@sjcrh/proteinpaint-client 2.184.0 → 2.185.0

package/dist/chunk-HROKXT4K.js

@@ -0,0 +1,14 @@
+// src/block.lazyload.js
+var Block;
+async function blocklazyload(arg) {
+  if (!Block) {
+    const b = await import("./block-IGBB4BJH.js");
+    Block = b.Block;
+  }
+  return new Block(arg);
+}
+
+export {
+  blocklazyload
+};
+//# sourceMappingURL=chunk-HROKXT4K.js.map

package/dist/chunk-HTMXVOTH.js

@@ -0,0 +1,482 @@
+import {
+  renderTable
+} from "./chunk-YWUVCXFS.js";
+import {
+  clusterMethodLst,
+  distanceMethodLst
+} from "./chunk-6ZCHECOT.js";
+import {
+  METABOLITE_INTENSITY,
+  NUMERIC_DICTIONARY_TERM,
+  PROTEOME_ABUNDANCE
+} from "./chunk-EGWVYY7K.js";
+import {
+  select_default
+} from "./chunk-I6Y4O3RR.js";
+import {
+  __export
+} from "./chunk-HFNDKYVF.js";
+
+// plots/matrix/hierCluster.interactivity.js
+var hierCluster_interactivity_exports = {};
+__export(hierCluster_interactivity_exports, {
+  addSelectedRowsOptions: () => addSelectedRowsOptions,
+  addSelectedSamplesOptions: () => addSelectedSamplesOptions,
+  getAllChildrenClusterIds: () => getAllChildrenClusterIds,
+  getClusterFromLeftDendrogram: () => getClusterFromLeftDendrogram,
+  getClusterFromTopDendrogram: () => getClusterFromTopDendrogram,
+  setClusteringBtn: () => setClusteringBtn,
+  showTable4selectedRows: () => showTable4selectedRows,
+  showTable4selectedSamples: () => showTable4selectedSamples,
+  triggerZoomBranch: () => triggerZoomBranch
+});
+function getAllChildrenClusterIds(clickedClusterId, left) {
+  const mergedClusters = left ? this.hierClusterData.clustering.row.mergedClusters : this.hierClusterData.clustering.col.mergedClusters;
+  const children = mergedClusters.get(clickedClusterId).childrenClusters || [];
+  let allChildren = [...children];
+  for (const child of children) {
+    allChildren = allChildren.concat(this.getAllChildrenClusterIds(child, left));
+  }
+  return allChildren;
+}
+function addSelectedSamplesOptions(clickedSampleNames, event) {
+  const l = this.settings.matrix.controlLabels;
+  const ss = this.opts.allow2selectSamples;
+  const optionArr = [
+    {
+      label: "Zoom in",
+      callback: () => {
+        this.triggerZoomBranch(this, clickedSampleNames);
+      }
+    },
+    {
+      label: `List ${clickedSampleNames.length} ${l.samples}`,
+      callback: () => this.showTable4selectedSamples(clickedSampleNames)
+    }
+  ];
+  if (ss) {
+    optionArr.push({
+      label: ss.buttonText || `Select ${l.samples}`,
+      callback: async () => {
+        const samples = clickedSampleNames.map((c) => this.data.samples[c]);
+        ss.callback({
+          samples: await this.app.vocabApi.convertSampleId(samples, ss.attributes),
+          source: ss.defaultSelectionLabel || `Selected ${l.samples} from gene expression`
+        });
+      }
+    });
+  } else {
+    if (this.state.nav && this.state.nav.header_mode !== "hidden") {
+      const samples = clickedSampleNames.map((c) => this.sampleOrder.find((s) => s.row.sample == c).row);
+      for (const s of samples) {
+        if (!s.sampleId) s.sampleId = s.sample;
+      }
+      optionArr.push({
+        label: "Add to a group",
+        callback: async () => {
+          const group = {
+            name: "Group",
+            items: samples
+          };
+          this.addGroup(group);
+        }
+      });
+    }
+  }
+  this.mouseout();
+  this.dom.tip.hide();
+  this.dom.dendroClickMenu.d.selectAll("*").remove();
+  this.dom.dendroClickMenu.d.selectAll("div").data(optionArr).enter().append("div").attr("class", "sja_menuoption").style("border-radius", "0px").html((d) => d.label).attr("data-testid", (d) => `hierCluster_dendro_menu_${d.label.split(" ")[0]}`).on("click", (event2) => {
+    this.dom.dendroClickMenu.d.selectAll("*").remove();
+    event2.target.__data__.callback();
+  });
+  this.dom.dendroClickMenu.show(event.clientX, event.clientY);
+}
+function addSelectedRowsOptions(clickedRowNames, event) {
+  const rowType = this.config.dataType == "geneExpression" ? "genes" : this.config.dataType == "metaboliteIntensity" ? "metabolites" : this.config.dataType == "proteomeAbundance" ? "proteins" : "items";
