@sjcrh/proteinpaint-client 2.182.0 → 2.183.0

package/dist/chunk-APOHXHKH.js

@@ -0,0 +1,526 @@
+import {
+  setComputedConfig
+} from "./chunk-77ZJGPK2.js";
+import {
+  MatrixControls
+} from "./chunk-ZGT4XP5J.js";
+import {
+  matrix_data_exports
+} from "./chunk-WPHOEG56.js";
+import {
+  matrix_layout_exports
+} from "./chunk-36DYWBU7.js";
+import {
+  matrix_serieses_exports
+} from "./chunk-D4QFQQWJ.js";
+import {
+  matrix_legend_exports
+} from "./chunk-DNCSPTOQ.js";
+import {
+  matrix_groups_exports
+} from "./chunk-QRIRWDIW.js";
+import {
+  setMatrixDom
+} from "./chunk-VYIO7T6J.js";
+import {
+  setInteractivity
+} from "./chunk-DTDQKGIQ.js";
+import {
+  setRenderers
+} from "./chunk-YALAQWX4.js";
+import {
+  MatrixCluster
+} from "./chunk-A5TSPTYC.js";
+import {
+  PlotBase,
+  TwRouter,
+  getCombinedTermFilter,
+  rebaseGroupFilter,
+  routedTermTypes,
+  sayerror,
+  svgLegend
+} from "./chunk-OXJ2TWDO.js";
+import {
+  copyMerge,
+  deepEqual,
+  getCompInit
+} from "./chunk-MVTCBVSX.js";
+import {
+  dt2label,
+  mclass,
+  morigin
+} from "./chunk-XYFDBYOY.js";
+import {
+  convertUnits
+} from "./chunk-TV74I3Y5.js";
+import {
+  select_default
+} from "./chunk-NDWTN4U5.js";
+
+// plots/matrix/matrix.xtw.ts
+var addons;
+async function getTermGroups(termgroups, app) {
+  const termGroups = structuredClone(termgroups);
+  if (!addons)
+    addons = {
+      QualTWValues: discreteAddons,
+      QualTWPredefinedGS: discreteAddons,
+      QualTWCustomGS: discreteAddons,
+      NumTWRegularBin: discreteAddons,
+      NumTWCustomBin: discreteAddons,
+      NumTWCont: continuousAddons,
+      TermCollectionTWCont: TermCollectionContAddons
+    };
+  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) {
+      const inputTw = tw.getTw?.() || tw;
+      xtwlst.push(
+        inputTw.type in opts.addons && routedTermTypes.has(inputTw.term.type) ? await TwRouter.init(inputTw, opts) : inputTw
+      );
+    }
+    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)} ${this.term.unit}` : cell.key.toFixed(2);
+        cell.height = renderV >= 0 ? t.scales.pos(renderV) : t.scales.neg(renderV);
+        cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
+        cell.y = renderV >= 0 ? t.counts.posMaxHt + twSettings.contBarGap - cell.height : t.counts.posMaxHt + twSettings.contBarGap;
+        cell.convertedValueLabel = !vc ? "" : convertUnits(cell.key, vc.fromUnit, vc.toUnit, vc.scaleFactor);
+      }
+    }
+  }
+};
+var TermCollectionContAddons = {
+  setCellProps: {
+    value: function(cell, anno, value, s, t, self2, width, height, dx, _dy, _i) {
+      const tw = this.getTw();
+      const twSpecificSettings = self2.config.settings.matrix.twSpecificSettings;
+      if (!twSpecificSettings[tw.$id]) twSpecificSettings[tw.$id] = {};
+      const twSettings = twSpecificSettings[tw.$id];
+      if (!twSettings.contBarH) twSettings.contBarH = s.barh;
+      if (!("gap" in twSettings)) twSettings.contBarGap = 4;
+      const isNegative = value.value < 0;
+      if (isNegative) {
+        cell.height = t.scales.neg ? t.scales.neg(value.value) - t.scales.neg(0) : 0;
+        cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
+        const cumulativeHeight = t.scales.neg ? t.scales.neg(value.pre_val_sum) - t.scales.neg(0) : 0;
+        cell.y = t.counts.posMaxHt + twSettings.contBarGap + (t.scales.neg ? t.scales.neg(0) : 0) + cumulativeHeight;
+      } else {
+        cell.height = t.scales.pos(value.value) - t.scales.pos(0);
+        cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
+        const cumulativeHeight = t.scales.pos(value.pre_val_sum) - t.scales.pos(0);
+        cell.y = t.counts.posMaxHt + twSettings.contBarGap - t.scales.pos(0) - cumulativeHeight - cell.height;
+      }
+      cell.label = value.label;
+      cell.fill = twSettings[value.label]?.color || value.color || tw.term.propsByTermId?.[value.label]?.color;
+      cell.value = value.value;
+      return {
+        ref: t.ref,
+        group: tw.$id,
+        value: value.label,
+        order: -1,
+        entry: { key: value.label, label: value.label, fill: cell.fill }
+      };
+    }
+  }
+};
+
+// plots/matrix/matrix.js
+var Matrix = class _Matrix extends PlotBase {
+  static type = "matrix";
+  configTermKeys = ["termgroups.lst", "divideBy"];
+  constructor(opts) {
