@sjcrh/proteinpaint-client 2.187.0 → 2.188.1

package/dist/chunk-2QQO4RRD.js

@@ -0,0 +1,2681 @@
+import {
+  addNewGroup,
+  fillTermWrapper,
+  getFilter,
+  getSamplelstTW,
+  newSandboxDiv,
+  renderTable,
+  rgb2hex,
+  table2col,
+  termsettingInit
+} from "./chunk-2XPDA6NL.js";
+import {
+  Menu
+} from "./chunk-HYOEWQ5P.js";
+import {
+  icons
+} from "./chunk-KWM6B3NL.js";
+import {
+  dofetch3
+} from "./chunk-MYWJQRTD.js";
+import {
+  NUMERIC_DICTIONARY_TERM,
+  TermTypes,
+  isNumericTerm
+} from "./chunk-FDK4UJMN.js";
+import {
+  dt2label,
+  dtcnv,
+  dtgeneexpression,
+  dtmetaboliteintensity,
+  dtproteomeabundance,
+  dtsnvindel,
+  mclass
+} from "./chunk-X7GDCYND.js";
+import {
+  format
+} from "./chunk-OAWQ6LOO.js";
+import {
+  pointer_default,
+  select_default
+} from "./chunk-I6Y4O3RR.js";
+
+// plots/matrix/matrix.interactivity.js
+var inputIndex = 0;
+var svgIcons = {
+  externalLink: ""
+  //`<svg xmlns="http://www.w3.org/2000/svg" height="16" width="16" viewBox="0 0 512 512" transform="scale(0.8)" style="display: inline-block; position:relative; top: -2px; left:4px;" ><!--!Font Awesome Free 6.5.0 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free Copyright 2023 Fonticons, Inc.--><path d="M320 0c-17.7 0-32 14.3-32 32s14.3 32 32 32h82.7L201.4 265.4c-12.5 12.5-12.5 32.8 0 45.3s32.8 12.5 45.3 0L448 109.3V192c0 17.7 14.3 32 32 32s32-14.3 32-32V32c0-17.7-14.3-32-32-32H320zM80 32C35.8 32 0 67.8 0 112V432c0 44.2 35.8 80 80 80H400c44.2 0 80-35.8 80-80V320c0-17.7-14.3-32-32-32s-32 14.3-32 32V432c0 8.8-7.2 16-16 16H80c-8.8 0-16-7.2-16-16V112c0-8.8 7.2-16 16-16H192c17.7 0 32-14.3 32-32s-14.3-32-32-32H80z"/></svg>`
+};
+function setInteractivity(self) {
+  let t;
+  self.delayedMouseoutHandler = () => {
+    if (t) clearTimeout(t);
+    t = setTimeout(self.mouseout, 500);
+  };
+  self.showCellInfo = function(event2) {
+    if (self.activeLabel || self.zoomArea) return;
+    if (event2.target.__data__?.isLegendItem) {
+      return;
+    }
+    if (!(event2.target.tagName == "rect" || event2.target.tagName == "image")) {
+      const d2 = event2.target.__data__;
+      const grp = d2?.grp;
+      if (grp?.legendData) {
+        if (event2.target.closest(".sjpp-matrix-series-group-label-g")) self.displaySampleGroupInfo(event2, grp);
+      }
+      return;
+    }
+    if (event2.target.tagName !== "rect" && !self.imgBox) self.imgBox = event2.target.getBoundingClientRect();
+    const d = event2.target.tagName == "rect" ? event2.target.__data__ : self.getImgCell(event2);
+    if (!d || !d.term || !d.sample) {
+      self.dom.tip.hide();
+      self.mouseout();
+      return;
+    }
+    const x = self.dimensions.xOffset + self.dimensions.seriesXoffset;
+    const y = self.dimensions.yOffset;
+    const s = self.settings.matrix;
+    const l = s.controlLabels;
+    const twSpecificSettings = self.config.settings.matrix.twSpecificSettings;
+    const twBarh = twSpecificSettings[d.tw.$id]?.contBarH;
+    const twGap = twSpecificSettings[d.tw.$id]?.contBarGap;
+    self.dom.rowBeam.attr("x", x).attr("y", y + d.seriesY).attr("height", twBarh ? twBarh + 2 * twGap : d.t.grp.type == "hierCluster" ? s.clusterRowh : s.rowh).style("display", "");
+    self.dom.colBeam.attr("x", x + d.x).attr("y", y).style("display", "");
+    self.dom.matrixCellHoverOver.clear();
+    const table = table2col({ holder: self.dom.matrixCellHoverOver.d.append("div") });
+    if (d.term.type == "geneVariant" && d.tw.q?.type == "values") {
+      {
+        const [c1, c2] = table.addRow();
+        c1.html(l.Sample);
+        c2.html(d.row._ref_.label || d.value?.sample);
+      }
+      {
+        const [c1, c2] = table.addRow();
+        c1.html("Gene");
+        c2.html(d.term.name);
+      }
+      const siblingCellLabels = {};
+      if (d.siblingCells)
+        for (const c of d.siblingCells) {
+          if (c.$id != d.$id) continue;
+          const v = c.value;
+          const p = v.pairlst;
+          const dtLabel = v.origin ? `${v.origin} ${dt2label[v.dt]}` : dt2label[v.dt];
+          const label = getLabel(c, v, p);
+          const color = c.fill == v.color || v.class == "Blank" ? "" : c.fill;
+          if (!siblingCellLabels[dtLabel]) {
+            siblingCellLabels[dtLabel] = [{ label, color }];
+          } else {
+            siblingCellLabels[dtLabel].push({ label, color });
+          }
+        }
+      for (const [dtLabel, classArray] of Object.entries(siblingCellLabels).sort((a, b) => b.length - a.length)) {
+        const [c1, c2] = table.addRow();
+        c1.html(dtLabel);
+        c2.html(`<span style="display:inline-block; width:12px; height:12px; background-color:${classArray[0].color}" ></span>
+					${classArray[0].label}`);
+        for (const classType of classArray.slice(1)) {
+          const [c12, c22] = table.addRow();
+          c12.html("");
+          c22.html(`<span style="display:inline-block; width:12px; height:12px; background-color:${classType.color}" ></span>
+						${classType.label}`);
+        }
+      }
+    } else {
+      {
+        const [c1, c2] = table.addRow();
+        c1.html(l.Sample);
+        c2.html(d.row._ref_.label);
+      }
+      let survivalInfo;
+      if (d.term.type == TermTypes.SURVIVAL && d.exitCodeKey) {
+        survivalInfo = d.term.values?.[d.exitCodeKey]?.label || d.exitCodeKey;
+      }
+      if (survivalInfo || d.convertedValueLabel || d.label || d.label === 0) {
+        if (d.term.type == TermTypes.GENE_EXPRESSION) {
+          {
+            const [c1, c2] = table.addRow();
+            c1.html("Gene");
+            c2.html(d.term.gene);
+          }
+          {
+            const colorSquare = d.tw?.q?.convert2ZScore && d.tw.q.mode == "continuous" || d.tw.q.mode !== "continuous" ? `<span style="display:inline-block; width:12px; height:12px; background-color:${d.fill == "#fff" || d.fill == "transparent" ? "" : d.fill}" ></span>` : "";
+            const [c1, c2] = table.addRow();
+            c1.html("Gene Expression");
+            c2.html(
+              `${colorSquare} ${d.convertedValueLabel || d.label}${d.tw?.q?.convert2ZScore && d.tw.q.mode == "continuous" && d.zscoreLabel ? d.zscoreLabel : ""}`
+            );
+          }
+        } else if (d.term.type == TermTypes.METABOLITE_INTENSITY) {
+          {
+            const [c1, c2] = table.addRow();
+            c1.html("Metabolite");
+            c2.html(d.term.name);
+          }
+          {
+            const colorSquare = d.tw?.q?.convert2ZScore && d.tw.q.mode == "continuous" || d.tw.q.mode !== "continuous" ? `<span style="display:inline-block; width:12px; height:12px; background-color:${d.fill == "#fff" || d.fill == "transparent" ? "" : d.fill}" ></span>` : "";
+            const [c1, c2] = table.addRow();
+            c1.html("Metabolite Intensity");
+            c2.html(
+              `${colorSquare} ${d.convertedValueLabel || d.label}${d.tw?.q?.convert2ZScore && d.tw.q.mode == "continuous" && d.zscoreLabel ? d.zscoreLabel : ""}`
+            );
+          }
+        } else if (d.term.type == TermTypes.PROTEOME_ABUNDANCE) {
+          {
+            const [c1, c2] = table.addRow();
+            c1.html("gene");
+            c2.html(d.term.name);
+          }
+          {
+            const colorSquare = d.tw?.q?.convert2ZScore && d.tw.q.mode == "continuous" || d.tw.q.mode !== "continuous" ? `<span style="display:inline-block; width:12px; height:12px; background-color:${d.fill == "#fff" || d.fill == "transparent" ? "" : d.fill}" ></span>` : "";
+            const [c1, c2] = table.addRow();
+            c1.html("Protein Abundance");
+            c2.html(
+              `${colorSquare} ${d.convertedValueLabel || d.label}${d.tw?.q?.convert2ZScore && d.tw.q.mode == "continuous" && d.zscoreLabel ? d.zscoreLabel : ""}`
+            );
+          }
+        } else if (d.term.type == TermTypes.SURVIVAL) {
+          {
+            const [c1, c2] = table.addRow();
+            c1.html(d.term.name);
+            c2.html(`<span style="display:inline-block; width:12px; height:12px; background-color:${d.fill == "#fff" || d.fill == "transparent" ? "" : d.fill}" ></span>
+							${survivalInfo || d.label}`);
+          }
+          const timeToEventKey = "Time to Event: " + (d.timeToEventKey ? d.timeToEventKey + (d.term.unit ? ` ${d.term.unit}` : "") : (d.convertedValueLabel || d.label) + (d.tw?.q?.convert2ZScore && d.tw.q.mode == "continuous" && d.zscoreLabel ? d.zscoreLabel : ""));
+          {
+            const [c1, c2] = table.addRow();
+            c1.html("");
+            c2.html(timeToEventKey);
+          }
+        } else if (d.term.type == TermTypes.TERM_COLLECTION) {
+          const renderedValues = d.row[d.$id].renderedValues;
+          const sortedRenderedValues = renderedValues.filter((rv) => rv.value !== 0).sort((a, b) => b.value - a.value);
+          for (const renderedValue of sortedRenderedValues) {
+            const colorSquare = `<span style="display:inline-block; width:12px; height:12px; background-color:${renderedValue.color}"></span>`;
+            const [c1, c2] = table.addRow();
+            c1.html(`${colorSquare} ${renderedValue.label}`);
+            c2.html(`${renderedValue.value.toFixed(2)}%`);
+          }
+        } else {
+          const colorSquare = d.tw?.q?.convert2ZScore && d.tw.q.mode == "continuous" || d.tw.q.mode !== "continuous" ? `<span style="display:inline-block; width:12px; height:12px; background-color:${d.fill == "#fff" || d.fill == "transparent" ? "" : d.fill}" ></span>` : "";
+          const [c1, c2] = table.addRow();
+          c1.html(d.term.name);
+          c2.html(
+            `${colorSquare} ${d.convertedValueLabel || d.label}${d.tw?.q?.convert2ZScore && d.tw.q.mode == "continuous" && d.zscoreLabel ? d.zscoreLabel : ""}`
+          );
+        }
+      }
+    }
+    self.dom.matrixCellHoverOver.show2(event2.clientX, event2.clientY);
+    self.dom.mainG.on("mouseout", self.mouseout);
+  };
+  self.getImgCell = function(event2) {
+    if (!self.imgBox) {
+      if (event2.target.tagName == "image") self.imgBox = event2.target.getBoundingClientRect();
+      else return;
+    }
+    const y = event2.clientY - self.imgBox.y - event2.target.clientTop;
+    const d = event2.target.__data__.find((series) => series.hoverY0 <= y && y <= series.hoverY1);
+    if (!d) return;
+    const { xMin, dx } = self.dimensions;
+    const x2 = event2.clientX - self.imgBox.x - event2.target.clientLeft + xMin;
+    for (const cell of d.cells) {
+      const min = cell.x;
+      const max = cell.x + dx;
+      if (min <= x2 && x2 <= max) return cell;
+    }
+    return null;
+  };
+  self.mouseout = function() {
+    if (!self.activeLabel && self.dom.tip) self.dom.tip.hide();
+    delete self.imgBox;
+    if (self.dom.colBeam) self.dom.colBeam.style("display", "none");
+    if (self.dom.rowBeam) self.dom.rowBeam.style("display", "none");
+    if (self.dom.matrixCellHoverOver) self.dom.matrixCellHoverOver.clear();
+  };
+  self.mouseclick = async function(event2, data) {
+    const q = self.state.termdbConfig.queries;
+    if (!q) return;
+    if (!(q.singleSampleGenomeQuantification || q.singleSampleMutation || q.NIdata || q.DZImages)) return;
+    self.dom.mainG.on("mouseout", null);
+    delete self.imgBox;
+    const sampleData = data || event2.target.__data__;
+    if (!sampleData) return;
+    const s = self.config.settings.matrix;
+    const sample = {
+      sample_id: sampleData.row._ref_.label
+    };
+    const geneName = sampleData.term?.type == "geneVariant" ? sampleData.term.name : null;
+    self.dom.clickMenu.clear();
+    self.dom.dendroClickMenu.clear();
+    self.dom.brushMenu.clear();
+    self.dom.matrixCellHoverOver.clear();
+    if (self.dom.sampleListMenu) self.dom.sampleListMenu.destroy();
+    if (q.singleSampleGenomeQuantification) {
+      for (const k in q.singleSampleGenomeQuantification) {
+        const menuDiv = self.dom.clickMenu.d.append("div").attr("class", "sja_menuoption sja_sharp_border").attr("data-testid", "sjpp-ssgp-menu-btn").text(k).on("click", async (event3) => {
+          const sandbox = newSandboxDiv(self.opts.plotDiv || select_default(self.opts.holder.node().parentNode));
+          sandbox.header.text(sample.sample_id);
+          await (await import("./plot.ssgq-FHE5KU5C.js")).plotSingleSampleGenomeQuantification(
+            self.state.termdbConfig,
+            self.state.vocab.dslabel,
+            k,
+            sample,
+            sandbox.body.append("div").style("margin", "20px"),
+            self.app.opts.genome,
+            geneName
+          );
+          menuDiv.remove();
+          self.dom.clickMenu.d.selectAll("*").remove();
+        });
+      }
+    }
+    if (q?.singleSampleMutation) {
+      const menuDiv = self.dom.clickMenu.d.append("div").attr("class", "sja_menuoption sja_sharp_border").attr("data-testid", "oncoMatrix_termLabel_disco_button").text("Disco plot").on("click", async (event3) => {
+        const sandbox = newSandboxDiv(self.opts.plotDiv || select_default(self.opts.holder.node().parentNode));
+        sandbox.header.text(sample.sample_id);
+        (await import("./plot.disco-2RPNPX6E.js")).default(
+          self.state.termdbConfig,
+          self.state.vocab.dslabel,
+          sample,
+          sandbox.body,
+          self.app.opts.genome
+        );
+        menuDiv.remove();
+        self.dom.clickMenu.d.selectAll("*").remove();
+      });
+    }
+    if (q.DZImages) {
+      const menuDiv = self.dom.clickMenu.d.append("div").attr("class", "sja_menuoption sja_sharp_border").attr("data-testid", "oncoMatrix_termLabel_dzi_button").style("display", "none").text(`${q.DZImages.type} Images (0)`);
+      const data2 = await dofetch3("sampledzimages", {
+        body: {
+          genome: self.app.opts.genome.name,
+          dslabel: self.state.vocab.dslabel,
+          sample_id: sample.sample_id
+        }
+      });
+      if (data2.sampleDZImages?.length > 0) {
+        menuDiv.style("display", "block");
+        menuDiv.text(`${q.DZImages.type} Images (${data2.sampleDZImages.length})`);
+        menuDiv.on("click", async (_) => {
+          const sandbox = newSandboxDiv(self.opts.plotDiv || select_default(self.opts.holder.node().parentNode));
+          sandbox.header.text(sample.sample_id);
+          (await import("./plot.dzi-7VTYYGGW.js")).default(
+            self.state.vocab.dslabel,
+            sandbox.body,
+            self.app.opts.genome,
+            sample.sample_id,
+            data2.sampleDZImages
+          );
+          menuDiv.remove();
+          self.dom.clickMenu.d.selectAll("*").remove();
+        });
+      }
+    }
+    if (q.NIdata) {
+      for (const [queryKey, ref] of Object.entries(q.NIdata)) {
+        const menuDiv = self.dom.clickMenu.d.append("div").attr("class", "sja_menuoption sja_sharp_border").text("Neuro Image: " + queryKey).on("click", async () => {
+          self.dom.clickMenu.clear();
+          const config = {
+            chartType: "brainImaging",
+            queryKey,
+            settings: {
+              brainImaging: {