+  const optionArr = [
+    {
+      label: `List ${clickedRowNames.length} ${rowType}`,
+      callback: () => this.showTable4selectedRows(clickedRowNames, rowType)
+    }
+  ];
+  if (this.config.dataType == "geneExpression" && this.app.opts.genome.termdbs) {
+    const minGeneCutoff = this.app.opts.genome.termdbs.msigdb.geneORAparam.minCutoff;
+    const maxGeneCutoff = this.app.opts.genome.termdbs.msigdb.geneORAparam.maxCutoff;
+    optionArr.push({
+      label: `Gene set overrepresentation analysis`,
+      disabled: clickedRowNames.length < minGeneCutoff || clickedRowNames.length > maxGeneCutoff,
+      callback: () => {
+        if (clickedRowNames.length < minGeneCutoff || clickedRowNames.length > maxGeneCutoff) return;
+        this.dom.dendroClickMenu.d.selectAll("*").remove();
+        const lst = [];
+        for (const x of clickedRowNames) {
+          const j = this.terms?.find?.((t) => t.tw.$id == x);
+          if (j) {
+            const n = j.tw?.term?.gene;
+            if (n) lst.push(n);
+          }
+        }
+        const config = {
+          chartType: "geneORA",
+          geneORAparams: {
+            sample_genes: lst.join(","),
+            genome: this.app.vocabApi.opts.state.vocab.genome
+          }
+        };
+        this.app.dispatch({
+          type: "plot_create",
+          config
+        });
+      }
+    });
+  }
+  this.mouseout();
+  this.dom.tip.hide();
+  this.dom.dendroClickMenu.d.selectAll("*").remove();
+  this.dom.dendroClickMenu.d.selectAll("div").data(optionArr).enter().append("div").attr("class", (d) => d.disabled ? "sja_menuoption_not_interactive" : "sja_menuoption").style("opacity", (d) => d.disabled ? 0.5 : 1).style("border-radius", "0px").html(
+    (d) => d.disabled ? `${d.label} <span style="font-size: 0.6em; display: block; margin-left: 2px; margin-top: 2px;">Only available when 15 - 500 genes selected</span>` : d.label
+  ).attr("data-testid", (d) => `hierCluster_dendro_menu_${d.label.split(" ")[0]}`).on("click", (event2) => {
+    if (event2.target.__data__?.callback) event2.target.__data__.callback();
+  });
+  this.dom.dendroClickMenu.show(event.clientX, event.clientY);
+}
+function triggerZoomBranch(self, clickedSampleNames) {
+  if (self.zoomArea) {
+    self.zoomArea.remove();
+    delete self.zoomArea;
+  }
+  const c = {
+    startCell: self.serieses[0].cells.find((d2) => d2.sample == clickedSampleNames[0]),
+    endCell: self.serieses[0].cells.find((d2) => d2.sample == clickedSampleNames[clickedSampleNames.length - 1])
+  };
+  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];
+  const colw = self.computedSettings.colw || self.settings.matrix.colw;
+  const maxZoomLevel = s.colwMax / colw;
+  const minZoomLevel = s.colwMin / colw;
+  const tentativeZoomLevel = Math.max(
+    1,
+    s.zoomLevel * d.mainw / Math.max(c.endCell.x - c.startCell.x, 2 * d.colw) * 0.7
+  );
+  const zoomLevel = Math.max(minZoomLevel, Math.min(tentativeZoomLevel, maxZoomLevel));
+  self.app.dispatch({
+    type: "plot_edit",
+    id: self.id,
+    config: {
+      settings: {
+        matrix: {
+          zoomLevel,
+          zoomCenterPct: 0.5,
+          //zoomLevel < 1 && d.mainw >= d.zoomedMainW ? 0.5 : zoomCenter / d.mainw,
+          zoomIndex,
+          zoomGrpIndex: centerCell.grpIndex
+        }
+      }
+    }
+  });
+  self.resetInteractions();
+}
+function showTable4selectedSamples(clickedSampleNames) {
+  const templates = this.state.termdbConfig.urlTemplates;
+  const rows = templates?.sample ? clickedSampleNames.map((c) => [
+    { value: this.hierClusterData.bySampleId[c].label, url: `${templates.sample.base}${c}` }
+  ]) : clickedSampleNames.map((c) => [{ value: this.hierClusterData.bySampleId[c].label }]);
+  const columns = [{ label: this.settings.matrix.controlLabels.Sample }];
+  renderTable({
+    rows,
+    columns,
+    div: this.dom.dendroClickMenu.clear().d.append("div").style("margin", "10px"),
+    showLines: true,
+    maxHeight: "35vh",
+    resize: true
+  });
+}