+    super(opts);
+    this.type = _Matrix.type;
+    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 = await 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);
+        const warnings = this.data.warnings.join("\n");
+        this.dom.warningDiv.style("display", warnings.length ? "" : "none").html(warnings);
+        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 = 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-APOHXHKH.js.map

package/dist/chunk-APOHXHKH.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/matrix/matrix.xtw.ts", "../plots/matrix/matrix.js"],
+  "sourcesContent": ["import type { ContinuousXTW, DiscreteXTW, CollectionCont, TermCollectionTransformedValue } from '#tw'\nimport { TwRouter, routedTermTypes } from '#tw'\nimport type { TermWrapper } from '#types'\nimport { convertUnits } from '#shared/helpers.js'\n\nlet addons\n\nexport async function getTermGroups(termgroups, app) {\n\tconst termGroups = structuredClone(termgroups)\n\t// should only set the addons once, it should not vary from one call to the next\n\tif (!addons)\n\t\taddons = {\n\t\t\tQualTWValues: discreteAddons,\n\t\t\tQualTWPredefinedGS: discreteAddons,\n\t\t\tQualTWCustomGS: discreteAddons,\n\t\t\tNumTWRegularBin: discreteAddons,\n\t\t\tNumTWCustomBin: discreteAddons,\n\t\t\tNumTWCont: continuousAddons,\n\t\t\tTermCollectionTWCont: TermCollectionContAddons\n\t\t}\n\n\tconst opts = {\n\t\tvocabApi: app.vocabApi,\n\t\taddons\n\t}\n\n\tfor (const [origIndex, tG] of termGroups.entries()) {\n\t\ttG.origIndex = origIndex\n\t\tif (tG.type == 'hierCluster') continue\n\t\tconst xtwlst: (MatrixTWObj | TermWrapper)[] = []\n\t\tfor (const tw of tG.lst) {\n\t\t\tconst inputTw = tw.getTw?.() || tw\n\t\t\txtwlst.push(\n\t\t\t\tinputTw.type in opts.addons && routedTermTypes.has(inputTw.term.type)\n\t\t\t\t\t? await TwRouter.init(inputTw, opts)\n\t\t\t\t\t: inputTw\n\t\t\t)\n\t\t}\n\t\ttG.lst = xtwlst\n\t}\n\treturn termGroups\n}\n\nexport type SetCellPropsSignature = {\n\tvalue: (\n\t\t/** a plain object for matrix cell data to be rendered, including sibling cells */\n\t\tcell: any,\n\t\tanno: any,\n\t\tvalue: string | number,\n\t\ts: any,\n\t\tt: any,\n\t\tself: any,\n\t\twidth: number,\n\t\theight: number,\n\t\tdx: number,\n\t\tdy: number,\n\t\ti: number\n\t) => any\n}\n\ninterface MatrixTWObj {\n\tsetCellProps: SetCellPropsSignature\n}\n\nconst discreteAddons: MatrixTWObj = {\n\tsetCellProps: {\n\t\tvalue: function (\n\t\t\tthis: DiscreteXTW,\n\t\t\tcell: any,\n\t\t\tanno: any,\n\t\t\tvalue: string | number,\n\t\t\ts: any,\n\t\t\tt: any,\n\t\t\tself: any,\n\t\t\twidth: number,\n\t\t\theight: number,\n\t\t\tdx: number,\n\t\t\tdy: number,\n\t\t\ti: number\n\t\t) {\n\t\t\tconst tw = this.getTw()\n\t\t\tconst key = anno.key\n\t\t\tconst values = tw.term.values || {}\n\t\t\tcell.label = 'label' in anno ? anno.label : values[key]?.label ? values[key].label : key\n\t\t\tconst tw$id = tw.$id\n\t\t\tcell.fill =\n\t\t\t\tself.config.settings.matrix.twSpecificSettings?.[tw$id!]?.[key]?.color ||\n\t\t\t\tanno.color ||\n\t\t\t\tvalues[anno.key]?.color ||\n\t\t\t\tself.data.refs.byTermId?.[tw$id!]?.bins?.find(b => anno.key == b.name)?.color\n\t\t\t// only for numeric terms for now\n\t\t\t// TODO: should also consider categorical term.values[*].order\n\t\t\tcell.order = t.ref.bins ? t.ref.bins.findIndex(bin => bin.name == key) : 0\n\n\t\t\tcell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace\n\t\t\tcell.y = height * i\n\t\t\tconst group = tw.legend?.group || tw$id\n\t\t\treturn { ref: t.ref, group, value: key, entry: { key, label: cell.label, fill: cell.fill } }\n\t\t}\n\t}\n}\n\nconst continuousAddons: MatrixTWObj = {\n\tsetCellProps: {\n\t\tvalue: function (\n\t\t\tthis: ContinuousXTW,\n\t\t\tcell: any,\n\t\t\tanno: any,\n\t\t\tvalue: string | number,\n\t\t\ts: any,\n\t\t\tt: any,\n\t\t\tself: any,\n\t\t\twidth: number,\n\t\t\theight: number,\n\t\t\tdx: number,\n\t\t\tdy: number,\n\t\t\ti: number\n\t\t) {\n\t\t\tconst tw = this.getTw()\n\t\t\tconst key = anno.key\n\t\t\tconst values = tw.term.values || {}\n\t\t\tcell.label = 'label' in anno ? anno.label : values[key]?.label ? values[key].label : key\n\t\t\tcell.fill = anno.color || values[anno.key]?.color\n\t\t\tconst tw$id = tw.