+                brainImageL: ref.parameters.l,
+                brainImageF: ref.parameters.f,
+                brainImageT: ref.parameters.t
+              }
+            },
+            selectedSampleFileNames: [sample.sample_id + ".nii"]
+          };
+          self.app.dispatch({
+            type: "plot_create",
+            config
+          });
+        });
+      }
+    }
+    const l = self.settings.matrix.controlLabels;
+    const table = table2col({ holder: self.dom.clickMenu.d.append("div").append("span") });
+    const templates = self.state.termdbConfig.urlTemplates;
+    if (templates?.sample) {
+      const name = sampleData[templates.sample.namekey] || sampleData.sample || sampleData.row.sample;
+      const [c1, c2] = table.addRow();
+      c1.html(l.Sample);
+      c2.html(
+        `<a href="${templates.sample.base}${name}" target="_blank">${sampleData.row._ref_.label} ${svgIcons.externalLink}</a>`
+      );
+    } else {
+      const [c1, c2] = table.addRow();
+      c1.html(l.Sample);
+      c2.html(sampleData.row._ref_.label || sampleData.value.sample);
+    }
+    if (sampleData.term?.type == "geneVariant" && sampleData.tw.q?.type == "values") {
+      if (sampleData.value) {
+        if (templates?.gene) {
+          const name = self.data.refs.byTermId[sampleData.tw.$id][templates.gene.namekey];
+          const [c1, c2] = table.addRow();
+          c1.html("Gene");
+          c2.html(
+            `<a href="${templates.gene.base}${name}" target="_blank">${sampleData.tw.term.name} ${svgIcons.externalLink}</a>`
+          );
+        } else {
+          const [c1, c2] = table.addRow();
+          c1.html("Gene");
+          c2.html(sampleData.term.name);
+        }
+        const siblingCellLabels = {};
+        for (const c of sampleData.siblingCells) {
+          if (c.$id != sampleData.$id) continue;
+          const v = c.value;
+          const p = v.pairlst;
+          const dtLabel = v.origin ? `${v.origin} ${dt2label[v.dt]}` : dt2label[v.dt];
+          const label = getLabel(c, v, p);
+          const color = c.fill == v.color || v.class == "Blank" ? "" : c.fill;
+          if (!siblingCellLabels[dtLabel]) {
+            siblingCellLabels[dtLabel] = [{ label, color }];
+          } else {
+            siblingCellLabels[dtLabel].push({ label, color });
+          }
+        }
+        for (const [dtLabel, classArray] of Object.entries(siblingCellLabels).sort((a, b) => b.length - a.length)) {
+          const [c1, c2] = table.addRow();
+          c1.html(dtLabel);
+          c2.html(`<span style="display:inline-block; width:12px; height:12px; background-color:${classArray[0].color}" ></span>
+						${classArray[0].label}`);
+          for (const classType of classArray.slice(1)) {
+            const [c12, c22] = table.addRow();
+            c12.html("");
+            c22.html(`<span style="display:inline-block; width:12px; height:12px; background-color:${classType.color}" ></span>
+							${classType.label}`);
+          }
+        }
+      }
+    } else if (sampleData.term) {
+      let survivalInfo;
+      if (sampleData.term.type == TermTypes.SURVIVAL && sampleData.exitCodeKey) {
+        survivalInfo = sampleData.term.values?.[sampleData.exitCodeKey]?.label || sampleData.exitCodeKey;
+      }
+      if (survivalInfo || sampleData.convertedValueLabel || sampleData.label || sampleData.label === 0) {
+        if (sampleData.term.type == TermTypes.GENE_EXPRESSION) {
+          {
+            const [c1, c2] = table.addRow();
+            c1.html("Gene");
+            c2.html(sampleData.term.name);
+          }
+          {
+            const colorSquare = sampleData.tw?.q?.convert2ZScore && sampleData.tw.q.mode == "continuous" || sampleData.tw.q.mode !== "continuous" ? `<span style="display:inline-block; width:12px; height:12px; background-color:${sampleData.fill == "#fff" || sampleData.fill == "transparent" ? "" : sampleData.fill}" ></span>` : "";
+            const [c1, c2] = table.addRow();
+            c1.html("Gene Expression");
+            c2.html(
+              `${colorSquare} ${sampleData.convertedValueLabel || sampleData.label}${sampleData.tw?.q?.convert2ZScore && sampleData.tw.q.mode == "continuous" && sampleData.zscoreLabel ? sampleData.zscoreLabel : ""}`
+            );
+          }
+        } else if (sampleData.term.type == TermTypes.METABOLITE_INTENSITY) {
+          {
+            const [c1, c2] = table.addRow();
+            c1.html("Metabolite");
+            c2.html(sampleData.term.name);
+          }
+          {
+            const colorSquare = sampleData.tw?.q?.convert2ZScore && sampleData.tw.q.mode == "continuous" || sampleData.tw.q.mode !== "continuous" ? `<span style="display:inline-block; width:12px; height:12px; background-color:${sampleData.fill == "#fff" || sampleData.fill == "transparent" ? "" : sampleData.fill}" ></span>` : "";
+            const [c1, c2] = table.addRow();
+            c1.html("Metabolite Intensity");
+            c2.html(
+              `${colorSquare} ${sampleData.convertedValueLabel || sampleData.label}${sampleData.tw?.q?.convert2ZScore && sampleData.tw.q.mode == "continuous" && sampleData.zscoreLabel ? sampleData.zscoreLabel : ""}`
+            );
+          }
+        } else if (sampleData.term.type == TermTypes.PROTEOME_ABUNDANCE) {
+          {
+            const [c1, c2] = table.addRow();
+            c1.html("Gene");
+            c2.html(sampleData.term.name);
+          }
+          {
+            const colorSquare = sampleData.tw?.q?.convert2ZScore && sampleData.tw.q.mode == "continuous" || sampleData.tw.q.mode !== "continuous" ? `<span style="display:inline-block; width:12px; height:12px; background-color:${sampleData.fill == "#fff" || sampleData.fill == "transparent" ? "" : sampleData.fill}" ></span>` : "";
+            const [c1, c2] = table.addRow();
+            c1.html("Protein Abundance");
+            c2.html(
+              `${colorSquare} ${sampleData.convertedValueLabel || sampleData.label}${sampleData.tw?.q?.convert2ZScore && sampleData.tw.q.mode == "continuous" && sampleData.zscoreLabel ? sampleData.zscoreLabel : ""}`
+            );
+          }
+        } else if (sampleData.term.type == TermTypes.SURVIVAL) {
+          {
+            const [c1, c2] = table.addRow();
+            c1.html(sampleData.term.name);
+            c2.html(`<span style="display:inline-block; width:12px; height:12px; background-color:${sampleData.fill == "#fff" || sampleData.fill == "transparent" ? "" : sampleData.fill}" ></span>
+							${survivalInfo || sampleData.label}`);
+          }
+          const timeToEventKey = "Time to Event: " + (sampleData.timeToEventKey ? sampleData.timeToEventKey + (sampleData.term.unit ? ` ${sampleData.term.unit}` : "") : (sampleData.convertedValueLabel || sampleData.label) + (sampleData.tw?.q?.convert2ZScore && sampleData.tw.q.mode == "continuous" && sampleData.zscoreLabel ? sampleData.zscoreLabel : ""));
+          {
+            const [c1, c2] = table.addRow();
+            c1.html("");
+            c2.html(timeToEventKey);
+          }
+        } else if (sampleData.term.type == TermTypes.TERM_COLLECTION) {
+          const renderedValues = sampleData.row[sampleData.$id].renderedValues;
+          const sortedRenderedValues = renderedValues.filter((rv) => rv.value !== 0).sort((a, b) => b.value - a.value);
+          for (const renderedValue of sortedRenderedValues) {
+            const colorSquare = `<span style="display:inline-block; width:12px; height:12px; background-color:${renderedValue.color}"></span>`;
+            const [c1, c2] = table.addRow();
+            c1.html(`${colorSquare} ${renderedValue.label}`);
+            c2.html(`${renderedValue.value.toFixed(2)}%`);
+          }
+        } else {
+          const colorSquare = sampleData.tw?.q?.convert2ZScore && sampleData.tw.q.mode == "continuous" || sampleData.tw.q.mode !== "continuous" ? `<span style="display:inline-block; width:12px; height:12px; background-color:${sampleData.fill == "#fff" || sampleData.fill == "transparent" ? "" : sampleData.fill}" ></span>` : "";
+          const [c1, c2] = table.addRow();
+          c1.html(sampleData.term.name);
+          c2.html(
+            `${colorSquare} ${sampleData.convertedValueLabel || sampleData.label}${sampleData.tw?.q?.convert2ZScore && sampleData.tw.q.mode == "continuous" && sampleData.zscoreLabel ? sampleData.zscoreLabel : ""}`
+          );
+        }
+      }
+    }
+    self.dom.clickMenu.show(event2.clientX, event2.clientY, false, true);
+  };
+  self.legendClick = function() {
+  };
+  self.svgMousemove = function(event2) {
+    if (!self.dragged) return;
+    const s = self.config.settings.matrix;
+    const d = self.dragged;
+    const x2 = !s.transpose ? d.x : d.x - d.clientX + event2.clientX;
+    const y2 = !s.transpose ? d.y - d.clientY + event2.clientY : d.y;
+    d.clone.attr("transform", `translate(${x2},${y2})`);
+  };
+  self.svgMouseup = function(event2) {
+    if (!self.dragged) return;
+    self.dragged.clone.remove();
+    delete self.dragged;
+    delete self.clicked;
+  };
+  self.getVisibleCenterCell = function(dx) {
+    const d = self.dimensions;
+    if (d.seriesXoffset <= 0 && d.mainw >= d.zoomedMainW) {
+      return self.sampleOrder[Math.floor(self.sampleOrder.length / 2)];
+    }
+    const w = 0.5 * d.mainw - d.seriesXoffset - dx;
+    const i = Math.round(w / d.dx);
+    return self.sampleOrder[i];
+  };
+  setTermActions(self);
+  setTermGroupActions(self);
+  setSampleGroupActions(self);
+  setZoomPanActions(self);
+  setResizeHandler(self);
+  setLengendActions(self);
+  setMutationSelectionActions(self);
+}
+function setResizeHandler(self) {
+  let resizeId;
+  select_default(window).on(`resize.sjpp-${self.id}`, () => {
+    if (resizeId) clearTimeout(resizeId);
+    if (self.dimensions && self.layout) resizeId = setTimeout(resize, 200);
+  });
+  function resize() {
+    if (self.dimensions && self.layout) self.main();
+  }
+}
+function setTermActions(self) {
+  setLabelDragEvents(self, "term");
+  self.setPill = function(appState) {
+    self.pill = termsettingInit({
+      tip: self.customTipApi,
+      menuOptions: "all",
+      menuLayout: "horizontal",
+      vocabApi: self.app.vocabApi,
+      vocab: appState.vocab,
+      activeCohort: appState.activeCohort,
+      numericEditMenuVersion: ["discrete", "continuous"],
+      usecase: { target: "matrix" },
+      getBodyParams: () => {
+        const currentGeneNames = [];
+        for (const g of self.config.termgroups) {
+          if (self.chartType == "hierCluster" && g.type != "hierCluster") continue;
+          for (const t of g.lst) {
+            if (t.term.chr) {
+              currentGeneNames.push(`${t.term.chr}:${t.term.start}-${t.term.stop}`);
+            } else if (t.term.gene) {
+              currentGeneNames.push(t.term.gene);
+            }
+          }
+        }
+        if (currentGeneNames.length) return { currentGeneNames };
+        return {};
+      },
+      //holder: {}, //self.dom.inputTd.append('div'),
+      //debug: opts.debug,
+      renderAs: "none",
+      callback: (tw) => {
+        if (tw && !tw.q) throw "data.q{} missing from pill callback";
+        const t = self.activeLabel || self.lastactiveLabel;
+        if (tw) {
+          tw.label = t.tw.label;
+          if (t && t.tw) tw.$id = t.tw.$id;
+          const legendValueFilter = self.mayRemoveTvsEntry(tw);
+          self.pill.main(Object.assign({ filter: self.state.filter }, tw));
+          self.app.dispatch({
+            type: "plot_nestedEdits",
+            id: self.opts.id,
+            edits: [
+              {
+                nestedKeys: ["termgroups", t.grpIndex, "lst", t.lstIndex],
+                value: tw
+              },
+              {
+                nestedKeys: ["legendValueFilter"],
+                value: legendValueFilter
+              }
+            ]
+          });
+        } else {
+          self.removeTerm();
+        }
+        self.dom.tip.hide();
+      }
+    });
+  };
+  self.getMenuOptions = function(t) {
+    return self.config.chartType == "hierCluster" && t.grp.type === "hierCluster" ? "{remove,}" : t.tw.term.type == "geneVariant" ? "{edit,replace,remove}" : t.tw.term.type == "termCollection" ? "{edit,replace,remove}" : "*";
+  };
+  self.showTermMenu = async function(event2) {
+    const t = event2.target.__data__;
+    if (!t || !t.tw || !t.grp) return;
+    const s = self.settings.matrix;
+    const l = s.controlLabels;
+    self.activeLabel = t;
+    self.dom.menutop.style("display", "").selectAll("*").remove();
+    self.dom.menubody.style("padding", 0).selectAll("*").remove();
+    const termMenuWaitDiv = self.dom.menutop.append("div").style("display", "block").text("Loading...");
+    self.dom.tip.show(event2.clientX - 20, event2.clientY - 20);
+    const pillArg = Object.assign(
+      { menuOptions: self.getMenuOptions(t), filter: self.state.filter },
+      t.tw ? t.tw : { term: null, q: null }
+    );
+    mayAddEditMsg(pillArg, t);
+    await self.pill.main(pillArg);
+    termMenuWaitDiv.remove();
+    self.dom.shortcutDiv = self.dom.menutop.append("div").style("z-index", 1e4);
+    self.showShortcuts(t, self.dom.shortcutDiv);
+    self.dom.twMenuDiv = self.dom.menutop.append("div");
+    const labelEditDiv = self.dom.twMenuDiv.append("div").style("text-align", "center");
+    if (t.tw?.term?.type) labelEditDiv.append("span").text(`${l.Term} `);
+    const twlabel = t.tw.label || t.tw.term.name;
+    const vartype = t.tw.term.type == "geneVariant" || t.tw.term.type == TermTypes.GENE_EXPRESSION ? "gene" : t.tw.term.type == TermTypes.METABOLITE_INTENSITY ? "metabolite" : t.tw.term.type == TermTypes.PROTEOME_ABUNDANCE ? "protein" : "variable";
+    if (t.tw?.term?.type)
+      self.dom.twLabelInput = labelEditDiv.append("input").attr("type", "text").attr("size", twlabel.length + 3).attr("aria-label", `Type to edit the ${vartype} label`).style("padding", "1px 5px").style("text-align", "center").property("value", twlabel).on("input", () => {
+        const value = self.dom.twLabelInput.property("value");
+        self.dom.twLabelInput.attr("size", value.length + 3);
+        self.dom.twLabelEditBtn.style("display", value.trim() === twlabel ? "none" : "inline");
+      });
+    if (t.tw?.term?.type)
+      self.dom.twLabelEditBtn = labelEditDiv.append("button").style("display", "none").style("margin-left", "5px").html("submit").on("click", () => {
+        if (twlabel != self.dom.twLabelInput.property("value").trim()) self.updateTermLabel();
+        self.dom.tip.hide();
+      });
+    if (vartype == "gene") {
+      if (t.tw.term.type == "geneVariant") {
+        self.dom.gbButton = labelEditDiv.append("button").style("text-align", "center").html("Lollipop").attr("data-testid", "oncoMatrix_cell_lollipop_button").on("click", async () => {
+          await self.launchGB(t);
+          self.dom.tip.hide();
+        });
+      }
+    }
+    if (self.state.termdbConfig.urlTemplates?.gene && vartype == "gene") {
+      const templates = self.state.termdbConfig.urlTemplates;