+function showTable4selectedRows(clickedRowNames, rowType) {
+  const templates = this.state.termdbConfig.urlTemplates;
+  const rows = [];
+  if (templates?.gene && this.config.dataType == "geneExpression" && this.hierClusterData.byTermId) {
+    for (const i of clickedRowNames) {
+      const genesymbol = this.terms.find((t) => t.tw?.$id == i)?.tw?.term?.gene;
+      if (!genesymbol) continue;
+      const gencode = this.hierClusterData.byTermId[i]?.gencodeId;
+      if (gencode) {
+        rows.push([{ value: genesymbol, url: `${templates.gene.base}${gencode}` }]);
+      } else {
+        rows.push([{ value: genesymbol }]);
+      }
+    }
+  } else {
+    for (const i of clickedRowNames) {
+      const tw = this.terms.find((t) => t.tw?.$id == i)?.tw;
+      if (!tw) continue;
+      const n = tw.term?.gene || tw.term?.name;
+      if (!n) continue;
+      rows.push([{ value: n }]);
+    }
+  }
+  const div = this.dom.dendroClickMenu.clear().d.append("div").style("margin", "10px");
+  const buttonDiv = div.append("div").style("padding", "5px");
+  const copyButton = buttonDiv.append("button").html(`Copy ${rowType}`).attr("class", ".sja_menu_div button").style("margin-top", "2px").style("padding", "5px").on("click", () => {
+    const geneNames = rows.map((row) => row[0].value).join("\n");
+    navigator.clipboard.writeText(geneNames).then(() => {
+    }, console.warn);
+    copyButton.html(`Copy ${rowType}&nbsp;&check;`);
+  });
+  renderTable({
+    rows,
+    columns: [{ label: rowType }],
+    div: div.append("div"),
+    showLines: true,
+    maxHeight: "35vh",
+    resize: true
+  });
+}
+function getClusterFromTopDendrogram(event) {
+  if (event.target.tagName == "image") this.imgBox = event.target.getBoundingClientRect();
+  else return;
+  const y = event.clientY - this.imgBox.y - event.target.clientTop;
+  const xMin = this.dimensions.xMin;
+  const x = event.clientX - this.imgBox.x - event.target.clientLeft + xMin;
+  for (const [clusterId, cluster] of this.hierClusterData.clustering.col.mergedClusters) {
+    const { x1, y1, x2, y2, clusterY } = cluster.clusterPosition;
+    if (x1 <= x && x <= x2 && clusterY - 5 < y && y < clusterY + 5 || clusterY <= y && y <= y1 && x1 - 5 < x && x < x1 + 5 || clusterY <= y && y <= y2 && x2 - 5 < x && x < x2 + 5) {
+      return clusterId;
+    }
+  }
+}
+function getClusterFromLeftDendrogram(event) {
+  if (event.target.tagName == "image") this.imgBox = event.target.getBoundingClientRect();
+  else return;
+  const y = event.clientY - this.imgBox.y - event.target.clientTop;
+  const xMin = this.dimensions.xMin;
+  const x = event.clientX - this.imgBox.x - event.target.clientLeft + xMin;
+  for (const [clusterId, cluster] of this.hierClusterData.clustering.row.mergedClusters) {
+    const { x1, y1, x2, y2, clusterX } = cluster.clusterPosition;
+    if (y1 <= y && y <= y2 && clusterX - 5 < x && x < clusterX + 5 || clusterX <= x && x <= x1 && y1 - 5 < y && y < y1 + 5 || clusterX <= x && x <= x2 && y2 - 5 < y && y < y2 + 5) {
+      return clusterId;
+    }
+  }
+}
+function setClusteringBtn(holder, callback) {
+  const cl = this.config.settings.matrix.controlLabels;
+  const dataType = this.config.dataType;
+  const clusterRowLabel = dataType == "geneExpression" ? "Genes" : dataType == "metaboliteIntensity" ? "Metabolites" : dataType == "proteomeAbundance" ? "Proteins" : dataType == "numericDictTerm" ? "Variables" : "Rows";
+  const cluteringButtonLabel = dataType == "geneExpression" ? "Gene Expression Clustering" : dataType == "metaboliteIntensity" ? "Metabolite Intensity Clustering" : dataType == "proteomeAbundance" ? "Protein Abundance Clustering" : "Clustering";
+  holder.append("button").datum({
+    label: cluteringButtonLabel,
+    getCount: () => this.hcTermGroup?.lst.length || 0,
+    showCount: dataType == METABOLITE_INTENSITY || dataType == PROTEOME_ABUNDANCE || dataType == NUMERIC_DICTIONARY_TERM ? "append" : "hide",
+    rows: [
+      {
+        label: `Cluster ${cl.Samples}`,
+        title: `Option to enable ${cl.samples} clustering, instead of enabling ${cl.samples} sorting.`,