$id\n\t\t\tconst twSpecificSettings = self.config.settings.matrix.twSpecificSettings\n\t\t\tif (!twSpecificSettings[tw$id!]) twSpecificSettings[tw$id!] = {}\n\t\t\tconst twSettings = twSpecificSettings[tw$id!]\n\t\t\tif (!twSettings.contBarH) twSettings.contBarH = s.barh\n\t\t\tif (!('gap' in twSettings)) twSettings.contBarGap = 4\n\n\t\t\tconst specialValue = tw.term.values?.[cell.key]\n\n\t\t\t// handle uncomputable values\n\t\t\t// TODO: the server response data should not have uncomputable values when mode='continuous'\n\t\t\t// this may be implemented in getData(), but will require lots of testing since it is used\n\t\t\t// by multiple charts\n\t\t\tif (specialValue?.uncomputable) {\n\t\t\t\tcell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace\n\t\t\t\tcell.y = height * i\n\t\t\t\tcell.height = twSettings.contBarH\n\t\t\t\tcell.fill = 'transparent'\n\t\t\t\tcell.label = specialValue.label\n\t\t\t\tconst group = tw.legend?.group || tw.$id\n\t\t\t\treturn {\n\t\t\t\t\tref: t.ref,\n\t\t\t\t\tgroup,\n\t\t\t\t\tvalue: specialValue.label || specialValue.key,\n\t\t\t\t\tentry: { key, label: cell.label, fill: cell.fill }\n\t\t\t\t}\n\t\t\t}\n\n\t\t\t// TODO: may use color scale instead of bars\n\t\t\t// for bars, use a hardcoded color; TODO: allow a user to customize the bar color?\n\t\t\tcell.fill = self.config.settings.matrix.twSpecificSettings?.[tw$id!]?.contBarColor || '#555'\n\t\t\tif (s.transpose) {\n\t\t\t\tcell.height = t.scale(cell.key)\n\t\t\t\tcell.x = twSettings.contBarGap // - cell.width\n\t\t\t} else {\n\t\t\t\tconst vc = cell.term.valueConversion\n\t\t\t\tlet renderV = vc ? cell.key * vc.scaleFactor : cell.key\n\t\t\t\t// todo: convert from a boolean into maybe `q.units or q.transform: 'zscore' | ...`\n\t\t\t\tif (this.q.convert2ZScore) {\n\t\t\t\t\trenderV = (renderV - t.mean) / t.std\n\n\t\t\t\t\t// show positive z-score as soft red and negative z-score as soft blue\n\t\t\t\t\tcell.fill = renderV > 0 ? '#FF6666' : '#6666FF'\n\t\t\t\t\tcell.zscoreLabel = ` (Z-score: ${renderV.toFixed(2)})`\n\t\t\t\t}\n\t\t\t\tcell.label =\n\t\t\t\t\t'label' in anno\n\t\t\t\t\t\t? anno.label\n\t\t\t\t\t\t: values[key]?.label\n\t\t\t\t\t\t? values[key].label\n\t\t\t\t\t\t: this.term.unit\n\t\t\t\t\t\t? `${cell.key.toFixed(2)} ${this.term.unit}`\n\t\t\t\t\t\t: cell.key.toFixed(2)\n\t\t\t\tcell.height = renderV >= 0 ? t.scales.pos(renderV) : t.scales.neg(renderV)\n\t\t\t\tcell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace\n\t\t\t\tcell.y =\n\t\t\t\t\trenderV >= 0\n\t\t\t\t\t\t? t.counts.posMaxHt + twSettings.contBarGap - cell.height\n\t\t\t\t\t\t: t.counts.posMaxHt + twSettings.contBarGap\n\t\t\t\tcell.convertedValueLabel = !vc ? '' : convertUnits(cell.key, vc.fromUnit, vc.toUnit, vc.scaleFactor)\n\t\t\t}\n\t\t}\n\t}\n}\n\nconst TermCollectionContAddons = {\n\tsetCellProps: {\n\t\tvalue: function (\n\t\t\tthis: CollectionCont,\n\t\t\tcell: any,\n\t\t\tanno: any,\n\t\t\tvalue: TermCollectionTransformedValue,\n\t\t\ts: any,\n\t\t\tt: any,\n\t\t\tself: any,\n\t\t\twidth: number,\n\t\t\theight: number,\n\t\t\tdx: number,\n\t\t\t_dy: number,\n\t\t\t_i: number\n\t\t) {\n\t\t\t//\n\t\t\tconst tw = this.getTw() as CollectionCont\n\t\t\t//cell, tw, anno, value, s, t, self, width, height, dx, dy, i) {\n\t\t\tconst twSpecificSettings = self.config.settings.matrix.twSpecificSettings\n\t\t\tif (!twSpecificSettings[tw.$id]) twSpecificSettings[tw.$id] = {}\n\t\t\tconst twSettings = twSpecificSettings[tw.$id]\n\n\t\t\tif (!twSettings.contBarH) twSettings.contBarH = s.barh\n\t\t\tif (!('gap' in twSettings)) twSettings.contBarGap = 4\n\n\t\t\t// Determine if value is positive or negative\n\t\t\tconst isNegative = value.value < 0\n\n\t\t\tif (isNegative) {\n\t\t\t\t// For negative values, use the neg scale and position below the zero line\n\t\t\t\t// Height is the scale distance from 0 to the value\n\t\t\t\tcell.height = t.scales.neg ? t.scales.neg(value.value) - t.scales.neg(0) : 0\n\t\t\t\tcell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace\n\t\t\t\t// Position negative bars downward from the zero line\n\t\t\t\t// Cumulative height is the scale distance from 0 to pre_val_sum\n\t\t\t\tconst cumulativeHeight = t.scales.neg ? t.scales.neg(value.pre_val_sum) - t.scales.neg(0) : 0\n\t\t\t\tcell.y = t.counts.posMaxHt + twSettings.contBarGap + (t.scales.neg ? t.scales.neg(0) : 0) + cumulativeHeight\n\t\t\t} else {\n\t\t\t\t// For positive