+      self.dom.geneSummaryLink = labelEditDiv.append("div").style("display", "inline-block").style("margin-left", "5px").style("text-align", "center").style("color", "rgb(0, 0, 238)").style("cursor", "pointer").style("text-decoration", "underline").html(`${templates.gene.defaultText || ""}${svgIcons.externalLink}`).on("click", async () => {
+        const name = self.data.refs.byTermId[t.tw.$id][templates.gene.namekey];
+        window.open(`${templates.gene.base}${name}`, "_blank");
+        self.dom.tip.hide();
+      });
+    }
+    const twSpecificSettings = self.config.settings.matrix.twSpecificSettings;
+    if (!twSpecificSettings[t.tw.$id]) twSpecificSettings[t.tw.$id] = {};
+    const twSettings = twSpecificSettings[t.tw.$id];
+    const rowHeightColorEditDiv = self.dom.twMenuDiv.append("div").style("text-align", "center");
+    if (t.grp?.type !== "hierCluster" && t.tw?.q?.mode == "continuous") {
+      rowHeightColorEditDiv.append("span").text("Row Height");
+      self.dom.twRowheightInput = rowHeightColorEditDiv.append("input").attr("type", "number").attr("aria-label", `edit the row height`).style("padding", "1px 5px").style("text-align", "center").style("width", "60px").property("value", twSettings.contBarH).on("keyup", async (event3) => {
+        if (event3.code != "Enter") return;
+        const newBarh = parseFloat(self.dom.twRowheightInput.node().value);
+        twSettings.contBarH = newBarh;
+        self.app.dispatch({
+          type: "plot_edit",
+          id: self.opts.id,
+          config: { settings: { matrix: { twSpecificSettings } } }
+        });
+        self.dom.tip.hide();
+      });
+    }
+    if (t.grp?.type !== "hierCluster" && t.tw?.q?.mode == "continuous" && t.tw.term.type != "survival" && t.tw.term.type != "termCollection" && t.tw.q.convert2ZScore != true) {
+      rowHeightColorEditDiv.append("span").text("Bar Color");
+      self.dom.twRowColorInput = rowHeightColorEditDiv.append("input").attr("type", "color").attr("aria-label", `change the bar color`).style("padding", "1px 5px").attr("value", twSettings.contBarColor).on("change", async () => {
+        const color = self.dom.twRowColorInput.node().value;
+        twSettings.contBarColor = color;
+        self.app.dispatch({
+          type: "plot_edit",
+          id: self.opts.id,
+          config: { settings: { matrix: { twSpecificSettings } } }
+        });
+        self.dom.tip.hide();
+      });
+    }
+    if (self.config.settings.matrix.maxSample && t.counts.samples && t.allCounts.samples) {
+      self.dom.twMenuDiv.append("div").style("text-align", "center").style("margin", "5px").text(`#${l.samples}: ${t.counts.samples} rendered, ${t.allCounts.samples - t.counts.samples} not rendered`);
+    }
+    self.dom.twMenuBar = self.dom.twMenuDiv.append("div").style("text-align", "center");
+    const clickedElem = event2.target;
+    self.pill.showMenu(event2, clickedElem, self.dom.twMenuBar);
+    self.dom.grpMenuDiv = self.dom.menutop.append("div").style("margin-top", "10px");
+  };
+  self.launchGB = (t) => {
+    self.app.dispatch({
+      type: "plot_create",
+      config: {
+        chartType: "genomeBrowser",
+        snvindel: { shown: true },
+        geneSearchResult: { geneSymbol: t.tw.term.name }
+      }
+    });
+  };
+  self.updateTermLabel = () => {
+    const value = self.dom.twLabelInput.property("value").trim();
+    const t = self.activeLabel;
+    if (t.tw.label === value) return;
+    t.tw.label = value;
+    t.grp.lst[t.lstIndex] = t.tw;
+    self.app.dispatch({
+      type: "plot_nestedEdits",
+      id: self.opts.id,
+      edits: [
+        {
+          nestedKeys: ["termgroups", t.grpIndex],
+          value: t.grp
+        }
+      ]
+    });
+  };
+  self.showShortcuts = (t, div) => {
+    const l = self.settings.matrix.controlLabels;
+    div.style("text-align", "center");
+    const vartype = t.tw.term.type == "geneVariant" || t.tw.term.type == TermTypes.GENE_EXPRESSION ? "gene" : t.tw.term.type == TermTypes.METABOLITE_INTENSITY ? "metabolite" : t.tw.term.type == TermTypes.PROTEOME_ABUNDANCE ? "protein" : "variable";
+    const sortRevertable = self.type != "hierCluster" && t.tw.sortSamples?.priority !== void 0;
+    div.append("span").selectAll("div").data(
+      [
+        {
+          icon: "corner",
+          title: `Sort ${l.samples} against this ${vartype}, and position this ${vartype} at the top left corner`,
+          disabled: t.grp.lst.length < 1 || t.index === 0 && t.tw.sortSamples?.priority === 0 || self.type == "hierCluster",
+          handler: self.sortSamplesAgainstCornerTerm
+        },
+        {
+          icon: "left",
+          title: `Sort ${l.samples} against this ${vartype}`,
+          // should not disable sorting when hierCluster has top dendrogram
+          disabled: t.tw.sortSamples?.priority === 0 && !self.config.settings.hierCluster?.clusterSamples,
+          fill: sortRevertable ? "rgba(200,100,100,0.5)" : "",
+          handler: sortRevertable ? self.unsortSamplesAgainstTerm : self.sortSamplesAgainstTerm
+        },
+        {
+          html: "&nbsp;|&nbsp;"
+        },
+        {
+          icon: "up",
+          title: `Move this ${vartype} up`,
+          disabled: t.index === 0 || self.type == "hierCluster",
+          handler: self.moveTermUp
+        },
+        {
+          icon: "down",
+          title: `Move this ${vartype} down`,
+          disabled: t.index === t.grp.lst.length - 1 || self.type == "hierCluster",
+          handler: self.moveTermDown
+        }
+      ],
+      (d) => d.icon
+    ).enter().append("div").style("display", "inline-block").each(function(d) {
+      const elem = select_default(this);
+      if (d.icon) icons[d.icon](elem, d);
+      else elem.html(d.html);
+    });
+  };
+  self.sortSamplesAgainstCornerTerm = (event2) => {
+    event2.stopPropagation();
+    const t = self.activeLabel;
+    const termgroups = JSON.parse(JSON.stringify(self.termGroups));
+    const grp = termgroups[t.grpIndex];
+    const [tcopy, sorterTerms] = self.getSorterTerms(t);
+    const removed = grp.lst.splice(t.lstIndex, 1);
+    grp.lst.unshift(tcopy);
+    grp.sortTermsBy = "asListed";
+    for (const g of termgroups) {
+      if (g == grp) {
+        for (const [priority, tw] of g.lst.entries()) {
+          if (!tw.sortSamples) tw.sortSamples = { priority, by: "values" };
+          tw.sortSamples.priority = priority;
+        }
+      } else {
+        for (const tw of g.lst) {
+          if (!tw.sortSamples) continue;
+          tw.sortSamples.priority = sorterTerms.findIndex((t2) => t2.tw?.$id === tw.$id) + grp.lst.length;
+        }
+      }
+    }
+    self.app.dispatch({
+      type: "plot_edit",
+      id: self.opts.id,
+      config: {
+        termgroups,
+        settings: {
+          matrix: {
+            sortTermsBy: "asListed"
+          }
+        }
+      }
+    });
+    self.dom.tip.hide();
+  };
+  self.sortSamplesAgainstTerm = (event2) => {
+    event2?.stopPropagation();
+    const t = self.activeLabel;
+    const [tcopy] = self.getSorterTerms(t);
+    if (t.grp.type == "hierCluster") tcopy.sortSamples.by = "values";
+    const termgroups = self.termGroups;
+    termgroups[t.grpIndex].lst[t.lstIndex] = tcopy;
+    for (const g of termgroups) {
+      for (const tw of g.lst) {
+        if (!tw.sortSamples) continue;
+        if (tw.$id === t.tw.$id) {
+          tw.sortSamples.priority = 0;
+        } else tw.sortSamples.priority += 1;
+      }
+    }
+    if (self.chartType == "hierCluster") {
+      self.config.settings.hierCluster.clusterSamples = false;
+      self.config.settings.hierCluster.yDendrogramHeight = 0;
+    }
+    self.config.termgroups = termgroups;
+    self.app.dispatch({
+      type: "plot_edit",
+      id: self.opts.id,
+      config: self.config
+    });
+    self.dom.tip.hide();
+  };
+  self.unsortSamplesAgainstTerm = (event2, d) => {
+    event2.stopPropagation();
+    const t = self.activeLabel || d.data.t;
+    const [tcopy] = self.getSorterTerms(t);
+    const termgroups = self.termGroups;
+    termgroups[t.grpIndex].lst[t.lstIndex] = tcopy;
+    for (const g of termgroups) {
+      for (const tw of g.lst) {
+        if (!tw.sortSamples) continue;
+        if (tw.$id === t.tw.$id) {
+          delete tw.sortSamples;
+        } else if ("sortSamples" in tw && "priority" in tw.sortSamples) {
+          if (tw.sortSamples.priority > t.sortSamples?.priority) tw.sortSamples.priority -= 1;
+        }
+      }
+    }
+    self.app.dispatch({
+      type: "plot_edit",
+      id: self.opts.id,
+      config: {
+        termgroups
+      }
+    });
+    self.dom.tip.hide();
+  };
+  self.moveTermUp = (event2) => {
+    event2.stopPropagation();
+    const t = self.activeLabel;
+    const grp = self.termGroups[t.grpIndex];
+    grp.lst.splice(t.lstIndex, 1);
+    grp.lst.splice(t.lstIndex - 1, 0, t.tw);
+    grp.sortTermsBy = "asListed";
+    self.app.dispatch({
+      type: "plot_nestedEdits",
+      id: self.opts.id,
+      edits: [
+        {
+          nestedKeys: ["termgroups", t.grpIndex],
+          value: grp
+        },
+        {
+          nestedKeys: ["settings", "matrix", "sortTermsBy"],
+          value: "asListed"
+        }
+      ]
+    });
+    self.dom.tip.hide();
+  };
+  self.moveTermDown = (event2) => {
+    event2.stopPropagation();
+    const t = self.activeLabel;
+    const grp = self.termGroups[t.grpIndex];
+    grp.lst.splice(t.lstIndex, 1);
+    grp.lst.splice(t.lstIndex + 1, 0, t.tw);
+    grp.sortTermsBy = "asListed";
+    self.app.dispatch({
+      type: "plot_nestedEdits",
+      id: self.opts.id,
+      edits: [
+        {
+          nestedKeys: ["termgroups", t.grpIndex],
+          value: grp
+        },
+        {
+          nestedKeys: ["settings", "matrix", "sortTermsBy"],
+          value: "asListed"
+        }
+      ]
+    });
+    self.dom.tip.hide();
+  };
+  self.showTermEditMenu = async () => {
+    self.dom.menubody.selectAll("*").remove();
+    const t = self.activeLabel;
+    const s = self.config.settings.matrix;
+    const l = s.controlLabels;
+    if (t.tw.term.type == "geneVariant") {
+      const div = self.dom.menubody.append("div");
+      const label = div.append("label");
+      label.append("span").html(`Minimum # ${l.samples} to be visible`);
+      const minNumSamples = "minNumSamples" in t.tw ? t.tw.minNumSamples : "";
+      const input = label.append("input").attr("type", "number").style("margin-left", "5px").style("width", "50px").property("value", minNumSamples);
+      div.append("div").append("button").html("Submit").on("click", () => {
+        const value = input.property("value");
+        if (value === minNumSamples) return;
+        if (value === "") {
+          delete t.tw.minNumSamples;
+        } else {
+          t.tw.minNumSamples = Number(value);
+        }
+        self.app.dispatch({
+          type: "plot_nestedEdits",
+          id: self.opts.id,
+          edits: [
+            {
+              nestedKeys: ["termgroups", t.grpIndex, "lst", t.lstIndex],
+              value: t.tw
+            }
+          ]
+        });
+        self.dom.tip.hide();
+      });
+    } else {
+      await self.pill.main(
+        Object.assign({ menuOptions: self.getMenuOptions(t), filter: self.state.filter }, self.activeLabel.tw)
+      );
+      self.pill.showMenu();
+    }
+  };
+  self.showMoveMenu = async () => {
+    self.dom.menubody.selectAll("*").remove();
+    self.termBeingMoved = self.activeLabel;
+    const div = self.dom.menubody.append("div");
+    div.append("span").html("Click on another label");
+    self.makeInsertPosRadios(div);
+  };
+  self.showTermInsertMenu = () => {
+    self.dom.menubody.selectAll("*").remove();
+    self.dom.editbtns = self.dom.menubody.append("div");
+    self.dom.editbody = self.dom.menubody.append("div");
+    if (self.activeLabel.grp.type == "hierCluster") {
+      self.showDictTermSelection(self.dom.editbody);
+      return;
+    }
+    const grpNameDiv = self.dom.editbtns.append("div").style("margin", "10px 5px");
+    grpNameDiv.append("label").html(`Insert genes or variables in `);
+    self.dom.grpNameSelect = grpNameDiv.append("select").on("change", () => {
+      const value = self.dom.grpNameSelect.property("value");
+      self.dom.grpNameTextInput.property("disabled", value == "current").property("value", value == "current" ? self.activeLabel.grp.name : newGrpName);
+    });
+    self.dom.grpNameSelect.selectAll("option").data([
+      { label: "current", value: "current", selected: true },
+      { label: "new", value: "new" }
+    ]).enter().append("option").attr("selected", (d) => d.selected).html((d) => d.label);
+    grpNameDiv.append("span").html("&nbsp;group: &nbsp;");
+    let newGrpName = "";
+    self.dom.grpNameTextInput = grpNameDiv.append("input").attr("type", "text").property("disabled", true).property("value", self.activeLabel.grp.name).on("change", () => {
+      const name = self.dom.grpNameTextInput.property("value");
+      if (name == self.activeLabel.grp.name) {
+      } else {
+        newGrpName = self.dom.grpNameTextInput.property("value");
+      }
+    });
+    self.makeInsertPosRadios(self.dom.editbtns);
+    self.showDictTermSelection(self.dom.editbody);
+  };
+  self.makeInsertPosRadios = function(div) {
+    const insertPosInput = div.append("div").style("margin", "10px 5px");
+    insertPosInput.append("div").style("display", "inline-block").style("padding-right", "10px").html("Insert&nbsp");
+    const insertRadiosDiv = insertPosInput.append("div").style("display", "inline-block");
+    self.insertRadioId = `sjpp-matrix-${self.id}-insert-pos`;
+    const aboveLabel = insertRadiosDiv.append("label");
+    aboveLabel.append("input").attr("type", "radio").attr("value", "above").property("checked", true).attr("name", self.insertRadioId);
+    aboveLabel.append("span").html("above");
+    insertRadiosDiv.append("span").html("&nbsp;&nbsp");
+    const belowLabel = insertRadiosDiv.append("label");
+    belowLabel.append("input").attr("type", "radio").attr("value", "below").attr("name", self.insertRadioId);
+    belowLabel.append("span").html("&nbsp;below");
+  };
+  self.showDictTermSelection = async (holder) => {
+    const usecase = { target: "matrix", detail: "termgroups" };
+    if (self.chartType == "hierCluster") {
+      if (self.config.dataType == NUMERIC_DICTIONARY_TERM && (!self.activeLabel || self.activeLabel.grp.type == "hierCluster")) {
+        usecase.target = "numericDictTermCluster";
+        usecase.detail = { exclude: self.state.termdbConfig.numericDictTermCluster?.exclude };
+      } else if (self.config.dataType == TermTypes.METABOLITE_INTENSITY && (!self.activeLabel || self.activeLabel.grp.type == "hierCluster")) {
+        usecase.target = TermTypes.METABOLITE_INTENSITY;
+        usecase.detail = "term";
+      } else if (self.config.dataType == TermTypes.PROTEOME_ABUNDANCE && (!self.activeLabel || self.activeLabel.grp.type == "hierCluster")) {
+        usecase.target = TermTypes.PROTEOME_ABUNDANCE;