+        type: "checkbox",
+        chartType: "hierCluster",
+        settingsKey: "clusterSamples",
+        boxLabel: `Cluster ${cl.Samples} (Disable ${cl.Samples} Sorting)`,
+        callback: (checked) => {
+          if (!checked) {
+            this.config.settings.hierCluster.yDendrogramHeight = 0;
+            this.config.settings.hierCluster.clusterSamples = false;
+          } else {
+            this.config.divideBy = null;
+            this.config.settings.hierCluster.yDendrogramHeight = 200;
+            this.config.settings.hierCluster.clusterSamples = true;
+          }
+          this.app.dispatch({
+            type: "plot_edit",
+            id: this.id,
+            config: this.config
+          });
+        }
+      },
+      {
+        label: `Cluster ${clusterRowLabel}`,
+        title: `Option to enable ${clusterRowLabel} clustering, instead of enabling ${clusterRowLabel} sorting.`,
+        type: "checkbox",
+        chartType: "hierCluster",
+        settingsKey: "clusterRows",
+        boxLabel: `Cluster ${clusterRowLabel} (Disable ${clusterRowLabel} Sorting)`,
+        callback: (checked) => {
+          if (!checked) {
+            this.config.settings.hierCluster.clusterRows = false;
+            this.config.settings.hierCluster.sortClusterRows = "asListed";
+          } else {
+            this.config.settings.hierCluster.clusterRows = true;
+            this.config.settings.hierCluster.sortClusterRows = void 0;
+          }
+          this.app.dispatch({
+            type: "plot_edit",
+            id: this.id,
+            config: this.config
+          });
+        }
+      },
+      {
+        label: `Sort ${clusterRowLabel}`,
+        title: `Set how to order the ${clusterRowLabel} as rows`,
+        type: "radio",
+        chartType: "hierCluster",
+        settingsKey: "sortClusterRows",
+        options: [
+          { label: `By input ${clusterRowLabel} order`, value: "asListed" },
+          { label: `By ${clusterRowLabel} name`, value: "byName" }
+        ],
+        styles: { padding: 0, "padding-right": "10px", margin: 0, display: "inline-block" },
+        getDisplayStyle(plot) {
+          return plot.settings.hierCluster.clusterRows ? "none" : "table-row";
+        }
+      },
+      {
+        label: "Z-score Transformation",
+        title: `Option to do Z-score transformation`,
+        type: "checkbox",
+        chartType: "hierCluster",
+        settingsKey: "zScoreTransformation",
+        boxLabel: `Perform Z-score Transformation`,
+        callback: (checked) => {
+          if (!checked) {
+            this.config.settings.hierCluster.zScoreTransformation = false;
+            this.config.settings.hierCluster.colorScale = "whiteRed";
+          } else {
+            this.config.settings.hierCluster.zScoreTransformation = true;
+            this.config.settings.hierCluster.colorScale = "blueWhiteRed";
+          }
+          this.app.dispatch({
+            type: "plot_edit",
+            id: this.id,
+            config: this.config
+          });
+        }
+      },
+      {
+        label: `Clustering Method`,
+        title: `Sets which clustering method to use`,
+        type: "radio",
+        chartType: "hierCluster",
+        settingsKey: "clusterMethod",
+        options: clusterMethodLst
+      },
+      {
+        label: `Distance Method`,
+        title: `Sets which distance method to use for clustering`,
+        type: "radio",
+        chartType: "hierCluster",
+        settingsKey: "distanceMethod",
+        options: distanceMethodLst
+      },
+      {
+        label: `Column Dendrogram Height`,
+        title: `The maximum height to render the column dendrogram`,
+        type: "number",
+        chartType: "hierCluster",
+        settingsKey: "yDendrogramHeight",
+        getDisplayStyle(plot) {
+          return plot.settings.hierCluster.clusterSamples ? "table-row" : "none";
+        }
+      },
+      {
+        label: `Row Dendrogram Width`,
+        title: `The maximum width to render the row dendrogram`,
+        type: "number",
+        chartType: "hierCluster",