values, use the pos scale and position above the zero line\n\t\t\t\t// Height is the scale distance from 0 to the value\n\t\t\t\tcell.height = t.scales.pos(value.value) - t.scales.pos(0)\n\t\t\t\tcell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace\n\t\t\t\t// Position positive bars upward from the zero line\n\t\t\t\t// Cumulative height is the scale distance from 0 to pre_val_sum\n\t\t\t\tconst cumulativeHeight = t.scales.pos(value.pre_val_sum) - t.scales.pos(0)\n\t\t\t\tcell.y = t.counts.posMaxHt + twSettings.contBarGap - t.scales.pos(0) - cumulativeHeight - cell.height\n\t\t\t}\n\n\t\t\tcell.label = value.label\n\t\t\tcell.fill = twSettings[value.label]?.color || value.color || tw.term.propsByTermId?.[value.label]?.color\n\t\t\tcell.value = value.value\n\n\t\t\t// return the corresponding legend item data\n\t\t\treturn {\n\t\t\t\tref: t.ref,\n\t\t\t\tgroup: tw.$id,\n\t\t\t\tvalue: value.label,\n\t\t\t\torder: -1,\n\t\t\t\tentry: { key: value.label, label: value.label, fill: cell.fill }\n\t\t\t}\n\t\t}\n\t}\n}\n", "import { getCompInit, copyMerge, deepEqual } from '#rx'\nimport { setMatrixDom } from './matrix.dom'\nimport { setInteractivity } from './matrix.interactivity'\nimport { setRenderers } from './matrix.renderers'\nimport { MatrixCluster } from './matrix.cluster'\nimport { MatrixControls } from './matrix.controls'\nimport * as matrixData from './matrix.data'\nimport * as matrixLayout from './matrix.layout'\nimport * as matrixSerieses from './matrix.serieses'\nimport * as matrixLegend from './matrix.legend'\nimport * as matrixGroups from './matrix.groups'\nimport { setComputedConfig } from './matrix.config'\nimport { getTermGroups } from './matrix.xtw'\nimport svgLegend from '#dom/svg.legend'\nimport { mclass, dt2label, morigin, dtsnvindel, dtcnv } from '#shared/common.js'\nimport { select } from 'd3-selection'\nimport { sayerror } from '#dom'\nimport { getCombinedTermFilter } from '#filter'\nimport { rebaseGroupFilter } from '../../mass/groups.js'\nimport { PlotBase } from '#plots/PlotBase.js'\n\nexport class Matrix extends PlotBase {\n\tstatic type = 'matrix'\n\tconfigTermKeys = ['termgroups.lst', 'divideBy']\n\n\tconstructor(opts) {\n\t\tsuper(opts)\n\t\tthis.type = Matrix.type\n\t\tthis.holderTitle = 'Sample Matrix'\n\t\tthis.optionalFeatures = JSON.parse(sessionStorage.getItem('optionalFeatures') || `{}`)?.matrix || []\n\t\tsetInteractivity(this)\n\t\tsetRenderers(this)\n\t}\n\n\tasync init(appState) {\n\t\tconst opts = this.opts\n\t\tif (opts.reactsTo) this.reactsTo = opts.reactsTo\n\t\tthis.setDom = setMatrixDom\n\t\tthis.setDom(opts)\n\n\t\tthis.config = appState.plots.find(p => p.id === this.id)\n\t\tthis.settings = Object.assign({}, this.config.settings.matrix)\n\t\tthis.computed = {} // will hold settings/configuration/data that are computed or derived from other data\n\t\tif (this.dom.header) this.dom.header.html(this.config.preBuiltPlotTitle || this.holderTitle)\n\n\t\tthis.setControls(appState)\n\t\tthis.clusterRenderer = new MatrixCluster({ holder: this.dom.cluster, app: this.app, parent: this })\n\t\tthis.legendRenderer = svgLegend({\n\t\t\tholder: this.dom.legendG,\n\t\t\trectFillFxn: d => d.color,\n\t\t\ticonStroke: '#aaa',\n\t\t\thandlers: {\n\t\t\t\tlegend: {\n\t\t\t\t\tclick: this.legendClick\n\t\t\t\t}\n\t\t\t},\n\t\t\tsettings: {\n\t\t\t\tisExcludedAttr: 'isExcluded'\n\t\t\t},\n\t\t\tnote: 'CLICK A ROW LABEL OR ITEM TO APPLY FILTERING'\n\t\t})\n\n\t\t// enable embedding of termsetting and tree menu inside self.dom.menu\n\t\tthis.customTipApi = this.dom.tip.getCustomApi({\n\t\t\td: this.dom.menubody,\n\t\t\tclear: event => {\n\t\t\t\tif (event?.target) this.dom.menutop.style('display', 'none')\n\t\t\t\tthis.dom.menubody.selectAll('*').remove()\n\t\t\t\treturn this.customTipApi\n\t\t\t},\n\t\t\tshow: () => {\n\t\t\t\tthis.dom.menubody.style('display', 'block')\n\t\t\t},\n\t\t\thide: () => {\n\t\t\t\t//this.dom.menubody.style('display', 'none')\n\t\t\t}\n\t\t})\n\n\t\tthis.setPill(appState)\n\n\t\t/*\n\t\tLevels of mclass overrides, from more general to more specific. Same logic for dt2label\n\n\t\t1. server-level:\n\t\t  - specified as serverconfig.commonOverrides\n\t\t  - applied to the mclass from #shared/common on server startup\n\t\t  - applies to all datasets and charts\n\t\t  - overrides are applied to the static