+        usecase.detail = "term";
+      } else {
+        usecase.target = self.activeLabel.tw.term.type;
+        usecase.detail = "term";
+      }
+    }
+    const termdb = await import("./app-GTHYSGWI.js");
+    holder.selectAll("*").remove();
+    termdb.appInit({
+      holder: holder.append("div"),
+      vocabApi: self.app.vocabApi,
+      state: {
+        vocab: self.state.vocab,
+        activeCohort: self.activeCohort,
+        nav: {
+          header_mode: "search_only"
+        },
+        tree: {
+          usecase
+        },
+        ...!self.activeLabel || self.activeLabel.grp.type == "hierCluster" ? { selectedTerms: self.hcTermGroup.lst.map((t) => t.term) } : {}
+      },
+      tree: {
+        submit_lst
+      },
+      search: {
+        handleGeneVariant: (term) => submit_lst([term])
+      }
+    });
+  };
+  async function submit_lst(termlst) {
+    const newterms = await Promise.all(
+      termlst.map(async (_term) => {
+        const term = structuredClone(_term);
+        const tw = "id" in term ? { id: term.id, term } : { term };
+        await fillTermWrapper(tw, self.app.vocabApi);
+        return tw;
+      })
+    );
+    const t = self.activeLabel;
+    const termgroups = self.termGroups;
+    const isNumericDictTermCBut = self.config.dataType == NUMERIC_DICTIONARY_TERM && !t;
+    const isMetaboliteIntensityCBut = self.config.dataType == TermTypes.METABOLITE_INTENSITY && !t;
+    const isProteomeAbundanceCBut = self.config.dataType == TermTypes.PROTEOME_ABUNDANCE && !t;
+    if (isNumericDictTermCBut || isMetaboliteIntensityCBut || isProteomeAbundanceCBut || t.grp.type == "hierCluster") {
+      const grp = isNumericDictTermCBut || isMetaboliteIntensityCBut || isProteomeAbundanceCBut ? termgroups[0] : termgroups[t.grpIndex];
+      grp.lst.splice(0, grp.lst.length, ...newterms);
+      self.app.dispatch({
+        type: "plot_nestedEdits",
+        id: self.opts.id,
+        edits: [
+          {
+            nestedKeys: [
+              "termgroups",
+              isNumericDictTermCBut || isMetaboliteIntensityCBut || isProteomeAbundanceCBut ? 0 : t.grpIndex,
+              "lst"
+            ],
+            value: grp.lst
+          }
+        ]
+      });
+    } else if (self.dom.grpNameSelect.property("value") == "current") {
+      const pos = self.insertRadioId && select_default(`input[name='${self.insertRadioId}']:checked`)?.property("value");
+      const grp = termgroups[t.grpIndex];
+      const i = pos == "above" ? t.lstIndex : t.lstIndex + 1;
+      grp.lst.splice(i, 0, ...newterms);
+      self.app.dispatch({
+        type: "plot_nestedEdits",
+        id: self.opts.id,
+        edits: [
+          {
+            nestedKeys: ["termgroups", t.grpIndex, "lst"],
+            value: grp.lst
+          }
+        ]
+      });
+    } else {
+      const pos = self.insertRadioId && select_default(`input[name='${self.insertRadioId}']:checked`)?.property("value");
+      const i = pos == "above" ? t.grpIndex : t.grpIndex + 1;
+      termgroups.splice(i, 0, {
+        name: self.dom.grpNameTextInput.property("value"),
+        lst: newterms
+      });
+      self.app.dispatch({
+        type: "plot_edit",
+        id: self.opts.id,
+        config: { termgroups }
+      });
+    }
+    self.dom.tip.hide();
+  }
+  self.showSortMenu = () => {
+    const t = self.activeLabel;
+    self.dom.menubody.selectAll("*").remove();
+    self.dom.menubody.append("div").style("margin-top", "10px").style("text-align", "center").html(t.tw.term.name);
+    self.moveInput = void 0;
+    self.showSortOptions(t);
+  };
+  self.showTermMoveOptions = (t) => {
+    const moveDiv = self.dom.menubody.append("div").style("margin-top", "10px");
+    const moveLabel = moveDiv.append("label");
+    self.moveInput = moveLabel.append("input").attr("type", "checkbox").style("text-align", "center");
+    moveLabel.append("span").html(`&nbsp;move this row&nbsp;`);
+    const movePos = moveDiv.append("select");
+    movePos.selectAll("option").data([
+      { label: "before", value: 0 },
+      { label: "after", value: 1 }
+    ]).enter().append("option").attr("value", (d) => d.value).html((d) => d.label);
+    moveDiv.append("span").html("&nbsp;");
+    const otherTermsInGrp = t.grp.lst.filter((tw) => tw.$id != t.tw.$id).map((tw) => {
+      return { label: tw.term.name, value: tw.$id };
+    });
+    const moveTarget = moveDiv.append("select");
+    moveTarget.selectAll("option").data([{ label: "all", value: "*" }, ...otherTermsInGrp]).enter().append("option").attr("value", (d) => d.value).html((d) => d.label);
+  };
+  self.showSortOptions = (t) => {
+    const sortColDiv = self.dom.menubody.append("div").style("margin-top", "10px");
+    const sortColLabel = sortColDiv.append("label");
+    const sortColInput = sortColLabel.append("input").attr("type", "checkbox").property("checked", true).style("text-align", "center");
+    const l = self.settings.matrix.controlLabels;
+    sortColLabel.append("span").html(`&nbsp;sort ${l.samples} against (in order of priority):`);
+    const tcopy = self.showSorterTerms(sortColDiv, t);
+    self.dom.menubody.append("button").html("Apply").on("click", () => {
+      const matrix = JSON.parse(JSON.stringify(self.config.settings.matrix)) || {};
+      delete tcopy.div;
+      delete tcopy.up;
+      delete tcopy.down;
+      delete tcopy.delete;
+      if (sortColInput.property("checked") || self.moveInput?.property("checked")) {
+        self.app.dispatch({
+          type: "plot_nestedEdits",
+          id: self.opts.id,
+          edits: [
+            {
+              nestedKeys: ["termgroups", t.grpIndex, "lst", t.lstIndex],
+              value: tcopy
+            }
+          ]
+        });
+      }
+      self.dom.tip.hide();
+    });
+  };
+  self.showSorterTerms = (sortColDiv, t) => {
+    const [tcopy, sorterTerms] = self.getSorterTerms(t);
+    const s = self.settings.matrix;
+    const l = s.controlLabels;
+    sortColDiv.append("div").style("margin", "5px").style("padding", "5px 10px").selectAll("div").data(sorterTerms, (s2) => s2.$id).enter().append("div").style("width", "fit-content").style("margin", "3px").style("cursor", "default").style("padding", "3px 10px").style("border-radius", "5px").style("color", "black").style("background-color", "rgb(238, 238, 238)").each(function(st, i) {
+      st.sortSamples.priority = i;
+      st.div = select_default(this);
+      const label = st.$id == "sample" ? `${l.Sample} name` : st.term.name;
+      st.div.append("span").style("margin-right", "10px").html(label);
+      st.up = st.div.append("span").html(" &#9650; ").style("display", i === 0 ? "none" : "inline").style("color", "#555").on("click", () => {
+        this.parentNode.insertBefore(this, this.previousSibling);
+        sorterTerms.splice(st.priority, 1);
+        sorterTerms.splice(st.priority - 1, 0, st);
+        updateSorterDivStyles();
+      });
+      st.down = st.div.append("span").html(" &#9660; ").style("display", i < sorterTerms.length - 1 ? "inline" : "none").style("color", "#555").on("click", () => {
+        this.parentNode.insertBefore(this, this.nextSibling.nextSibling);
+        sorterTerms.splice(st.priority, 1);
+        sorterTerms.splice(st.priority + 1, 0, st);
+        updateSorterDivStyles();
+      });
+      st.delete = st.div.append("span").html(" &#10005; ").style("display", "inline").style("color", "rgb(255, 100, 100)").on("click", () => {
+        st.div.remove();
+        sorterTerms.splice(st.priority, 1);
+        updateSorterDivStyles();
+      });
+    });
+    function updateSorterDivStyles() {
+      for (const [i, st] of sorterTerms.entries()) {
+        st.priority = i;
+        st.up.style("display", st.priority > 0 ? "inline" : "none");
+        st.down.style("display", st.priority < sorterTerms.length - 1 ? "inline" : "none");
+      }
+    }
+    return tcopy;
+  };
+  self.getSorterTerms = (t) => {
+    const sorterTerms = [
+      ...self.termOrder.filter((t2) => t2.tw.sortSamples).map((t2) => JSON.parse(JSON.stringify(t2.tw))).sort((a, b) => a.sortSamples.priority - b.sortSamples.priority),
+      ...self.config.settings.matrix.sortSamplesTieBreakers.map((st) => JSON.parse(JSON.stringify(st)))
+    ];
+    const s = self.settings.matrix;
+    const activeOption = s.sortOptions[s.sortSamplesBy];
+    if (!activeOption) {
+      throw `unsupported s.sortSamplesBy='${s.sortSamplesBy}'`;
+    }
+    const matchingSortSamples = activeOption.sortPriority?.find((o) => o.types.includes(t.tw?.term?.type))?.tiebreakers[0];
+    const sortSamples = matchingSortSamples ? {} : t.tw?.term?.type == "geneVariant" && t.tw?.q?.type == "values" ? {
+      by: "class",
+      order: [
+        "Fuserna",
+        "CNV_homozygous_deletion",
+        "CNV_amplification",
+        "CNV_loss",
+        "CNV_amp",
+        "CNV_loh",
+        // truncating
+        "F",
+        "N",
+        // indel
+        "D",
+        "I",
+        // point
+        "M",
+        "P",
+        "L",
+        // noncoding
+        "Utr3",
+        "Utr5",
+        "S",
+        "Intron",
+        "WT",
+        "Blank"
+      ]
+    } : { by: "values" };
+    const i = sorterTerms.findIndex((st) => st.$id === t.tw?.$id);
+    const tcopy = JSON.parse(JSON.stringify(t.tw || {}));
+    tcopy.sortSamples = sortSamples;
+    if (i == -1) {
+      sorterTerms.unshift(tcopy);
+    } else {
+      if (sortSamples.order) tcopy.sortSamples.order = sortSamples.order;
+    }
+    return [tcopy, sorterTerms];
+  };
+  self.removeTerm = () => {
+    const t = self.activeLabel;
+    const legendValueFilter = self.mayRemoveTvsEntry(t.tw);
+    const termgroups = self.termGroups;
+    const grp = termgroups[t.grpIndex];
+    grp.lst.splice(t.lstIndex, 1);
+    if (grp.lst.length) {
+      self.app.dispatch({
+        type: "plot_nestedEdits",
+        id: self.opts.id,
+        edits: [
+          {
+            nestedKeys: ["termgroups", t.grpIndex, "lst"],
+            value: grp.lst
+          },
+          {
+            nestedKeys: ["legendValueFilter"],
+            value: legendValueFilter
+          }
+        ]
+      });
+    } else {
+      termgroups.splice(t.grpIndex, 1);
+      self.app.dispatch({
+        type: "plot_edit",
+        id: self.opts.id,
+        config: {
+          termgroups,
+          legendValueFilter
+        }
+      });
+    }
+    self.dom.tip.hide();
+  };
+  self.removeTermGroup = () => {
+    const t = self.activeLabel;
+    const termgroups = self.termGroups;
+    termgroups.splice(t.grpIndex, 1);
+    self.app.dispatch({
+      type: "plot_edit",
+      id: self.opts.id,
+      config: { termgroups }
+    });
+    self.dom.tip.hide();
+  };
+  self.mayRemoveTvsEntry = (tw) => {
+    if (!self.config.legendValueFilter?.lst.length) return self.config.legendValueFilter;
+    const lst = structuredClone(self.config.legendValueFilter.lst);
+    const items = lst.filter(
+      (f) => f.tvs?.term.type === tw?.term.type && (("id" in f.tvs.term || "id" in tw.term) && f.tvs.term.id === tw.term.id || f.tvs.term.name === tw.term.name)
+    );
+    if (!items.length) return self.config.legendValueFilter;
+    else {
+      for (const t of items) {
+        const tvs = t.tvs;
+        if (tvs.term.type != tw.term.type) continue;
+        if (("id" in tvs.term || "id" in tw.term) && tvs.term.id !== tw.term.id) continue;
+        else if (tvs.term.name != tw.term.name) continue;
+        const i = lst.findIndex((t2) => t2 === tvs);
+        lst.splice(i, 1);
+      }
+    }
+    return { in: true, join: "and", type: "tvslst", lst };
+  };
+}
+function setSampleGroupActions(self) {
+  self.showSampleGroupMenu = function(event2) {
+    const d = event2.target.__data__;
+    if (!d) return;
+    self.activeLabel = d;
+    self.dom.menutop.selectAll("*").remove();
+    self.dom.menubody.style("padding", 0).selectAll("*").remove();
+    const options = JSON.parse(JSON.stringify(self.config.menuOpts?.sampleGroup || [])).map((d2) => {
+      d2.callback = self[d2.callback];
+      return d2;
+    });
+    const menuOptions = [...options, { label: "Delete", callback: self.removeSampleGroup }];
+    self.dom.menutop.append("div").selectAll(":scope>.sja_menuoption").data(menuOptions).enter().append("div").attr("class", "sja_menuoption sja_sharp_border").style("display", "block").html((d2) => d2.label).on("click", (event3, d2) => {
+      event3.stopPropagation();
+      d2.callback(d2);
+    });
+    self.dom.tip.showunder(event2.target);
+  };
+  self.showNewChartMenu = () => {
+    self.dom.menubody.selectAll("*").remove();
+  };
+  self.launchSurvivalPlot = async (menuOpt) => {
+    self.dom.menubody.selectAll("*").remove();
+    self.dom.menubody.append("div").style("padding-top", "10px").html(`Use "<b>${self.config.divideBy.term.name}</b>" to`);
+    const radioDiv = self.dom.menubody.append("div").style("padding", "0 10px");
+    const radioName = "sjpp-matrix-surv-termnum-" + inputIndex++;
+    const label1 = radioDiv.append("label");
+    label1.append("input").attr("type", "radio").attr("name", radioName).attr("value", "term2").property("checked", true);
+    label1.append("span").html(" overlay");
+    const label2 = radioDiv.append("label").style("margin-left", "10px");
+    label2.append("input").attr("type", "radio").attr("name", radioName).attr("value", "term0");
+    label2.append("span").html(" divide");
+    self.dom.menubody.append("div").style("padding-bottom", "10px").html(`the selected survival variable below:`);
+    const termdb = await import("./app-GTHYSGWI.js");
+    termdb.appInit({
+      holder: self.dom.menubody.append("div"),
+      vocabApi: self.app.vocabApi,
+      state: {
+        vocab: self.state.vocab,
+        activeCohort: self.state.activeCohort,
+        nav: {
+          header_mode: "search_only"
+        },
+        tree: { usecase: { target: "survival", detail: "term" } }
+      },
+      tree: {
+        click_term: (term) => {
+          self.dom.tip.hide();
+          const termNum = radioDiv.select(`input[name='${radioName}']:checked`).property("value");
+          self.dom.menubody.selectAll("*").remove();
+          const config = {
+            chartType: "survival",
+            term,
+            [termNum]: JSON.parse(JSON.stringify(self.config.divideBy)),
+            insertBefore: self.id
+          };
+          if (menuOpt.config) {
+            Object.assign(config, menuOpt.config);
+          }
+          self.app.dispatch({ type: "plot_create", config });
+        }
+      }
+    });
+  };
+  self.removeSampleGroup = () => {
+    if (!self.config.divideBy) return;
+    const tw = self.activeLabel.grp.tw;
+    const term = tw.term;
+    if (term.type == "categorical" || term.type == "survival") {
+      term.$id = tw.$id;
+      const filterGrpIndex = self.config.legendValueFilter.lst.findIndex((l) => l.legendGrpName == tw.term.id);
+      if (filterGrpIndex == -1) {
+        const filterNew = {
+          legendGrpName: tw.term.id,
+          type: "tvs",
+          tvs: {
+            isnot: true,
+            term,
