclass, dt2label, morigin };
+    for (const k in commonKeys) {
+      const v = commonKeys[k];
+      this[k] = copyMerge({}, v, appState.termdbConfig[k] || {}, appState.termdbConfig.matrix?.[k] || {});
+    }
+  }
+  setControls(appState) {
+    this.controlsRenderer = new MatrixControls(
+      {
+        app: this.app,
+        id: this.id,
+        parent: this,
+        holder: this.dom.controls,
+        getSvg: () => this.dom.svg.node()
+      },
+      appState
+    );
+  }
+  // reactsTo(action) {
+  // 	// note: a parent app or 'plot' component is expected to already have
+  // 	// a comprehensive reactsTo() call to filter the actions for this component,
+  // 	// so only farther selective action filters should be applied here as needed
+  // 	return true
+  // }
+  getState(appState) {
+    const config = appState.plots.find((p) => p.id === this.id);
+    const filter0 = appState.termfilter.filter0;
+    this.prevFilter0 = this.state?.filter0;
+    const parentConfig = appState.plots.find((p) => p.id === this.parentId);
+    const termfilter = getCombinedTermFilter(appState, config.filter || parentConfig?.filter);
+    return {
+      isVisible: true,
+      config,
+      filter: termfilter.filter,
+      filter0,
+      // read-only, invisible filter currently only used for gdc dataset
+      hasVerifiedToken: this.app.vocabApi.hasVerifiedToken(),
+      tokenVerificationMessage: this.app.vocabApi.tokenVerificationMessage,
+      vocab: appState.vocab,
+      termdbConfig: appState.termdbConfig,
+      clusterMethod: config.settings.hierCluster?.clusterMethod,
+      distanceMethod: config.settings.hierCluster?.distanceMethod,
+      clusterSamples: config.settings.hierCluster?.clusterSamples,
+      clusterRows: config.settings.hierCluster?.clusterRows,
+      zScoreTransformation: config.settings.hierCluster?.zScoreTransformation,
+      nav: appState.nav,
+      groups: rebaseGroupFilter(appState)
+    };
+  }
+  async main() {
+    try {
+      this.config = await this.getMutableConfig();
+      if (this.mayRequireToken()) return;
+      const termGroups = getTermGroups(this.config.termgroups, this.app);
+      const prevTranspose = this.settings.transpose;
+      Object.assign(this.settings, structuredClone(this.config.settings), this.controlsRenderer.getSettings());
+      this.dom.loadingDiv.selectAll("*").remove();
+      this.dom.loadingDiv.html("").style("display", "").style("position", "relative").style("left", "45%");
+      this.dom.svg.style("opacity", 0.1).style("pointer-events", "none");
+      delete this.clickedClusterIds;
+      delete this.clickedLeftClusterIds;
+      try {
+        setComputedConfig(this.config);
+        const promises = [];
+        if (this.setHierClusterData) promises.push(this.setHierClusterData());
+        promises.push(this.setData());
+        this.dom.loadingDiv.html("Processing data ...");
+        await Promise.all(promises);
+        this.applyLegendValueFilter();
+        if (this.combineData) this.combineData();
+        this.app.save({ type: "plot_edit", id: this.id, config: this.config });
+      } catch (e) {
+        if (e == "no data") {
+          this.showNoMatchingDataMessage();
+          return;
+        } else if (this.app.isAbortError(e)) {
+          return;
+        } else {
+          this.dom.svg.style("display", "none");
+          throw e;
+        }
+      }
+      this.termGroups = termGroups;
+      this.dom.loadingDiv.html("Updating ...").style("display", "");
+      this.termOrder = this.getTermOrder(this.data);
+      this.sampleGroups = this.getSampleGroups(this.hierClusterSamples || this.data);
+      this.sampleOrder = this.getSampleOrder(this.data);
+      this.setLayout();
+      if (this.setHierColorScale) this.setHierColorScale(this.hierClusterData.clustering);