common.mclass object\n\t\t\n\t\t2. dataset-level: \n\t\t  - specified as termdb.mclass in the dataset's js file\n\t\t  - applied to the termdbConfig.mclass payload as returned from the /termdb?getTermdbConfig=1 route\n\t\t  - applies to all charts rendered for only the dataset/dslabel\n\t\t  - overrides are applied to a copy of common.mclass, not the original \"static\" object\n\n\t\t3. chart-level: \n\t\t  - specified as termdb[chartType].mclass in the dataset's js file\n\t\t  - applied to the termdbConfig[chartType].mclass payload as returned from the /termdb?getTermdbConfig=1 route\n\t\t  - applies to only the specific chart type as rendered for the dataset/dslabel\n\t\t  - overrides are applied to a copy of common.mclass + termdb.mclass\n\n\t\t!!! NOTE: \n\t\t\tBoolean configuration flags for mutually exclusive values may cause conflicting configurations\n\t\t\tin the resulting merged overrides, as outputted by rx.copyMerge()\n\t\t!!!\n\t\t*/\n\t\tconst commonKeys = { mclass, dt2label, morigin }\n\t\tfor (const k in commonKeys) {\n\t\t\tconst v = commonKeys[k]\n\t\t\tthis[k] = copyMerge({}, v, appState.termdbConfig[k] || {}, appState.termdbConfig.matrix?.[k] || {})\n\t\t}\n\t}\n\n\tsetControls(appState) {\n\t\t//if (this.opts.controls) return\n\t\tthis.controlsRenderer = new MatrixControls(\n\t\t\t{\n\t\t\t\tapp: this.app,\n\t\t\t\tid: this.id,\n\t\t\t\tparent: this,\n\t\t\t\tholder: this.dom.controls,\n\t\t\t\tgetSvg: () => this.dom.svg.node()\n\t\t\t},\n\t\t\tappState\n\t\t)\n\t}\n\n\t// reactsTo(action) {\n\t// \t// note: a parent app or 'plot' component is expected to already have\n\t// \t// a comprehensive reactsTo() call to filter the actions for this component,\n\t// \t// so only farther selective action filters should be applied here as needed\n\t// \treturn true\n\t// }\n\n\tgetState(appState) {\n\t\tconst config = appState.plots.find(p => p.id === this.id)\n\t\tconst filter0 = appState.termfilter.filter0\n\t\tthis.prevFilter0 = this.state?.filter0 // will be used to detect cohort change\n\n\t\tconst parentConfig = appState.plots.find(p => p.id === this.parentId)\n\t\tconst termfilter = getCombinedTermFilter(appState, config.filter || parentConfig?.filter)\n\t\treturn {\n\t\t\tisVisible: true,\n\t\t\tconfig,\n\t\t\tfilter: termfilter.filter,\n\t\t\tfilter0, // read-only, invisible filter currently only used for gdc dataset\n\t\t\thasVerifiedToken: this.app.vocabApi.hasVerifiedToken(),\n\t\t\ttokenVerificationMessage: this.app.vocabApi.tokenVerificationMessage,\n\t\t\tvocab: appState.vocab,\n\t\t\ttermdbConfig: appState.termdbConfig,\n\t\t\tclusterMethod: config.settings.hierCluster?.clusterMethod,\n\t\t\tdistanceMethod: config.settings.hierCluster?.distanceMethod,\n\t\t\tclusterSamples: config.settings.hierCluster?.clusterSamples,\n\t\t\tclusterRows: config.settings.hierCluster?.clusterRows,\n\t\t\tzScoreTransformation: config.settings.hierCluster?.zScoreTransformation,\n\t\t\tnav: appState.nav,\n\t\t\tgroups: rebaseGroupFilter(appState)\n\t\t}\n\t}\n\n\tasync main() {\n\t\ttry {\n\t\t\tthis.config = await this.getMutableConfig()\n\t\t\tif (this.mayRequireToken()) return\n\t\t\t// do not assign this.termgroups until the data request is complete, to avoid stale value in a race condition;\n\t\t\t// this termGroups value is directly associated with the submitted data request, and the response will match\n\t\t\t// the tw.$id's in these term groups\n\t\t\tconst termGroups = await getTermGroups(this.config.termgroups, this.app)\n\n\t\t\tconst prevTranspose = this.settings.transpose\n\t\t\t// controlsRenderer.getSettings() supplies settings that are not tracked in the global app and plot state\n\t\t\t// use structuredClone to avoid overwriting of original settings.matrix\n\t\t\tObject.assign(this.settings, structuredClone(this.config.settings), this.controlsRenderer.getSettings())\n\n\t\t\tthis.dom.loadingDiv.selectAll('*').remove()\n\t\t\tthis.dom.loadingDiv.html('').style('display', '').style('position', 'relative').style('left', '45%')\n\t\t\tthis.dom.svg.style('opacity', 0.1).style('pointer-events', 'none')\n\n\t\t\t// reset highlighted top/left dendrogram children to black when data request is triggered\n\t\t\tdelete this.clickedClusterIds\n\t\t\tdelete this.clickedLeftClusterIds\n\n\t\t\ttry {\n\t\t\t\tsetComputedConfig(this.config)\n\t\t\t\tconst promises = []\n\t\t\t\t// get the data\n\t\t\t\tif (this.setHierClusterData) promises.push(this.setHierClusterData())\n\t\t\t\tpromises.push(this.setData())\n\t\t\t\tthis.dom.loadingDiv.html('Processing data ...')