+            values: [{ key: self.activeLabel.grp.id }]
+          }
+        };
+        self.config.legendValueFilter.lst.push(filterNew);
+      } else {
+        self.config.legendValueFilter.lst[filterGrpIndex].tvs.values.push({ key: self.activeLabel.grp.id });
+      }
+    } else if (isNumericTerm(term)) {
+      term.$id = tw.$id;
+      const filterNew = {
+        legendGrpName: tw.term.id || tw.term.name,
+        type: "tvs",
+        tvs: {
+          isnot: true,
+          term,
+          ranges: [self.data.refs.byTermId[tw.$id].bins.find((b) => self.activeLabel.grp.id == b.name)]
+        }
+      };
+      self.config.legendValueFilter.lst.push(filterNew);
+    }
+    self.app.dispatch({
+      type: "plot_edit",
+      id: self.id,
+      config: { legendValueFilter: self.config.legendValueFilter }
+    });
+    self.dom.tip.hide();
+  };
+  self.showDeletedSampleGroups = () => {
+    if (!self.config.divideBy) return;
+    const tw = self.activeLabel?.grp?.tw || self.config.divideBy;
+    self.config.legendValueFilter.lst = self.config.legendValueFilter.lst.filter(
+      (l) => l.legendGrpName !== tw.term.id && l.legendGrpName != tw.term.name
+    );
+    self.app.dispatch({
+      type: "plot_edit",
+      id: self.id,
+      config: { legendValueFilter: self.config.legendValueFilter }
+    });
+    self.dom.tip.hide();
+  };
+  self.displaySampleGroupInfo = (event2, grp) => {
+    const l = self.settings.matrix.controlLabels;
+    const n = grp.lst.length;
+    self.dom.menutop.selectAll("*").remove();
+    self.dom.menubody.selectAll("*").remove();
+    self.dom.menubody.append("div").style("text-align", "center").html(`<b>${grp.name}</b> (${n} ${n < 2 ? l.sample : l.samples})`);
+    const div = self.dom.menubody.append("div").style("max-width", "400px").style("padding", "5px");
+    for (const key in event2.target.__data__.grp.legendData) {
+      const g = event2.target.__data__.grp.legendData[key];
+      div.append("div").style("padding-top", "10px").html(`<b>${g.name}</b>`);
+      const t = div.append("table");
+      for (const i of g.items) {
+        const tr = t.append("tr");
+        tr.append("td").append("div").style("width", "12px").style("height", "12px").style("background-color", i.color).style("border", `1px soloid ${i.stroke}`);
+        tr.append("td").html(i.text);
+      }
+    }
+    self.dom.tip.show(event2.clientX, event2.clientY);
+  };
+  self.legendItemSorter = (a, b) => {
+    if (a.order && b.order) return a.order - b.order;
+    if (Number.isFinite(a.order) || b.order == -1) return -1;
+    if (Number.isFinite(b.order) || a.order == -1) return 1;
+    if (a.count) return b.count - a.count;
+    if (Number.isFinite(a.count)) return -1;
+    if (Number.isFinite(b.count)) return 1;
+    return 0;
+  };
+  self.handleLegendItemClick = (d) => {
+    const dvt = structuredClone(self.config.divideBy || {});
+    const id = "id" in dvt ? dvt.id : dvt.name;
+    if (d.termid == id) {
+      if (!dvt.exclude) dvt.exclude = [];
+      const i = dvt.exclude?.indexOf(d.key);
+      if (i == -1) dvt.exclude.push(d.key);
+      else dvt.exclude.splice(i, 1);
+      self.app.dispatch({
+        type: "plot_edit",
+        id: self.id,
+        config: {
+          divideBy: dvt
+        }
+      });
+    }
+  };
+  self.handleLegendMouseover = (event2, d) => {
+    const dvt = structuredClone(self.config.divideBy || {});
+    const id = "id" in dvt ? dvt.id : dvt.name;
+    if (d.termid == id) {
+      self.dom.menutop.selectAll("*").remove();
+      self.dom.menubody.selectAll("*").remove();
+      self.dom.menubody.html(`Click to ${d.isExcluded ? "show" : "hide"}`);
+      self.dom.tip.show(event2.clientX, event2.clientY);
+    }
+  };
+}
+function setTermGroupActions(self) {
+  setLabelDragEvents(self, "termGrp");
+  self.showTermGroupMenu = function(event2) {
+    const d = event2.target.tagName.toLowerCase() == "tspan" ? event2.target.parentNode.__data__ : event2.target.__data__;
+    if (!d) return;
+    self.activeLabel = d;
+    self.dom.menutop.style("display", "").selectAll("*").remove();
+    self.showTermGroupInputs(self.dom.menutop.append("div"));
+    self.dom.tip.showunder(event2.target);
+  };
+  self.showTermGroupInputs = function(div) {
+    const holder = div;
+    const labelEditDiv = holder.append("div").style("text-align", "center");
+    labelEditDiv.append("span").text("Group ");
+    self.dom.grpNameInput = labelEditDiv.append("input").attr("type", "text").attr("size", (self.activeLabel.grp.name?.length || 0) + 5).style("padding", "1px 5px").style("text-align", "center").property("value", self.activeLabel.grp.name).on("input", () => {
+      const value = self.dom.grpNameInput.property("value");
+      self.dom.grpNameInput.attr("size", value.length + 5);
+      self.dom.grpEditBtn.style("display", value === self.activeLabel.grp.name ? "none" : "");
+    });
+    self.dom.grpEditBtn = labelEditDiv.append("button").style("display", "none").style("margin-left", "5px").html("submit").on("click", () => {
+      self.updateTermGrpName();
+      self.dom.tip.hide();
+    });
+    self.dom.menubody.style("padding", 0).selectAll("*").remove();
+    const menuOptions = [{ label: "Add Rows", callback: self.showTermInsertMenu }];
+    if (self.chartType != "hierCluster") {
+      menuOptions.push(
+        { label: "Edit", callback: self.showTermGroupEditMenu }
+        //{ label: 'Sort', callback: self.showSortMenu },
+      );
+    }
+    if (self.activeLabel.grp.type != "hierCluster") {
+      menuOptions.push({ label: "Delete", callback: self.removeTermGroup });
+    }
+    holder.append("div").style("text-align", "center").selectAll(":scope>.sja_menuoption").data(menuOptions).enter().append("div").attr("class", "sja_menuoption sja_sharp_border").style("display", "inline-block").html((d) => d.label).on("click", (event2, d) => {
+      event2.stopPropagation();
+      self.dom.menutop.style("display", "none");
+      d.callback(d);
+    });
+  };
+  self.updateTermGrpName = () => {
+    const value = self.dom.grpNameInput.property("value");
+    const t = self.activeLabel;
+    if (t.grp.name === value) return;
+    t.grp.name = value;
+    self.app.dispatch({
+      type: "plot_nestedEdits",
+      id: self.opts.id,
+      edits: [
+        {
+          nestedKeys: ["termgroups", t.grpIndex],
+          value: t.grp
+        }
+      ]
+    });
+  };
+  self.showTermGroupEditMenu = async () => {
+    self.dom.menubody.selectAll("*").remove();
+    const menu = self.dom.menubody.append("div").style("padding", "5px");
+    menu.append("div").style("width", "100%").style("font-weight", 600).html("Group options");
+    const label = menu.append("div").append("label");
+    const l = self.settings.matrix.controlLabels;
+    label.append("span").html(
+      `Minimum # of mutated ${l.samples} for the ${l.term.charAt(0).toLowerCase() + l.term.slice(1)} to be visible `
+    ).attr("aria-label", `May be overridden by a row-specific minNumSamples`);
+    const minNumSampleInput = label.append("input").attr("type", "number").style("margin-left", "5px").style("width", "50px").property("value", self.activeLabel.grp.settings?.minNumSamples || 0);
+    menu.append("div").append("button").html("Submit").on("click", () => {
+      const settings = self.activeLabel.grp.settings || {};
+      settings.minNumSamples = minNumSampleInput.property("value");
+      self.app.dispatch({
+        type: "plot_nestedEdits",
+        id: self.id,
+        edits: [
+          {
+            nestedKeys: ["termgroups", self.activeLabel.grpIndex, "settings"],
+            value: settings
+          }
+        ]
+      });
+    });
+  };
+  self.removeTermGroup = () => {
+    const termgroups = self.termGroups;
+    termgroups.splice(self.activeLabel.grpIndex, 1);
+    self.app.dispatch({
+      type: "plot_edit",
+      id: self.id,
+      config: {
+        termgroups
+      }
+    });
+    self.dom.tip.hide();
+  };
+  const labelParentSelectors = ["series", "series-group", "term", "term-group"].map((d) => `.sjpp-matrix-${d}-label-g`).join(",");
+  self.enableTextHighlight = (event2) => {
+    select_default(event2.target.closest(labelParentSelectors)).selectAll(".sjpp-matrix-label text").style("-webkit-user-select", "auto").style("-moz-user-select", "auto").style("-ms-user-select", "auto").style("user-select", "auto");
+    select_default("body").on("mouseup.sjppMatrixLabelText", self.disableTextHighlight);
+  };
+  self.disableTextHighlight = (event2) => {
+    select_default(event2.target.closest(labelParentSelectors)).selectAll(".sjpp-matrix-label text").style("-webkit-user-select", "none").style("-moz-user-select", "none").style("-ms-user-select", "none").style("user-select", "none");
+    select_default("body").on("mouseup.sjppMatrixLabelText", null);
+  };
+}
+function setLabelDragEvents(self, prefix) {
+  self[`${prefix}LabelMousedown`] = (event2, d) => {
+    self.clicked = { event: event2, d };
+  };
+  self[`${prefix}LabelMouseover`] = (event2, t) => {
+    if (prefix == "term" && event2.target.__data__?.tw && event2.target.__data__.grp) {
+      if (event2.target.__data__.grp.type == "hierCluster") {
+        return;
+      }
+      if (self.activeLabel || self.zoomArea) {
+        return;
+      }
+      self.dom.menutop.selectAll("*").remove();
+      self.dom.menubody.selectAll("*").remove();
+      const groupName = event2.target.__data__.grp.name;
+      const termName = event2.target.__data__.tw.term.name;
+      const titleDiv = self.dom.menubody.append("div").style("text-align", "left").style("font-size", "1.1em").html(groupName ? `<b>${groupName}: ${termName}</b>` : `<b>${termName}</b>`);
+      const div = self.dom.menubody.append("div").style("max-width", "400px");
+      const data = event2.target.__data__;
+      if (data.tw.term.type == "geneVariant" && data.tw.q?.type == "values") {
+        const notTestedSum = Object.values(data.counts.subGroupCounts).reduce(
+          (sum, curr) => sum + curr.samplesNotTested,
+          0
+        );
+        titleDiv.append("div").style("text-align", "left").style("font-size", "0.9em").html(`(tested ${self.samples.length - notTestedSum} of ${self.samples.length})`);
+        for (const [grpName, counts] of Object.entries(data.counts.subGroupCounts)) {
+          const groupSampleTotal = self.sampleGroups.find((g) => g.name == grpName).lst.length;
+          const mRate = groupSampleTotal - counts.samplesNotTested ? counts.samplesTotal / (groupSampleTotal - counts.samplesNotTested) : 0;
+          div.append("div").style("padding-top", "10px").html(
+            grpName ? `<b>${grpName}</b>: Mutated samples (${counts.samplesTotal} of ${groupSampleTotal - counts.samplesNotTested}, ${format(".1%")(mRate)})` : `<b>Mutated samples (${counts.samplesTotal} of ${groupSampleTotal - counts.samplesNotTested}, ${format(".1%")(mRate)})`
+          );
+          const t2 = div.append("table").style("margin-left", "15px");
+          for (const [classType, num] of Object.entries(counts.classes).sort((a, b) => b[1] - a[1])) {
+            const tr = t2.append("tr");
+            tr.append("td").append("div").style("width", "12px").style("height", "12px").style("background-color", mclass[classType].color);
+            tr.append("td").html(`${mclass[classType].label}: ${num}`);
+          }
+          if (counts.notTestedClasses) {
+            div.append("div").style("margin-left", "15px").style("padding-top", "12px").html("<b> Not counted:</b>");
+            const t3 = div.append("table").style("margin-left", "15px");
+            for (const [classType, num] of Object.entries(counts.notTestedClasses).sort((a, b) => b[1] - a[1])) {
+              const tr = t3.append("tr");
+              tr.append("td").append("div").style("width", "12px").style("height", "12px").style("background-color", mclass[classType].color);
+              tr.append("td").html(`${mclass[classType].label}: ${num}`);
+            }
+          }
+        }
+      } else if (!self.config.divideBy) {
+        const termLegend = self.legendData.find((t2) => t2.name == data.tw.term.name);
+        if (termLegend && termLegend.items) {
+          const t2 = div.append("table");
+          for (const classType of termLegend.items) {
+            const tr = t2.append("tr");
+            tr.append("td").append("div").style("width", "12px").style("height", "12px").style("background-color", classType.color);
+            tr.append("td").html(`${classType.key}: ${classType.count}`);
+          }
+        } else {
+          for (const [grpName, counts] of Object.entries(data.counts.subGroupCounts)) {
+            const groupSampleTotal = self.sampleGroups.find((g) => g.name == grpName).totalCountedValues;
+            div.append("div").style("padding-top", "10px").html(
+              grpName !== "" ? `<b>${grpName}</b>: ${counts.samplesTotal} of ${groupSampleTotal}` : `<b>${counts.samplesTotal} of ${groupSampleTotal}`
+            );
+            const t2 = div.append("table").style("margin-left", "15px");
+            for (const [classType, num] of Object.entries(counts.classes).sort((a, b) => b[1] - a[1])) {
+              const classColor = data.tw.term.values?.[classType]?.color;
+              if (!classColor) continue;
+              const tr = t2.append("tr");
+              tr.append("td").append("div").style("width", "12px").style("height", "12px").style("background-color", classColor);
+              tr.append("td").html(`${classType}: ${num}`);
+            }
+          }
+        }
+      } else {
+        for (const [grpName, counts] of Object.entries(data.counts.subGroupCounts)) {
+          const groupSampleTotal = self.sampleGroups.find((g) => g.name == grpName).totalCountedValues;
+          div.append("div").style("padding-top", "10px").html(
+            grpName !== "" ? `<b>${grpName}</b>: ${counts.samplesTotal} of ${groupSampleTotal}` : `<b>${counts.samplesTotal} of ${groupSampleTotal}`
+          );
+          const subGrp = self.sampleGroups.find((g) => g.name == grpName);
+          const termLegend = subGrp.legendData.find((t2) => t2.name == data.tw.term.name);
+          if (termLegend && termLegend.items) {
+            const t2 = div.append("table").style("margin-left", "15px");
+            for (const classType of termLegend.items) {
+              const tr = t2.append("tr");
+              tr.append("td").append("div").style("width", "12px").style("height", "12px").style("background-color", classType.color);
+              tr.append("td").html(`${classType.key}: ${classType.count}`);
+            }
+          } else {
+            const t2 = div.append("table").style("margin-left", "15px");
+            for (const [classType, num] of Object.entries(counts.classes).sort((a, b) => b[1] - a[1])) {
+              const classColor = data.tw.term.values?.[classType]?.color;
+              if (!classColor) continue;
+              const tr = t2.append("tr");
+              tr.append("td").append("div").style("width", "12px").style("height", "12px").style("background-color", classColor);