+      if (!this.sampleOrder?.length) {
+        this.showNoMatchingDataMessage();
+      }
+      this.controlsRenderer.main();
+      this.serieses = this.getSerieses(this.data);
+      this.dom.loadingDiv.html("Rendering ...");
+      if (this.plotDendrogramHclust) this.plotDendrogramHclust();
+      this.render();
+      this.mayDisplayCohortMessage();
+      this.dom.svg.style("display", "").style("opacity", 1).style("pointer-events", "");
+      const [xGrps, yGrps] = !this.settings.matrix.transpose ? ["sampleGrps", "termGrps"] : ["termGrps", "sampleGrps"];
+      const d = this.dimensions;
+      this.clusterRenderer.main({
+        settings: this.settings.matrix,
+        xGrps: this[xGrps],
+        yGrps: this[yGrps],
+        dimensions: d
+      });
+      this.legendRenderer(this.legendData, {
+        settings: Object.assign({}, this.settings.legend, {
+          svgw: Math.max(400, d.mainw + d.xOffset - this.settings.matrix.margin.right),
+          svgh: d.mainh + d.yOffset,
+          dimensions: d,
+          padleft: this.settings.legend.padleft
+          //+ d.xOffset
+        })
+      });
+      await this.adjustSvgDimensions(prevTranspose);
+      this.controlsRenderer.main();
+      if (this.data.removedHierClusterTerms) {
+        for (const r of this.data.removedHierClusterTerms) {
+          sayerror(this.dom.errorDiv, r.text + ": " + r.lst.join(", "));
+        }
+      }
+    } catch (e) {
+      const message = this.app.vocabApi.tokenVerificationMessage;
+      this.mayRequireToken(message);
+      if (!message) {
+        this.app.tip.hide();
+        this.dom.loadingDiv.style("display", "none");
+        throw e;
+      }
+    }
+    this.resetInteractions();
+  }
+  showNoMatchingDataMessage() {
+    this.forcedSampleCount = 0;
+    this.dom.svg.style("opacity", 1e-3).style("display", "none");
+    if (this.termOrder && this.dimensions) this.controlsRenderer.main({ sampleCount: 0 });
+    this.dom.loadingDiv.html("");
+    const div = this.dom.loadingDiv.append("div").style("display", "inline-block").style("text-align", "center").style("position", "relative").style("left", "-150px");
+    div.append("div").style("margin", "5px 10px").html("No matching cohort sample data for the current gene list.");
+    if (this.settings.matrix.showHints?.includes("genesetEdit")) {
+      const div1 = div.append("div").style("margin", "5px 10px");
+      div1.append("span").html("You may change the selected cohort,");
+      if (this.config.legendGrpFilter?.lst.length || this.config.legendValueFilter?.lst.length) {
+        const cnvBtn = this.controlsRenderer.btns.filter((d) => d.label == "CNV")?.node();
+        if (cnvBtn) {
+          div1.append("br");
+          div1.append("span").html("show hidden ");
+          div1.append("span").html("CNV").style("cursor", "pointer").style("text-decoration", "underline").on("click", () => {
+            cnvBtn.click();
+          });
+        }
+        const mutationBtn = this.controlsRenderer.btns.filter((d) => d.label == "Mutation")?.node();
+        if (cnvBtn && mutationBtn) div1.append("span").html(" or ");
+        if (mutationBtn) {
+          div1.append("span").style("cursor", "pointer").style("text-decoration", "underline").html("Mutation").on("click", () => {
+            mutationBtn.click();
+          });
+        }
+        if (cnvBtn || mutationBtn) div1.append("span").html(" data,");
+      }
+      div1.append("br");
+      div1.append("span").html("or edit the gene list from the ");
+      div1.append("span").style("cursor", "pointer").style("text-decoration", "underline").html("Gene Set Edit Group menu.").on("click", () => {
+        const GenesBtn = this.controlsRenderer.btns.filter((d) => d.label == "Genes")?.node().click();
+        const i = setInterval(() => {