\n\t\t\t\tawait Promise.all(promises)\n\t\t\t\tconst warnings = this.data.warnings.join('\\n')\n\t\t\t\tthis.dom.warningDiv.style('display', warnings.length ? '' : 'none').html(warnings)\n\t\t\t\tthis.applyLegendValueFilter() // need to applyLegendValueFiter before combineData to avoid error for hierCluster\n\t\t\t\tif (this.combineData) this.combineData()\n\t\t\t\t// tws in the config may be filled-in based on applicable server response data;\n\t\t\t\t// these filled-in config, such as tw.term.values|category2samplecount, will need to replace\n\t\t\t\t// the corresponding tracked state values in the app store, without causing unnecessary\n\t\t\t\t// dispatch notifications, so use app.save()\n\t\t\t\tthis.app.save({ type: 'plot_edit', id: this.id, config: this.config })\n\t\t\t} catch (e) {\n\t\t\t\tif (e == 'no data') {\n\t\t\t\t\tthis.showNoMatchingDataMessage()\n\t\t\t\t\treturn\n\t\t\t\t} else if (this.app.isAbortError(e)) {\n\t\t\t\t\t// ignore this error, but skip this update since a subsequent action is being processed\n\t\t\t\t\treturn\n\t\t\t\t} else {\n\t\t\t\t\tthis.dom.svg.style('display', 'none')\n\t\t\t\t\tthrow e\n\t\t\t\t}\n\t\t\t}\n\n\t\t\tthis.termGroups = termGroups // onl assign this as instance value after the data request, to prevent incorrect reference in a race condition\n\t\t\tthis.dom.loadingDiv.html('Updating ...').style('display', '')\n\t\t\tthis.termOrder = this.getTermOrder(this.data)\n\t\t\tthis.sampleGroups = this.getSampleGroups(this.hierClusterSamples || this.data)\n\t\t\tthis.sampleOrder = this.getSampleOrder(this.data)\n\t\t\t// even though there may not be sampleOrder (matrix columns) to render,\n\t\t\t// should still compute empty series data, legendData, etc to not break\n\t\t\t// controls/interactions handlers that use those data\n\t\t\tthis.setLayout()\n\t\t\tif (this.setHierColorScale) this.setHierColorScale(this.hierClusterData.clustering)\n\t\t\tif (!this.sampleOrder?.length) {\n\t\t\t\tthis.showNoMatchingDataMessage()\n\t\t\t\t// do not return early yet\n\t\t\t}\n\t\t\t// make sure computed dimensions are available from preceding steps, to use as control input values\n\t\t\tthis.controlsRenderer.main() // to update button count or cross out button labels\n\n\t\t\tthis.serieses = this.getSerieses(this.data)\n\t\t\t// TODO: may re-enable below if showing no-data message/suggestions is preferred over rendering empty matrix\n\t\t\t// can now return early before rendering computed data\n\t\t\t// if (!this.sampleOrder?.length) return\n\n\t\t\t// render the data\n\t\t\tthis.dom.loadingDiv.html('Rendering ...')\n\t\t\tif (this.plotDendrogramHclust) this.plotDendrogramHclust()\n\t\t\tthis.render()\n\t\t\tthis.mayDisplayCohortMessage()\n\t\t\tthis.dom.svg.style('display', '').style('opacity', 1).style('pointer-events', '')\n\n\t\t\tconst [xGrps, yGrps] = !this.settings.matrix.transpose ? ['sampleGrps', 'termGrps'] : ['termGrps', 'sampleGrps']\n\t\t\tconst d = this.dimensions\n\t\t\tthis.clusterRenderer.main({\n\t\t\t\tsettings: this.settings.matrix,\n\t\t\t\txGrps: this[xGrps],\n\t\t\t\tyGrps: this[yGrps],\n\t\t\t\tdimensions: d\n\t\t\t})\n\n\t\t\tthis.legendRenderer(this.legendData, {\n\t\t\t\tsettings: Object.assign({}, this.settings.legend, {\n\t\t\t\t\tsvgw: Math.max(400, d.mainw + d.xOffset - this.settings.matrix.margin.right),\n\t\t\t\t\tsvgh: d.mainh + d.yOffset,\n\t\t\t\t\tdimensions: d,\n\t\t\t\t\tpadleft: this.settings.legend.padleft //+ d.xOffset\n\t\t\t\t})\n\t\t\t})\n\t\t\tawait this.adjustSvgDimensions(prevTranspose)\n\t\t\tthis.controlsRenderer.main()\n\t\t\tif (this.data.removedHierClusterTerms) {\n\t\t\t\tfor (const r of this.data.removedHierClusterTerms) {\n\t\t\t\t\tsayerror(this.dom.errorDiv, r.text + ': ' + r.lst.join(', '))\n\t\t\t\t}\n\t\t\t}\n\t\t} catch (e) {\n\t\t\t// a new token message error may have been triggered by the data request here,\n\t\t\t// even if the initial state did not have a token message at the start of a dispatch\n\t\t\tconst message = this.app.vocabApi.tokenVerificationMessage\n\t\t\tthis.mayRequireToken(message)\n\t\t\tif (!message) {\n\t\t\t\tthis.app.tip.hide()\n\t\t\t\tthis.dom.loadingDiv.style('display', 'none')\n\t\t\t\tthrow e\n\t\t\t}\n\t\t}\n\n\t\tthis.resetInteractions()\n\t}\n\n\tshowNoMatchingDataMessage() {\n\t\tthis.forcedSampleCount = 0\n\t\tthis.dom.svg.style('opacity', 0.001).style('display', 'none')\n\t\t// an error on initial load/data request will cause computed data/settings to be empty,\n\t\t// which would cause input values to be empty for controls and likely thrown errors\n\t\tif (this.termOrder && this.dimensions) this.controlsRenderer.main({ sampleCount: 0 })\n\t\tthis.dom.loadingDiv.html('')\n\t\tconst div = this.dom.loadingDiv\n\t\t\t.append('div')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('text-align', 'center')\n\t\t\t.style('position', 'relative')\n\t\t\t.style('left', '-150px')\n\t\tdiv.append('div').style('margin', '5px 10px').html('No matching cohort sample data for the current gene list.')\n\n\t\tif (this.settings.matrix.showHints?.includes('genesetEdit')) {\n\t\t\tconst div1 = div.append('div').style('margin', '5px 10px')\n\t\t\tdiv1.append('span').html('You may change the selected cohort,')\n\n\t\t\tif (this.config.legendGrpFilter?.lst.length || this.config.legendValueFilter?.lst.length) {\n\t\t\t\tconst cnvBtn = this.controlsRenderer.btns.filter(d => d.label == 'CNV')?.node()\n\t\t\t\tif (cnvBtn) {\n\t\t\t\t\tdiv1.append('br')\n\t\t\t\t\tdiv1.append('span').html('show hidden ')\n\t\t\t\t\tdiv1\n\t\t\t\t\t\t.append('span')\n\t\t\t\t\t\t.html('CNV')\n\t\t\t\t\t\t.style('cursor', 'pointer')\n\t\t\t\t\t\t.style('text-decoration', 'underline')\n\t\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\t\tcnvBtn.click()\n\t\t\t\t\t\t})\n\t\t\t\t}\n\n\t\t\t\tconst mutationBtn = this.controlsRenderer.btns.filter(d => d.label == 'Mutation')?.node()\n\n\t\t\t\tif (cnvBtn && mutationBtn) div1.append('span').html(' or ')\n\t\t\t\tif (mutationBtn) {\n\t\t\t\t\tdiv1\n\t\t\t\t\t\t.append('span')\n\t\t\t\t\t\t.style('cursor', 'pointer')\n\t\t\t\t\t\t.style('text-decoration', 'underline')\n\t\t\t\t\t\t.html('Mutation')\n\t\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\t\tmutationBtn.click()\n\t\t\t\t\t\t})\n\t\t\t\t}\n\n\t\t\t\tif (cnvBtn || mutationBtn) div1.append('span').html(' data,')\n\t\t\t}\n\n\t\t\tdiv1.append('br')\n\t\t\tdiv1.append('span').html('or edit the gene list from the ')\n\t\t\tdiv1\n\t\t\t\t.append('span')\n\t\t\t\t.style('cursor', 'pointer')\n\t\t\t\t.style('text-decoration', 'underline')\n\t\t\t\t.html('Gene Set Edit Group menu.')\n\t\t\t\t.on('click', () => {\n\t\t\t\t\tconst GenesBtn = this.controlsRenderer.btns\n\t\t\t\t\t\t.filter(d => d.label == 'Genes')\n\t\t\t\t\t\t?.node()\n\t\t\t\t\t\t.click()\n\t\t\t\t\tconst i = setInterval(() => {\n\t\t\t\t\t\tconst editBtn = this.app.tip.d\n\t\t\t\t\t\t\t.selectAll('button')\n\t\t\t\t\t\t\t.filter(function () {\n\t\t\t\t\t\t\t\treturn this.innerHTML == 'Edit Group'\n\t\t\t\t\t\t\t})\n\t\t\t\t\t\t\t.node()\n\t\t\t\t\t\tif (editBtn) {\n\t\t\t\t\t\t\teditBtn.click()\n\t\t\t\t\t\t\tclearInterval(i)\n\t\t\t\t\t\t}\n\t\t\t\t\t}, 100)\n\t\t\t\t})\n\t\t}\n\t\tthis.dom.svg.style('display', 'none')\n\t}\n\n\tmayDisplayCohortMessage() {\n\t\tconst msg = deepEqual(this.state.filter0, this.prevFilter0) ? '' : 'The gene list is persisted across cohorts.'\n\t\tif (msg) {\n\t\t\tthis.dom.loadingDiv.html('')\n\t\t\tconst div = this.dom.loadingDiv\n\t\t\t\t.append('div')\n\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t.style('text-align', 'center')\n\t\t\t\t.style('position', 'relative')\n\t\t\t\t.style('left', '-150px')\n\t\t\tdiv.append('div').html(msg)\n\n\t\t\tif (this.settings.matrix.showHints?.includes('genesetEdit')) {\n\t\t\t\tconst div1 = div.append('div')\n\t\t\t\tdiv1.append('span').html(' You may edit the gene list from the ')\n\t\t\t\tdiv1\n\t\t\t\t\t.append('span')\n\t\t\t\t\t.style('cursor', 'pointer')\n\t\t\t\t\t.style('text-decoration', 'underline')\n\t\t\t\t\t.html('Gene Set Edit Group menu.')