+              tr.append("td").html(`${classType}: ${num}`);
+            }
+          }
+        }
+      }
+      self.dom.tip.show(event2.clientX, event2.clientY);
+    }
+    if (event2.target.innerHTML.includes("grouped by")) return;
+    if (event2.target.tagName === "text") {
+      select_default(event2.target).style("fill", "blue");
+    }
+    if (!self.dragged) return;
+    self.hovered = event2.target.__data__;
+  };
+  self[`${prefix}LabelMouseout`] = (event2) => {
+    select_default(event2.target).style("fill", "");
+  };
+  self[`${prefix}LabelMousemove`] = (event2, data) => {
+    const s = self.config.settings.matrix;
+    if (self.clicked && !self.dragged) {
+      self.dom[`${prefix}LabelG`].selectAll("text").style("-webkit-user-select", "none").style("-moz-user-select", "none").style("-ms-user-select", "none").style("user-select", "none");
+      const label = self.clicked.event.target.closest(".sjpp-matrix-label");
+      const t = label?.__data__;
+      if (!t) return;
+      if (self.type == "hierCluster" && t.tw && t.grp?.name == self.config.settings.hierCluster?.termGroupName) return;
+      const [x, y] = select_default(label).attr("transform").split("translate(")[1].split(")")[0].split(",").map(Number);
+      const node = label.cloneNode(true);
+      self.dom[`${prefix}LabelG`].node().prepend(node);
+      self.dragged = {
+        orig: label,
+        clone: select_default(node).style("cursor", "move").style("pointer-events", "none"),
+        node,
+        x,
+        y,
+        clientX: event2.clientX,
+        clientY: event2.clientY
+      };
+      self.dragged.clone.selectAll("text").style("fill", "red");
+    }
+    if (!self.dragged) return;
+    const d = self.dragged;
+    const x2 = !s.transpose ? d.x : d.x - d.clientX + event2.clientX;
+    const y2 = !s.transpose ? d.y - d.clientY + event2.clientY : d.y;
+    d.clone.attr("transform", `translate(${x2},${y2})`);
+  };
+  self[`${prefix}LabelMouseup`] = (event2) => {
+    delete self.clicked;
+    const s = self.config.settings.matrix;
+    if (self.dragged) {
+      self.dragged.clone.remove();
+      if (self.hovered) {
+        const d = self.dragged;
+        const t = d.orig.__data__;
+        const h = self.hovered;
+        if (prefix == "termGrp") {
+          const grp = self.config.termgroups.splice(t.grpIndex, 1)[0];
+          self.config.termgroups.splice(h.grpIndex, 0, grp);
+        } else {
+          for (const grp of self.config.termgroups) {
+            grp.lst.sort((a, b) => {
+              const a1 = self.termOrder.find((t2) => t2.tw.$id === a.$id);
+              const b1 = self.termOrder.find((t2) => t2.tw.$id === b.$id);
+              if (!a1 && !b1) return 0;
+              if (!a1) return 1;
+              if (!b1) return -1;
+              return a1.totalIndex - b1.totalIndex;
+            });
+          }
+          const tw = self.config.termgroups[t.grpIndex].lst.splice(t.index, 1)[0];
+          self.config.termgroups[h.grpIndex].lst.splice(h.index, 0, t.tw);
+          if (!self.config.termgroups[t.grpIndex].lst.length) self.config.termgroups.splice(t.grpIndex, 1);
+        }
+        const sortKey = prefix == "term" ? "sortTermsBy" : "sortTermGroupsBy";
+        self.app.dispatch({
+          type: "plot_edit",
+          id: self.id,
+          config: {
+            termgroups: self.config.termgroups,
+            settings: {
+              matrix: {
+                [sortKey]: "asListed"
+              }
+            }
+          }
+        });
+      }
+      self.dom[`${prefix}LabelG`].selectAll("text").style("fill", "").style("-webkit-user-select", "").style("-moz-user-select", "").style("-ms-user-select", "").style("user-select", "");
+      delete self.dragged;
+    } else if (prefix == "term") {
+      self.showTermMenu(event2);
+    } else {
+      self.showTermGroupMenu(event2);
+    }
+  };
+}
+function setZoomPanActions(self) {
+  self.resetInteractions = function() {
+    if (self.zoomArea) {
+      self.zoomArea.remove();
+      delete self.zoomArea;
+      select_default("body").on("mouseup.matrixZoom", null);
+    }
+    delete self.clickedSeriesCell;
+  };
+  self.seriesesGMousedown = function(event2) {
+    event2.stopPropagation();
+    self.resetInteractions();
+    const startCell = self.getCellByPos(event2);
+    if (!startCell) return;
+    self.clickedSeriesCell = { event: event2, startCell };
+    if (self.settings.matrix.mouseMode == "pan") {
+      self.seriesesGdragInit();
+    } else {
+      self.zoomPointer = pointer_default(event2, self.dom.seriesesG.node());
+      self.dom.seriesesG.on("mousemove", self.seriesesGoutlineZoom).on("mouseup", self.seriesesGtriggerZoom).on("contextmenu", self.resetInteractions);
+    }
+    self.dom.mainG.selectAll("text").style("-webkit-user-select", "none").style("-moz-user-select", "none").style("-ms-user-select", "none").style("user-select", "none");
+  };
+  self.getCellByPos = function(event2) {
+    const s = self.settings.matrix;
+    const d = self.dimensions;
+    if (event2.target.tagName == "rect") {
+      if (event2.target.__data__?.sample) return event2.target.__data__;
+      if (event2.target.__data__?.xg) {
+        const width = event2.clientX - event2.target.getBoundingClientRect().x + d.seriesXoffset;
+        const i = Math.floor(width / d.dx);
+        return self.sampleOrder[i];
+      }
+    }
+    if (event2.target.tagName == "image" && s.useCanvas) {
+      return self.getImgCell(event2);
+    }
+  };
+  self.seriesesGdragInit = function() {
+    select_default("body").on("mousemove.sjppMatrixDrag", self.seriesesGdrag).on("mouseup.sjppMatrixDrag", self.seriesesGcancelDrag);
+    const s = self.settings.matrix;
+    const d = self.dimensions;
+    const c = self.clickedSeriesCell;
+    c.dxPad = 20;
+    c.dxMax = -d.seriesXoffset;
+    c.dxMaxPad = c.dxMax + c.dxPad;
+    c.dxMin = d.mainw - d.zoomedMainW - d.seriesXoffset;
+    c.dxMinPad = c.dxMin - c.dxPad;
+    const halfw = 0.5 * d.mainw;
+    c.center = {
+      max: halfw + (d.zoomedMainW - d.mainw),
+      min: halfw
+    };
+  };
+  self.seriesesGdrag = function(event2) {
+    const s = self.settings.matrix;
+    const c = self.clickedSeriesCell;
+    const d = self.dimensions;
+    const dx = event2.clientX - c.event.clientX;
+    if (Math.abs(dx) < 1) return;
+    if (dx < c.dxMinPad || dx > c.dxMaxPad) return;
+    self.clickedSeriesCell.dx = dx;
+    self.translateElems(dx, d, s, c);
+  };
+  self.translateElems = function(dx, d, s, c) {
+    self.dom.seriesesG.attr("transform", `translate(${d.xOffset + d.seriesXoffset + dx},${d.yOffset})`);
+    self.layout.top.attr.adjustBoxTransform(dx);
+    self.layout.btm.attr.adjustBoxTransform(dx);
+    const computedCenter = s.zoomCenterPct * d.mainw - d.seriesXoffset - dx;
+    self.controlsRenderer.svgScrollApi.update({ zoomCenter: computedCenter });
+  };
+  self.seriesesGcancelDrag = function(event2) {
+    select_default("body").on("mousemove.sjppMatrixDrag", null).on("mouseup.sjppMatrixDrag", null);
+    const s = self.settings.matrix;
+    const d = self.dimensions;
+    const cc = self.clickedSeriesCell;
+    const _dx = event2.clientX - cc.event.clientX;
+    const dx = Math.min(cc.dxMax, Math.max(_dx, cc.dxMin));
+    if (Math.abs(_dx) < 1 || Math.abs(dx) < 1) {
+      self.translateElems(0, d, s, cc);
+      return;
+    }
+    self.translateElems(dx, d, s, cc);
+    const c = self.getVisibleCenterCell(dx);
+    self.app.dispatch({
+      type: "plot_edit",
+      id: self.id,
+      config: {
+        settings: {
+          matrix: {
+            zoomCenterPct: 0.5,
+            zoomIndex: c.totalIndex,
+            zoomGrpIndex: c.grpIndex
+          }
+        }
+      }
+    });
+  };
+  self.seriesesGoutlineZoom = function(event2) {
+    if (!self.clickedSeriesCell) return;
+    const s = self.config.settings.matrix;
+    const e = self.clickedSeriesCell.event;
+    if (self.clickedSeriesCell && !self.zoomArea) {
+      self.zoomArea = self.dom.seriesesG.append("rect").attr("fill", "rgba(50, 50, 50, 0.3)");
+      select_default("body").on("mouseup.matrixZoom", self.mouseup);
+      self.dom.mainG.selectAll("text").style("-webkit-user-select", "none").style("-moz-user-select", "none").style("-ms-user-select", "none").style("user-select", "none");
+    }
+    const dx = event2.clientX - e.clientX;
+    const dy = event2.clientY - e.clientY;
+    const x = dx > 0 ? self.zoomPointer[0] : self.zoomPointer[0] + dx + 3;
+    self.zoomWidth = Math.abs(dx);
+    self.zoomArea.attr("transform", `translate(${x},0)`).attr("width", Math.max(0, self.zoomWidth - 2)).attr("height", self.dimensions.mainh);
+    if (!self.clickedSeriesCell.endCell) self.clickedSeriesCell.endCell = self.getCellByPos(event2);
+  };
+  self.seriesesGtriggerZoom = function(event2) {
+    event2.stopPropagation();
+    self.dom.seriesesG.on("mousemove", null).on("mouseup", null);
+    select_default("body").on("mouseup.matrixZoom", null);
+    self.dom.mainG.selectAll("text").style("-webkit-user-select", "").style("-moz-user-select", "").style("-ms-user-select", "").style("user-select", "");
+    const c = self.clickedSeriesCell;
+    const endCell = self.getCellByPos(event2);
+    if (!c || !c.startCell) {
+      self.dom.mainG.on("mouseout", null);
+      delete self.clickedSeriesCell;
+      return;
+    } else if (!c.endCell || endCell === c.startCell) {
+      self.dom.mainG.on("mouseout", null);
+      self.dom.tip.hide();
+      const cell = event2.target.tagName == "rect" ? event2.target.__data__ : c.startCell;
+      if (cell) {
+        if (self.opts.cellClick) {
+          self.opts.cellClick(
+            structuredClone({
+              sampleData: cell.row,
+              term: cell.term,
+              value: cell.value,
+              s: cell.s,
+              t: cell.t,
+              siblingCells: cell.siblingCells.filter((c2) => c2 !== cell).map((c2) => ({
+                term: c2.term,
+                value: c2.value,
+                s: c2.s,
+                t: c2.t
+              }))
+            })
+          );
+        } else {
+          self.mouseclick(event2, cell);
+        }
+      }
+      delete self.clickedSeriesCell;
+      delete self.zoomArea;
+      return;
+    }
+    const s = self.settings.matrix;
+    const l = s.controlLabels;
+    c.endCell = endCell;
+    const ss = self.opts.allow2selectSamples;
+    const startCellTouched = c.startCell.totalIndex < c.endCell.totalIndex ? c.startCell : c.endCell;
+    const endCellTouched = c.startCell.totalIndex < c.endCell.totalIndex ? c.endCell : c.startCell;
+    const samplesSet = /* @__PURE__ */ new Set();
+    for (let i = startCellTouched.totalIndex; i <= endCellTouched.totalIndex; i++) {
+      samplesSet.add(self.sampleOrder[i].row);
+    }
+    const samples = [...samplesSet];
+    const optionArr = [
+      {
+        label: "Zoom in",
+        callback: self.triggerZoomArea
+      },
+      {
+        label: `List ${samples.length} ${l.samples}`,
+        callback: () => {
+          self.resetInteractions();
+          self.dom.tip.hide();
+          showTable(self, samples, event2.clientX, event2.clientY);
+        }
+      }
+    ];
+    if (ss) {
+      optionArr.push({
+        label: ss.buttonText || `Select ${l.Samples}`,
+        callback: async () => {
+          ss.callback({
+            samples: await self.app.vocabApi.convertSampleId(samples, ss.attributes),
+            source: `Selected ${l.samples} from OncoMatrix`
+          });
+          self.zoomArea.remove();
+          delete self.zoomArea;
+          delete self.clickedSeriesCell;
+        }
+      });
+    } else {
+      if (self.state.nav && self.state.nav.header_mode !== "hidden") {
+        for (const s2 of samples) {
+          if (!s2.sampleId) s2.sampleId = s2.sample;
+        }
+        optionArr.push({
+          label: "Add to a group",
+          callback: async () => {
+            self.resetInteractions();
+            const group = {
+              name: "Group",
+              items: samples
+            };
+            self.addGroup(group);
+          }
+        });
+      }
+    }
+    self.dom.dendroClickMenu.clear();
+    self.dom.clickMenu.clear();
+    self.mouseout();
+    self.dom.tip.hide();
+    self.dom.brushMenu.clear();
+    self.dom.brushMenu.d.selectAll("div").data(optionArr).enter().append("div").attr("class", "sja_menuoption").style("border-radius", "0px").html((d) => d.label).on("click", (event3) => {
+      self.dom.brushMenu.d.selectAll("*").remove();
+      event3.target.__data__.callback();
+    });
+    self.dom.brushMenu.show(event2.clientX, event2.clientY);
+  };
+  const showTable = function(self2, samples, x, y) {
+    delete self2.clickedSeriesCell;
+    const templates = self2.state.termdbConfig.urlTemplates;
+    const rows = templates?.sample ? samples.map((c) => [{ value: c._ref_.label, url: `${templates.sample.base}${c.sample}` }]) : samples.map((c) => [{ value: c._ref_.label }]);
+    const columns = [{ label: self2.settings.matrix.controlLabels.Samples }];
+    if (!self2.dom.sampleListMenu) self2.dom.sampleListMenu = new Menu({ padding: "5px" });
+    else self2.dom.sampleListMenu.clear();
+    const div = self2.dom.sampleListMenu.d.append("div");
+    renderTable({
+      rows,
+      columns,
+      div,
+      showLines: true,
+      maxWidth: columns.length * "30" + "vw",
+      maxHeight: "35vh",
+      resize: true
+    });
+    self2.dom.sampleListMenu.show(x, y);
+  };
+  self.addGroup = async function(group) {
+    const tw = getSamplelstTW([group]);
+    const filter = getFilter(tw);
+    addNewGroup(self.app, filter, self.state.groups);
+  };
+  self.triggerZoomArea = function() {
+    if (self.zoomArea) {
+      self.zoomArea.remove();
+      delete self.zoomArea;
+    }
+    const c = self.clickedSeriesCell;
+    delete self.clickedSeriesCell;
+    const s = self.settings.matrix;
+    const d = self.dimensions;
+    const start = c.startCell.totalIndex < c.endCell.totalIndex ? c.startCell : c.endCell;
+    const zoomIndex = Math.floor(start.totalIndex + Math.abs(c.endCell.totalIndex - c.startCell.totalIndex) / 2);
+    const centerCell = self.sampleOrder[zoomIndex] || self.getImgCell(event);
+    const colw = self.computedSettings.colw || self.settings.matrix.colw;
+    const maxZoomLevel = s.colwMax / colw;
+    const minZoomLevel = s.colwMin / colw;
+    const tentativeZoomLevel = s.zoomLevel * d.mainw / self.zoomWidth * 0.75;
+    const zoomLevel = Math.max(minZoomLevel, Math.min(tentativeZoomLevel, maxZoomLevel));
+    const zoomCenter = centerCell.totalIndex * d.dx + (centerCell.grpIndex - 1) * s.colgspace + d.seriesXoffset;
+    self.app.dispatch({
+      type: "plot_edit",
+      id: self.id,
+      config: {
+        settings: {
+          matrix: {
+            zoomLevel,
+            // try to keep the center of the grey zoom rectangle in the same position before and after zoom
+            // this could aslo support mouse scroll zoom in the future.