+          const editBtn = this.app.tip.d.selectAll("button").filter(function() {
+            return this.innerHTML == "Edit Group";
+          }).node();
+          if (editBtn) {
+            editBtn.click();
+            clearInterval(i);
+          }
+        }, 100);
+      });
+    }
+    this.dom.svg.style("display", "none");
+  }
+  mayDisplayCohortMessage() {
+    const msg = !this.prevFilter0 || deepEqual(this.state.filter0, this.prevFilter0) ? "" : "The gene list is persisted across cohorts.";
+    if (msg) {
+      this.dom.loadingDiv.html("");
+      const div = this.dom.loadingDiv.append("div").style("display", "inline-block").style("text-align", "center").style("position", "relative").style("left", "-150px");
+      div.append("div").html(msg);
+      if (this.settings.matrix.showHints?.includes("genesetEdit")) {
+        const div1 = div.append("div");
+        div1.append("span").html(" You may edit the gene list from the ");
+        div1.append("span").style("cursor", "pointer").style("text-decoration", "underline").html("Gene Set Edit Group menu.").on("click", () => {
+          const GenesBtn = this.controlsRenderer.btns.filter((d) => d.label == "Genes")?.node().click();
+          const i = setInterval(() => {
+            const editBtn = this.app.tip.d.selectAll("button").filter(function() {
+              return this.innerHTML == "Edit Group";
+            }).node();
+            if (editBtn) {
+              editBtn.click();
+              clearInterval(i);
+            }
+          }, 100);
+        });
+      }
+    }
+    this.dom.loadingDiv.style("display", msg ? "" : "none");
+  }
+  sampleKey(s) {
+    return s.row.sample;
+  }
+  sampleLabel(s) {
+    return s.label || s.row._ref_.label || "";
+  }
+  sampleGrpKey(s) {
+    return s.grp.name;
+  }
+  sampleGrpLabel(s) {
+    return s.grp.label || s.grp.name || "";
+  }
+  termKey(t) {
+    return t.tw.$id;
+  }
+  termLabel(t) {
+    return t.label;
+  }
+  termGrpKey(t) {
+    return t.grp.name;
+  }
+  termGrpLabel(t) {
+    return t.grp.label || t.grp.name || [{ text: "\u22EE", dx: 3, cls: "sjpp-exclude-svg-download" }];
+  }
+  destroy() {
+    select_default(window).on(`resize.sjpp-${self.id}`, null);
+  }
+};
+for (const m of [matrix_data_exports, matrix_groups_exports, matrix_layout_exports, matrix_serieses_exports, matrix_legend_exports]) {
+  for (const methodName in m) {
+    Matrix.prototype[methodName] = m[methodName];
+  }
+}
+var matrixInit = getCompInit(Matrix);
+var componentInit = matrixInit;
+function makeChartBtnMenu(holder, chartsInstance) {
+  chartsInstance.dom.tip.clear();
+  const menuDiv = holder.append("div");
+  if (chartsInstance.state.termdbConfig.matrixplots) {
+    for (const plot of chartsInstance.state.termdbConfig.matrixplots) {
+      menuDiv.append("button").style("margin", "10px").style("padding", "10px 15px").style("border-radius", "20px").style("border-color", "#ededed").style("display", "inline-block").text(plot.name).on("click", async () => {
+        chartsInstance.dom.tip.hide();
+        const config = await chartsInstance.app.vocabApi.getMatrixByName(plot.name);
+        config.preBuiltPlotTitle = plot.name;
+        chartsInstance.app.dispatch({
+          type: "plot_create",
+          config
+        });
+      });
+    }
+  }
+  const chart = {
+    clickTo: chartsInstance.showTree_selectlst,
+    chartType: "matrix",
+    usecase: { target: "matrix", detail: "termgroups" },
+    processSelection: (lst) => {
+      return [
+        {
+          name: "",
+          lst: lst.map((term) => {
+            return { term };
+          })
+        }
+      ];
+    }
+  };
+  chartsInstance.showTree_selectlst(chart);
+}
+
+export {
+  Matrix,
+  matrixInit,
+  componentInit,
+  makeChartBtnMenu
+};
+//# sourceMappingURL=chunk-H3BSKMND.js.map