\n\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\tconst GenesBtn = this.controlsRenderer.btns\n\t\t\t\t\t\t\t.filter(d => d.label == 'Genes')\n\t\t\t\t\t\t\t?.node()\n\t\t\t\t\t\t\t.click()\n\t\t\t\t\t\tconst i = setInterval(() => {\n\t\t\t\t\t\t\tconst editBtn = this.app.tip.d\n\t\t\t\t\t\t\t\t.selectAll('button')\n\t\t\t\t\t\t\t\t.filter(function () {\n\t\t\t\t\t\t\t\t\treturn this.innerHTML == 'Edit Group'\n\t\t\t\t\t\t\t\t})\n\t\t\t\t\t\t\t\t.node()\n\t\t\t\t\t\t\tif (editBtn) {\n\t\t\t\t\t\t\t\teditBtn.click()\n\t\t\t\t\t\t\t\tclearInterval(i)\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}, 100)\n\t\t\t\t\t})\n\t\t\t}\n\t\t}\n\t\tthis.dom.loadingDiv.style('display', msg ? '' : 'none')\n\t}\n\n\tsampleKey(s) {\n\t\treturn s.row.sample\n\t}\n\n\tsampleLabel(s) {\n\t\treturn s.label || s.row._ref_.label || ''\n\t}\n\n\tsampleGrpKey(s) {\n\t\treturn s.grp.name\n\t}\n\n\tsampleGrpLabel(s) {\n\t\treturn s.grp.label || s.grp.name || ''\n\t}\n\n\ttermKey(t) {\n\t\treturn t.tw.$id\n\t}\n\n\ttermLabel(t) {\n\t\treturn t.label\n\t}\n\n\ttermGrpKey(t) {\n\t\treturn t.grp.name\n\t}\n\n\ttermGrpLabel(t) {\n\t\treturn t.grp.label || t.grp.name || [{ text: '\u22EE', dx: 3, cls: 'sjpp-exclude-svg-download' }]\n\t}\n\tdestroy() {\n\t\tselect(window).on(`resize.sjpp-${self.id}`, null)\n\t}\n}\n\n// assign class prototype methods and props that are exported from other matrix.* code files\nfor (const m of [matrixData, matrixGroups, matrixLayout, matrixSerieses, matrixLegend]) {\n\tfor (const methodName in m) {\n\t\tMatrix.prototype[methodName] = m[methodName]\n\t}\n}\n\nexport const matrixInit = getCompInit(Matrix)\n// this alias will allow abstracted dynamic imports\nexport const componentInit = matrixInit\n\nexport function makeChartBtnMenu(holder, chartsInstance) {\n\t/*\n\tholder: the holder in the tooltip\n\tchartsInstance: MassCharts instance\n\t\ttermdbConfig is accessible at chartsInstance.state.termdbConfig{}\n\t\tmass option is accessible at chartsInstance.app.opts{}\n\t*/\n\tchartsInstance.dom.tip.clear()\n\tconst menuDiv = holder.append('div')\n\tif (chartsInstance.state.termdbConfig.matrixplots) {\n\t\tfor (const plot of chartsInstance.state.termdbConfig.matrixplots) {\n\t\t\t/* plot: \n\t\t\t{\n\t\t\t\tname=str\n\t\t\t}\n\t\t\t*/\n\t\t\tmenuDiv\n\t\t\t\t.append('button')\n\t\t\t\t.style('margin', '10px')\n\t\t\t\t.style('padding', '10px 15px')\n\t\t\t\t.style('border-radius', '20px')\n\t\t\t\t.style('border-color', '#ededed')\n\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t.text(plot.name)\n\t\t\t\t.on('click', async () => {\n\t\t\t\t\tchartsInstance.dom.tip.hide()\n\t\t\t\t\tconst config = await chartsInstance.app.vocabApi.getMatrixByName(plot.name)\n\t\t\t\t\t//add pre-built plot name to config to be shown in the sandbox header\n\t\t\t\t\tconfig.preBuiltPlotTitle = plot.name\n\t\t\t\t\tchartsInstance.app.dispatch({\n\t\t\t\t\t\ttype: 'plot_create',\n\t\t\t\t\t\tconfig\n\t\t\t\t\t})\n\t\t\t\t})\n\t\t}\n\t}\n\n\tconst chart = {\n\t\tclickTo: chartsInstance.showTree_selectlst,\n\t\tchartType: 'matrix',\n\t\tusecase: { target: 'matrix', detail: 'termgroups' },\n\t\tprocessSelection: lst => {\n\t\t\treturn [\n\t\t\t\t{\n\t\t\t\t\tname: '',\n\t\t\t\t\tlst: lst.map(term => {\n\t\t\t\t\t\treturn { term }\n\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t]\n\t\t}\n\t}\n\tchartsInstance.showTree_selectlst(chart)\n}\n"],
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+  "names": ["self"]
+}

package/dist/chunk-AQ4OP4GR.js

@@ -0,0 +1,39 @@
+import {
+  isNumeric
+} from "./chunk-TV74I3Y5.js";
+
+// common/urlmap.js
+function urlmap_default(search = "", log = console.warn) {
+  const location = search ? { search } : window.location;
+  const urlp = /* @__PURE__ */ new Map();
+  for (const s of location.search.substr(1).split("&")) {
+    if (!s) continue;
+    const l = s.split("=");
+    if (l.length == 2 && l[0] != "" && l[1] != "") {
+      let value = decodeURIComponent(l[1]);
+      if (
+        // assume JSON encoding when the string is enclosed by matching characters below
+        value.startsWith('"') && value.endsWith('"') || value.startsWith("{") && value.endsWith("}") || value.startsWith("[") && value.endsWith("]")
+      ) {
+        try {
+          value = JSON.parse(value);
+        } catch (e) {
+          log(e);
+        }
+      } else if (isNumeric(value)) {
+        value = Number(value);
+      }
+      urlp.set(l[0].toLowerCase(), value);
+    } else if (l.length > 2) {
+      log(`unexpected '=' character in the URL parameter value for '${l[0]}'`);
+    } else {
+      log(`Invalid url parameter: '${s}'`);
+    }
+  }
+  return urlp;
+}
+
+export {
+  urlmap_default
+};
+//# sourceMappingURL=chunk-AQ4OP4GR.js.map