+            zoomCenterPct: zoomLevel < 1 && d.mainw >= d.zoomedMainW ? 0.5 : zoomCenter / d.mainw,
+            zoomIndex,
+            zoomGrpIndex: centerCell.grpIndex
+          }
+        }
+      }
+    });
+    self.resetInteractions();
+  };
+}
+function setLengendActions(self) {
+  self.legendLabelMouseover = (event2) => {
+    const targetData = event2.target.__data__;
+    if (!targetData || targetData.dt == dtgeneexpression || targetData.dt == dtmetaboliteintensity || targetData.dt == dtproteomeabundance) {
+      return;
+    }
+    if (!targetData.isLegendItem && !targetData.dt) {
+      return;
+    }
+    const legendGrpHidden = self.config.legendGrpFilter.lst.find(
+      (f) => f.dt?.includes(targetData.dt) && (!f.origin || f.origin == targetData.origin)
+    ) && true;
+    if (targetData.isLegendItem && legendGrpHidden) {
+      return;
+    }
+    const term = self.termOrder.find((t) => t.tw.$id == targetData.$id);
+    if (term?.tw?.q?.type == "predefined-groupset" || term?.tw?.q?.type == "custom-groupset") {
+      return;
+    }
+    if (event2.target.nodeName == "rect") select_default(event2.target).style("cursor", "pointer");
+    else select_default(event2.target).style("fill", "blue").style("cursor", "pointer");
+  };
+  self.legendLabelMouseout = (event2) => {
+    select_default(event2.target).style("fill", "");
+  };
+  self.legendLabelMouseup = (event2) => {
+    const targetData = event2.target.__data__;
+    if (!targetData || targetData.dt == dtgeneexpression || targetData.dt == dtmetaboliteintensity || targetData.dt == dtproteomeabundance) {
+      return;
+    }
+    if (event2.target.className.baseVal.includes("sjpp-color-scale") && targetData.dt == dtcnv) {
+      return;
+    }
+    const byOrigin = self.state.termdbConfig.assayAvailability?.byDt?.[parseInt(targetData.dt)]?.byOrigin;
+    const menuGrp = self.dom.legendMenu.clear();
+    if (!targetData.isLegendItem) {
+      if (!targetData.dt) {
+        return;
+      }
+      const legendGrpFilterIndex = self.config.legendGrpFilter.lst.findIndex(
+        (f) => f.dt.slice().sort().toString() === targetData.dt.slice().sort().toString() && (!byOrigin || f.origin == targetData.origin)
+      );
+      const legendFilterIndex2 = self.config.legendValueFilter.lst.findIndex(
+        (l) => l.legendGrpName == targetData.name && l.tvs.values.find((v) => targetData.dt.includes(v.dt) && (!byOrigin || v.origin == targetData.origin))
+      );
+      const div2 = menuGrp.d.append("div");
+      if (legendGrpFilterIndex == -1) {
+        if (targetData.dt.includes(dtsnvindel)) {
+          div2.append("div").attr("class", "sja_menuoption sja_sharp_border").text(`Show only truncating mutations`).on("click", () => {
+            showOnlyTrunc(menuGrp, targetData, self);
+          });
+          div2.append("div").attr("class", "sja_menuoption sja_sharp_border").text(`Show only protein-changing mutations`).on("click", () => {
+            showOnlyPC(menuGrp, targetData, self);
+          });
+        }
+        const onlyGeneGroupShown = self.legendData.filter(
+          (l) => l.dt && !l.crossedOut && (l.name == targetData.name || l.items.find((i) => !i.greyedOut && !i.crossedOut))
+        ).length <= 1;
+        div2.append("div").attr(
+          "class",
+          onlyGeneGroupShown ? "sja_menuoption_not_interactive sja_sharp_border" : "sja_menuoption sja_sharp_border"
+        ).text(`Do not show ${targetData.name}`).style("opacity", onlyGeneGroupShown ? "0.5" : "1").on("click", () => {
+          if (!onlyGeneGroupShown) showNone(menuGrp, targetData, self);
+        });
+      }
+      if (legendGrpFilterIndex !== -1 || legendFilterIndex2 !== -1) {
+        div2.append("div").attr("class", "sja_menuoption sja_sharp_border").text(`Show all ${targetData.name}`).on("click", () => {
+          showAll(menuGrp, targetData, self);
+        });
+      }
+      menuGrp.showunder(event2.target);
+      return;
+    }
+    const legendGrpHidden = self.config.legendGrpFilter.lst.find(
+      (f) => f.dt?.includes(targetData.dt) && (!f.origin || f.origin == targetData.origin)
+    ) && true;
+    if (targetData.isLegendItem && legendGrpHidden) {
+      return;
+    }
+    const term = self.terms.find((t) => t.tw.$id == targetData.$id);
+    if (term?.tw?.q?.type == "predefined-groupset" || term?.tw?.q?.type == "custom-groupset") {
+      return;
+    }
+    let legendFilterIndex;
+    if (targetData.dt) {
+      legendFilterIndex = self.config.legendValueFilter.lst.findIndex(
+        (l) => l.legendGrpName == targetData.termid && l.tvs.values.find(
+          (v) => v.dt == targetData.dt && (!byOrigin || v.origin == targetData.origin) && v.mclasslst[0] == targetData.key
+        )
+      );
+    } else {
+      const legendTerm = self.termOrder.find((to) => to.tw.$id == targetData.$id)?.tw?.term;
+      if (!legendTerm) {
+        return;
+      }
+      if (legendTerm.type == "categorical" || legendTerm.type == "survival") {
+        legendFilterIndex = self.config.legendValueFilter.lst.findIndex(
+          (l) => l.legendGrpName == targetData.termid && l.tvs.values.find((v) => v.key == targetData.key)
+        );
+      } else if (isNumericTerm(legendTerm)) {
+        legendFilterIndex = self.config.legendValueFilter.lst.findIndex(
+          (l) => l.legendGrpName == targetData.termid && l.tvs.ranges.find((r) => r.name == targetData.key)
+        );
+      }
+    }
+    const controlLabels = self.settings.matrix.controlLabels;
+    const div = menuGrp.d.append("div");
+    const addMenuOptions = (targetItemData) => {
+      const term2 = self.termOrder.find((t) => t.tw.$id == targetItemData.$id)?.tw?.term;
+      if (term2?.type !== "termCollection" && (!targetItemData.dt || self.type !== "hierCluster" || legendFilterIndex !== -1)) {
+        div.append("div").attr("class", "sja_menuoption sja_sharp_border").text(
+          targetItemData.dt ? legendFilterIndex == -1 ? `Hide ${controlLabels.samples} with ${mclass[targetItemData.key].label}` : `Show ${controlLabels.samples} with ${mclass[targetItemData.key].label}` : legendFilterIndex == -1 ? "Hide" : "Show"
+        ).on("click", () => {
+          menuGrp.hide();
+          if (legendFilterIndex == -1) {
+            if (targetItemData.dt) {
+              const filterNew = {
+                legendGrpName: targetItemData.termid,
+                type: "tvs",
+                tvs: {
+                  isnot: true,
+                  legendFilterType: "geneVariant_hard",
+                  // indicates this matrix legend filter is hard filter
+                  term: { type: "geneVariant" },
+                  values: [
+                    {
+                      dt: targetItemData.dt,
+                      origin: targetItemData.origin,
+                      mclasslst: [targetItemData.key]
+                    }
+                  ]
+                }
+              };
+              self.config.legendValueFilter.lst.push(filterNew);
+            } else {
+              const term3 = self.termOrder.find((t) => t.tw.$id == targetItemData.$id).tw.term;
+              if (term3.type == "categorical" || term3.type == "survival") {
+                term3.$id = targetItemData.$id;
+                const filterGrpIndex = self.config.legendValueFilter.lst.findIndex(
+                  (l) => l.legendGrpName == targetItemData.termid
+                );
+                if (filterGrpIndex == -1) {
+                  const filterNew = {
+                    legendGrpName: targetItemData.termid,
+                    type: "tvs",
+                    tvs: {
+                      isnot: true,
+                      term: term3,
+                      values: [{ key: targetItemData.key }]
+                    }
+                  };
+                  self.config.legendValueFilter.lst.push(filterNew);
+                } else {
+                  self.config.legendValueFilter.lst[filterGrpIndex].tvs.values.push({ key: targetItemData.key });
+                }
+              } else if (isNumericTerm(term3)) {
+                term3.$id = targetItemData.$id;
+                const filterNew = {
+                  legendGrpName: targetItemData.termid,
+                  type: "tvs",
+                  tvs: {
+                    isnot: true,
+                    term: term3,
+                    ranges: [self.data.refs.byTermId[targetItemData.$id].bins.find((b) => targetItemData.key == b.name)]
+                  }
+                };
+                self.config.legendValueFilter.lst.push(filterNew);
+              }
+            }
+          } else {
+            if (targetItemData.dt) self.config.legendValueFilter.lst.splice(legendFilterIndex, 1);
+            else {
+              const term3 = self.termOrder.find((t) => t.tw.$id == targetItemData.$id).tw.term;
+              if (term3.type == "categorical" || term3.type == "survival") {
+                const filterGrpIndex = self.config.legendValueFilter.lst.findIndex(
+                  (l) => l.legendGrpName == targetItemData.termid
+                );
+                const filterIndex = self.config.legendValueFilter.lst[filterGrpIndex].tvs.values.findIndex(
+                  (v) => v.key == targetItemData.key
+                );
+                self.config.legendValueFilter.lst[filterGrpIndex].tvs.values.splice(filterIndex, 1);
+              } else self.config.legendValueFilter.lst.splice(legendFilterIndex, 1);
+            }
+          }
+          if (self.state.config.settings.matrix.addMutationCNVButtons && self.chartType !== "hierCluster") {
+            if (targetItemData.dt == dtsnvindel) {
+              self.config.settings.matrix.showMatrixMutation = "bySelection";
+              const cl = self.settings.matrix.controlLabels;
+              if (self.legendData.find((l) => l.name == cl.Mutations)?.items?.length == self.config.legendValueFilter.lst.filter((l) => l.legendGrpName == cl.Mutations)?.length) {
+                self.config.settings.matrix.allMatrixMutationHidden = true;
+              } else self.config.settings.matrix.allMatrixMutationHidden = false;
+            }
+            if (targetItemData.dt == dtcnv) {
+              self.config.settings.matrix.showMatrixCNV = "bySelection";
+              if (self.legendData.find((l) => l.name == "CNV")?.items?.length == self.config.legendValueFilter.lst.filter((l) => l.legendGrpName == "CNV")?.length) {
+                self.config.settings.matrix.allMatrixCNVHidden = true;
+                if (self.config.settings.matrix.cellEncoding == "oncoprint")
+                  self.config.settings.matrix.cellEncoding = "single";
+              } else {
+                self.config.settings.matrix.allMatrixCNVHidden = false;
+                if (self.config.settings.matrix.cellEncoding !== "")
+                  self.config.settings.matrix.cellEncoding = "oncoprint";
+              }
+            }
+          }
+          self.app.dispatch({
+            type: "plot_edit",
+            id: self.id,
+            config: self.config
+          });
+        });
+      }
+      if (targetItemData.isLegendItem) {
+        if (targetItemData.dt && legendFilterIndex == -1 && term2?.type !== "termCollection") {
+          div.append("div").attr("class", "sja_menuoption sja_sharp_border").text(`Do not show ${mclass[targetItemData.key]?.label}`).on("click", () => {
+            menuGrp.hide();
+            const filterNew = {
+              legendGrpName: targetItemData.termid,
+              type: "tvs",
+              tvs: {
+                isnot: true,
+                legendFilterType: "geneVariant_soft",
+                // indicates this matrix legend filter is soft filter
+                term: { type: "geneVariant" },
+                values: [{ dt: targetItemData.dt, origin: targetItemData.origin, mclasslst: [targetItemData.key] }]
+              }
+            };
+            self.config.legendValueFilter.lst.push(filterNew);
+            if (self.state.config.settings.matrix.addMutationCNVButtons && self.chartType !== "hierCluster") {
+              if (targetItemData.dt == dtsnvindel) {
+                self.config.settings.matrix.showMatrixMutation = "bySelection";
+                const cl = self.settings.matrix.controlLabels;
+                if (self.legendData.find((l) => l.name == cl.Mutations)?.items?.length == self.config.legendValueFilter.lst.filter((l) => l.legendGrpName == cl.Mutations)?.length) {
+                  self.config.settings.matrix.allMatrixMutationHidden = true;
+                } else self.config.settings.matrix.allMatrixMutationHidden = false;
+              }
+              if (targetItemData.dt == dtcnv) {
+                self.config.settings.matrix.showMatrixCNV = "bySelection";
+                if (self.legendData.find((l) => l.name == "CNV")?.items?.length == self.config.legendValueFilter.lst.filter((l) => l.legendGrpName == "CNV")?.length) {
+                  self.config.settings.matrix.allMatrixCNVHidden = true;
+                  if (self.config.settings.matrix.cellEncoding == "oncoprint")
+                    self.config.settings.matrix.cellEncoding = "single";
+                } else self.config.settings.matrix.allMatrixCNVHidden = false;
+              }
+            }
+            self.app.dispatch({
+              type: "plot_edit",
+              id: self.id,
+              config: self.config
+            });
+          });
+        }
+        if (!targetItemData.dt && term2?.type !== "termCollection") {
+          div.append("div").attr("class", "sja_menuoption sja_sharp_border").text("Show only").on("click", () => {
+            menuGrp.hide();
+            const term3 = self.termOrder.find((t) => t.tw.$id == targetItemData.$id)?.tw?.term;
+            const legendGrp = self.legendData.find((lg) => lg.name == targetItemData.termid) || self.legendData.find((lg) => lg.$id == targetItemData.$id);
+            self.config.legendValueFilter.lst = self.config.legendValueFilter.lst.filter(
+              (l) => l.legendGrpName !== targetItemData.termid
+            );
+            if (term3.type == "categorical" || term3.type == "survival") {
+              term3.$id = targetItemData.$id;
+              for (const l of legendGrp.items) {
+                if (l.key == targetItemData.key) continue;
+                const filterGrpIndex = self.config.legendValueFilter.lst.findIndex(
+                  (l2) => l2.legendGrpName == targetItemData.termid
+                );
+                if (filterGrpIndex == -1) {
+                  const filterNew = {
+                    legendGrpName: targetItemData.termid,
+                    type: "tvs",
+                    tvs: {
+                      isnot: true,
+                      term: term3,
+                      values: [{ key: l.key }]
+                    }
+                  };
+                  self.config.legendValueFilter.lst.push(filterNew);
+                } else {
+                  self.config.legendValueFilter.lst[filterGrpIndex].tvs.values.push({ key: l.key });
+                }
+              }
+            } else if (isNumericTerm(term3)) {
+              term3.$id = targetItemData.$id;
+              for (const l of legendGrp.items) {
+                if (l.key == targetItemData.key) continue;
+                const filterNew = {
+                  legendGrpName: targetItemData.termid,
+                  type: "tvs",
+                  tvs: {
+                    isnot: true,
+                    term: term3,
+                    ranges: [self.data.refs.byTermId[targetItemData.$id].bins.find((b) => l.key == b.name)]
+                  }
+                };
+                if (!self.config.legendValueFilter.lst.length) self.config.legendValueFilter.lst = [filterNew];
+                else self.config.legendValueFilter.lst.push(filterNew);
+              }
+            }
+            self.app.dispatch({
+              type: "plot_edit",
+              id: self.id,
+              config: self.config
+            });
+          });
+        }
+        if (!targetItemData.dt && term2?.type !== "termCollection") {
+          div.append("div").attr("class", "sja_menuoption sja_sharp_border").text("Show all").on("click", () => {
+            menuGrp.hide();
+            self.config.legendValueFilter.lst = self.config.legendValueFilter.lst.filter(
+              (l) => l.legendGrpName !== targetItemData.termid
+            );
+            self.app.dispatch({
+              type: "plot_edit",
+              id: self.id,
+              config: self.config
+            });
+          });
+        }
+        if (!targetData.domain) {
+          div.append("span").text("Color").style("padding", "5px 10px").style("margin", "1px");
+          self.dom.legendColorInput = div.append("input").attr("type", "color").attr("aria-label", `change the bar color`).attr("value", targetData.color?.startsWith("rgb") ? rgb2hex(targetData.color) : targetData.color).on("change", async () => {
+            menuGrp.hide();
+            const color = self.dom.legendColorInput.node().value;
+            if (targetData.dt) {
+              if (!mclass[targetData.key].origColor) mclass[targetData.key].origColor = mclass[targetData.key].color;
+              mclass[targetData.key].color = color;
+              self.main();
+              return;
+            }
+            const twSpecificSettings = self.config.settings.matrix.twSpecificSettings;
+            if (!twSpecificSettings[targetData.$id]) twSpecificSettings[targetData.$id] = {};
+            const twSettings = twSpecificSettings[targetData.$id];
+            if (!twSettings[targetData.key]) twSettings[targetData.key] = {};
+            twSettings[targetData.key].color = color;
+            self.app.dispatch({
+              type: "plot_edit",
+              id: self.opts.id,
+              config: { settings: { matrix: { twSpecificSettings } } }
+            });
+          });
+          if (targetData.dt && mclass[targetData.key].origColor) {
+            const resetDiv = div.append("div").style("display", "inline-block");
+            const handler = () => {
+              menuGrp.hide();
+              mclass[targetData.key].color = mclass[targetData.key].origColor;
+              delete mclass[targetData.key].origColor;
+              self.main();
+            };
+            icons["restart"](resetDiv, { handler, title: "Reset to original color" });
+          }
+        }
+        menuGrp.showunder(event2.target);
+      }
+    };
+    if (targetData.parents) {
+      for (const p of targetData.parents) {
+        addMenuOptions(p);
+      }
+    } else {
+      addMenuOptions(targetData);
+    }
+  };
+}
+function setMutationSelectionActions(self) {
+  self.mutationSelectionActions = {
+    onlyTruncating: showOnlyTrunc,
+    onlyPC: showOnlyPC,
+    none: showNone,
+    all: showAll,
+    bySelection: showByLegendFilter
+  };
+  self.mutationControlCallback = (mutationSelection) => {
+    const menuGrp = self.dom.legendMenu.clear();
+    const targetData = self.legendData.find((l) => l.dt?.includes(dtsnvindel));
+    self.mutationSelectionActions[mutationSelection](menuGrp, targetData, self, "mutation");
+  };
+  self.CNVControlCallback = (CNVSelection) => {
+    const menuGrp = self.dom.legendMenu.clear();
+    const targetData = self.legendData.find((l) => l.dt?.includes(dtcnv));
+    self.mutationSelectionActions[CNVSelection](menuGrp, targetData, self, "CNV");
+  };
+  self.geneStyleControlCallback = (styleSelection) => {
+    const targetData = self.legendData.find((l) => l.dt?.includes(dtcnv));
+    if (styleSelection == "") showStackedStyle(targetData, self);
+    else if (styleSelection == "single") showSingleStyle(targetData, self);
+    else if (styleSelection == "oncoprint") showOncoprintStyle(targetData, self);
+  };
+}
+function showSingleStyle(targetData, self) {
+  if (self.state.config.settings.matrix.addMutationCNVButtons && self.chartType !== "hierCluster") {
+    if (targetData) {
+      const byOrigin = self.state.termdbConfig.assayAvailability?.byDt?.[parseInt(targetData.dt)]?.byOrigin;
+      const legendGrpFilterIndex = self.config.legendGrpFilter.lst.findIndex(
+        (f) => f.dt.slice().sort().toString() === targetData.dt.slice().sort().toString() && (!byOrigin || f.origin == targetData.origin)
+      );
+      if (legendGrpFilterIndex == -1) {
+        const filterNew = { dt: targetData.dt };
+        if (byOrigin) {
+          filterNew.origin = targetData.origin;
+        }
+        self.config.legendValueFilter.lst = self.config.legendValueFilter.lst.filter(
+          (f) => f.legendGrpName !== targetData.name
+        );
+        self.config.legendGrpFilter.lst.push(filterNew);
+      }
+    }
+    self.config.settings.matrix.cellEncoding = "single";
+  }
+  self.app.dispatch({
+    type: "plot_edit",
+    id: self.id,
+    config: self.config
+  });
+}
+function showOncoprintStyle(targetData, self) {
+  if (self.state.config.settings.matrix.addMutationCNVButtons && self.chartType !== "hierCluster") {
+    if (targetData) {
+      const byOrigin = self.state.termdbConfig.assayAvailability?.byDt?.[parseInt(targetData.dt)]?.byOrigin;
+      const legendGrpFilterIndex = self.config.legendGrpFilter.lst.findIndex(
+        (f) => f.dt.slice().sort().toString() === targetData.dt.slice().sort().toString() && (!byOrigin || f.origin == targetData.origin)
+      );
+      if (legendGrpFilterIndex !== -1) self.config.legendGrpFilter.lst.splice(legendGrpFilterIndex, 1);
+      self.config.legendValueFilter.lst = self.config.legendValueFilter.lst.filter(
+        (f) => f.legendGrpName !== targetData.name
+      );
+    }
+    self.config.settings.matrix.showMatrixCNV = "all";
+    self.config.settings.matrix.allMatrixCNVHidden = false;
+  }
+  self.config.settings.matrix.cellEncoding = "oncoprint";
+  self.app.dispatch({
+    type: "plot_edit",
+    id: self.id,
+    config: self.config
+  });
+}
+function showStackedStyle(targetData, self) {
+  if (self.state.config.settings.matrix.addMutationCNVButtons && self.chartType !== "hierCluster") {
+    if (targetData) {
+      const byOrigin = self.state.termdbConfig.assayAvailability?.byDt?.[parseInt(targetData.dt)]?.byOrigin;
+      const legendGrpFilterIndex = self.config.legendGrpFilter.lst.findIndex(
+        (f) => f.dt.slice().sort().toString() === targetData.dt.slice().sort().toString() && (!byOrigin || f.origin == targetData.origin)
+      );
+      if (legendGrpFilterIndex !== -1) self.config.legendGrpFilter.lst.splice(legendGrpFilterIndex, 1);
+      self.config.legendValueFilter.lst = self.config.legendValueFilter.lst.filter(
+        (f) => f.legendGrpName !== targetData.name
+      );
+    }
+  }
+  self.config.settings.matrix.cellEncoding = "";
+  self.app.dispatch({
+    type: "plot_edit",
+    id: self.id,
+    config: self.config
+  });
+}
+function showOnlyTrunc(menuGrp, targetData, self) {
+  menuGrp.hide();
+  if (targetData) {
+    self.config.legendValueFilter.lst = self.config.legendValueFilter.lst.filter(
+      (f) => f.legendGrpName !== targetData.name
+    );
+    self.config.legendGrpFilter.lst = self.config.legendGrpFilter.lst.filter(
+      (f) => !(f.dt.includes(dtsnvindel) && f.origin == targetData.origin)
+    );
+    const truncatingM = self.config.settings.matrix.truncatingMutations;
+    const controlLabels = self.config.settings.matrix.controlLabels;
+    for (const [k, v] of Object.entries(mclass)) {
+      if (truncatingM.includes(k) || v.dt != dtsnvindel) continue;
+      const filterNew = {
+        legendGrpName: targetData.origin ? `${targetData.origin[0].toUpperCase() + targetData.origin.slice(1)} ${controlLabels.Mutations}` : controlLabels.Mutations,
+        type: "tvs",
+        tvs: {
+          isnot: true,
+          legendFilterType: "geneVariant_soft",
+          term: { type: "geneVariant" },
+          values: [{ dt: dtsnvindel, origin: targetData.origin, mclasslst: [k] }]
+        }
+      };
+      self.config.legendValueFilter.lst.push(filterNew);
+    }
+  }
+  self.app.dispatch({
+    type: "plot_edit",
+    id: self.id,
+    config: self.config
+  });
+}
+function showOnlyPC(menuGrp, targetData, self) {
+  menuGrp.hide();
+  if (targetData) {
+    self.config.legendValueFilter.lst = self.config.legendValueFilter.lst.filter(
+      (f) => f.legendGrpName !== targetData.name
+    );
+    self.config.legendGrpFilter.lst = self.config.legendGrpFilter.lst.filter(
+      (f) => !(f.dt.includes(dtsnvindel) && f.origin == targetData.origin)
+    );
+    const proteinChangingMutations = self.config.settings.matrix.proteinChangingMutations;
+    const controlLabels = self.config.settings.matrix.controlLabels;
+    for (const [k, v] of Object.entries(mclass)) {
+      if (proteinChangingMutations.includes(k) || v.dt != dtsnvindel) continue;
+      const filterNew = {
+        legendGrpName: targetData.origin ? `${targetData.origin[0].toUpperCase() + targetData.origin.slice(1)} ${controlLabels.Mutations}` : controlLabels.Mutations,
+        type: "tvs",
+        tvs: {
+          isnot: true,
+          legendFilterType: "geneVariant_soft",
+          term: { type: "geneVariant" },
+          values: [{ dt: dtsnvindel, origin: targetData.origin, mclasslst: [k] }]
+        }
+      };
+      self.config.legendValueFilter.lst.push(filterNew);
+    }
+  }
+  self.app.dispatch({
+    type: "plot_edit",
+    id: self.id,
+    config: self.config
+  });
+}
+function showNone(menuGrp, targetData, self, target) {
+  menuGrp.hide();
+  if (targetData) {
+    const byOrigin = self.state.termdbConfig.assayAvailability?.byDt?.[parseInt(targetData.dt)]?.byOrigin;
+    const legendGrpFilterIndex = self.config.legendGrpFilter.lst.findIndex(
+      (f) => f.dt.slice().sort().toString() === targetData.dt.slice().sort().toString() && (!byOrigin || f.origin == targetData.origin)
+    );
+    if (legendGrpFilterIndex == -1) {
+      const filterNew = { dt: targetData.dt };
+      if (byOrigin) {
+        filterNew.origin = targetData.origin;
+      }
+      self.config.legendValueFilter.lst = self.config.legendValueFilter.lst.filter(
+        (f) => f.legendGrpName !== targetData.name
+      );
+      self.config.legendGrpFilter.lst.push(filterNew);
+    }
+  }
+  if (self.state.config.settings.matrix.addMutationCNVButtons && self.chartType !== "hierCluster" && (target == "CNV" || targetData?.dt?.includes(dtcnv)) && self.config.settings.matrix.cellEncoding == "oncoprint") {
+    self.config.settings.matrix.cellEncoding = "single";
+  }
+  self.app.dispatch({
+    type: "plot_edit",
+    id: self.id,
+    config: self.config
+  });
+}
+function getConfigForShowAll(self, targetData, target) {
+  if (targetData) {
+    const byOrigin = self.state.termdbConfig.assayAvailability?.byDt?.[parseInt(targetData.dt)]?.byOrigin;
+    const legendGrpFilterIndex = self.config.legendGrpFilter.lst.findIndex(
+      (f) => f.dt.slice().sort().toString() === targetData.dt.slice().sort().toString() && (!byOrigin || f.origin == targetData.origin)
+    );
+    const legendFilterIndex = self.config.legendValueFilter.lst.findIndex(
+      (l) => l.legendGrpName == targetData.name && l.tvs.values.find((v) => targetData.dt.includes(v.dt) && (!byOrigin || v.origin == targetData.origin))
+    );
+    if (legendGrpFilterIndex !== -1) self.config.legendGrpFilter.lst.splice(legendGrpFilterIndex, 1);
+    if (legendFilterIndex !== -1)
+      self.config.legendValueFilter.lst = self.config.legendValueFilter.lst.filter(
+        (f) => f.legendGrpName != targetData.name
+      );
+  }
+  const s = self.config.settings.matrix;
+  if (s.addMutationCNVButtons && self.chartType !== "hierCluster" && (target == "CNV" || targetData?.dt?.includes(dtcnv)) && s.cellEncoding !== "") {
+    s.cellEncoding = "oncoprint";
+  }
+  return self.config;
+}
+function showAll(menuGrp, targetData, self, target) {
+  menuGrp.hide();
+  self.app.dispatch({
+    type: "plot_edit",
+    id: self.id,
+    config: getConfigForShowAll(self, targetData, target)
+  });
+}
+function showByLegendFilter(menuGrp, targetData, self, target) {
+  menuGrp.hide();
+  const s = self.config.settings.matrix;
+  if (!targetData) {
+    if (s.addMutationCNVButtons && self.chartType !== "hierCluster" && target == "mutation") {
+      s.showMatrixMutation = "bySelection";
+    } else if (s.addMutationCNVButtons && self.chartType !== "hierCluster" && target == "CNV") {
+      s.showMatrixCNV = "bySelection";
+    }
+    self.app.dispatch({
+      type: "plot_edit",
+      id: self.id,
+      config: self.config
+    });
+    return;
+  }
+  self.app.tip.d.selectAll(".byLFClassDiv").remove();
+  const classDiv = self.app.tip.d.append("div").attr("class", "byLFClassDiv");
+  const checkboxName = Math.random().toString();
+  const mClassDiv = classDiv.selectAll(":scope>div").data(target == "mutation" ? s.mutationClasses : s.CNVClasses).enter().append("label").style("margin", "5px").style("margin-left", "30px").style("display", "block").each(function(d) {
+    const mclassDisabled = self.config.legendValueFilter.lst.find(
+      (f) => f.tvs.legendFilterType == "geneVariant_hard" && f.tvs.values[0].dt == mclass[d].dt && f.tvs.values[0].mclasslst.includes(d)
+    );
+    const mclassHidden = target == "mutation" ? s.hiddenMutations.includes(d) : s.hiddenCNVs.includes(d);
+    const oneClassDiv = select_default(this).attr("class", "sjpp_row_wrapper");
+    oneClassDiv.append("input").attr("type", "checkbox").attr("name", checkboxName).property("disabled", mclassDisabled ? true : false).property("checked", mclassDisabled || mclassHidden ? false : true).style("vertical-align", "top").style("margin-right", "3px").on("change", function() {
+      const anyChecked = mClassDiv.selectAll(`input[type='checkbox'][name='${checkboxName}']:checked`).empty();
+      applyBtn.property("disabled", anyChecked);
+    });
+    oneClassDiv.append("span").style("margin-left", "3px").html(mclass[d].label).style("text-decoration", mclassDisabled ? "line-through" : "");
+  });
+  const applyBtn = classDiv.append("button").property("disabled", true).style("margin-top", "3px").text("Apply").on("click", () => {
+    const checkedCheckboxes = mClassDiv.selectAll(`input[type='checkbox'][name='${checkboxName}']:checked`);
+    const checkedItems = checkedCheckboxes.nodes().map((c) => select_default(c).datum());
+    menuGrp.hide();
+    self.config.legendValueFilter.lst = self.config.legendValueFilter.lst.filter(
+      (f) => f.legendGrpName !== targetData.name || f.tvs.legendFilterType == "geneVariant_hard"
+    );
+    self.config.legendGrpFilter.lst = self.config.legendGrpFilter.lst.filter(
+      (f) => !(f.dt.includes(dtsnvindel) && targetData.dt.includes(dtsnvindel) || f.dt.includes(dtcnv) && targetData.dt.includes(dtcnv))
+    );
+    for (const item of target == "mutation" ? s.mutationClasses : s.CNVClasses) {
+      if (checkedItems.includes(item)) continue;
+      const filterNew = {
+        legendGrpName: targetData.name,
+        type: "tvs",
+        tvs: {
+          isnot: true,
+          legendFilterType: "geneVariant_soft",
+          // indicates this matrix legend filter is soft filter
+          term: { type: "geneVariant" },
+          values: [{ dt: mclass[item].dt, origin: targetData.origin, mclasslst: [item] }]
+        }
+      };
+      self.config.legendValueFilter.lst.push(filterNew);
+    }
+    if (self.state.config.settings.matrix.addMutationCNVButtons && self.chartType !== "hierCluster" && (target == "CNV" || targetData?.dt?.includes(dtcnv))) {
+      if (checkedItems.length == 0 && self.config.settings.matrix.cellEncoding == "oncoprint") {
+        self.config.settings.matrix.cellEncoding = "single";
+      } else if (checkedItems.length > 0 && self.config.settings.matrix.cellEncoding == "single") {
+        self.config.settings.matrix.cellEncoding = "oncoprint";
+      }
+    }
+    self.app.dispatch({
+      type: "plot_edit",
+      id: self.id,
+      config: self.config
+    });
+  });
+}
+function getLabel(c, v, p) {
+  let fusionLabel;
+  if (p)
+    fusionLabel = p[0].a.name && p[0].b.name ? p[0].a.name + "::" + p[0].b.name : p[0].a.name ? p[0].a.name + "::?" : p[0].b.name ? "?::" + p[0].b.name : "";
+  const label = c.t.grp.type == "hierCluster" ? v.value : v && v.dt == dtcnv && v.value ? `${mclass[v.class].label} (${v.value.toFixed(2)})` : p ? fusionLabel : v.mname ? `${v.mname} ${mclass[v.class].label}` : mclass[v.class].label;
+  return label;
+}
+function mayAddEditMsg(arg, t) {
+  if (!t.grp.valueFilter) return;
+  const editMsg = "Cannot edit variable because group value filter is in use.<br>Please add new variable/variable group to enable editing.";
+  arg.editMsg = editMsg;
+}
+
+export {
+  setInteractivity,
+  getConfigForShowAll,
+  showAll
+};
+//# sourceMappingURL=chunk-2QQO4RRD.js.map