+        settingsKey: "xDendrogramHeight",
+        getDisplayStyle(plot) {
+          return plot.settings.hierCluster.clusterRows ? "table-row" : "none";
+        }
+      },
+      {
+        label: `Z-score Cap`,
+        title: `Cap the Z-score scale to not exceed this absolute value`,
+        type: "number",
+        chartType: "hierCluster",
+        settingsKey: "zScoreCap"
+      },
+      {
+        label: `Color Scheme`,
+        title: `Sets which color scheme to use`,
+        type: "radio",
+        chartType: "hierCluster",
+        settingsKey: "colorScale",
+        options: [
+          {
+            label: "Blue-White-Red",
+            value: "blueWhiteRed",
+            title: `color scheme Blue-White-Red`
+          },
+          {
+            label: "Green-Black-Red",
+            value: "greenBlackRed",
+            title: `color scheme Green-Black-Red`
+          },
+          {
+            label: "Blue-Yellow-Red",
+            value: "blueYellowRed",
+            title: `color scheme Blue-Yellow-Red`
+          },
+          {
+            label: "Green-White-Red",
+            value: "greenWhiteRed",
+            title: `color scheme Green-White-Red`
+          },
+          {
+            label: "Blue-Black-Yellow",
+            value: "blueBlackYellow",
+            title: `color scheme Blue-Black-Yellow`
+          }
+        ]
+      }
+    ],
+    customInputs: updateClusteringControls
+  }).html((d) => d.label).style("margin", "2px 0").on("click", callback);
+}
+function updateClusteringControls(self, app, parent, table) {
+  if (parent.chartType == "hierCluster" && !parent.config.settings.hierCluster.zScoreTransformation) {
+    const zScoreCapControl = select_default(
+      table.selectAll("td").filter(function() {
+        return select_default(this).text() == "Z-score Cap";
+      }).node().closest("tr")
+    );
+    zScoreCapControl.style("display", "none");
+    const colorSchemeControl = select_default(
+      table.selectAll("td").filter(function() {
+        return select_default(this).text() == "Color Scheme";
+      }).node().closest("tr")
+    );
+    colorSchemeControl.style("display", "none");
+  }
+  if (parent.chartType == "hierCluster" && (parent.config.dataType == METABOLITE_INTENSITY || parent.config.dataType == PROTEOME_ABUNDANCE || parent.config.dataType == NUMERIC_DICTIONARY_TERM)) {
+    const geneInputTr = table.insert("tr", () => table.select("tr").node());
+    geneInputTr.append("td").attr("class", "sja-termdb-config-row-label").html("Hierarchical Clustering Term Set");
+    const td1 = geneInputTr.append("td").style("display", "block").style("padding", "5px 0px");
+    const editGrpDiv = td1.append("div").append("label");
+    const clusteringBtn = self.btns.node();
+    editGrpDiv.append("button").html("Edit Set").on("click", () => {
+      app.tip.clear();
+      const backDiv = app.tip.d.append("div").style("padding", "5px");
+      backDiv.attr("tabindex", 0).style("padding", "5px").style("text-decoration", "underline").style("cursor", "pointer").style("margin-bottom", "12px").html(`&#171; Back`).on("click", () => clusteringBtn.click()).on("keyup", (event) => {
+        if (event.key == "Enter") event.target.click();
+      });
+      const setEdiUiHolder = app.tip.d.append("div");
+      parent.showDictTermSelection(setEdiUiHolder);
+    });
+  }
+}
+
+export {
+  getAllChildrenClusterIds,
+  addSelectedSamplesOptions,
+  addSelectedRowsOptions,
+  triggerZoomBranch,
+  showTable4selectedSamples,
+  showTable4selectedRows,
+  getClusterFromTopDendrogram,
+  getClusterFromLeftDendrogram,
+  setClusteringBtn,
+  hierCluster_interactivity_exports
+};
+//# sourceMappingURL=chunk-HTMXVOTH.js.map

package/dist/chunk-HTMXVOTH.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/matrix/hierCluster.interactivity.js"],
+  "sourcesContent": ["import { renderTable } from '#dom'\nimport { clusterMethodLst, distanceMethodLst } from '#shared/clustering.js'\nimport { select } from 'd3-selection'\nimport { METABOLITE_INTENSITY, PROTEOME_ABUNDANCE, NUMERIC_DICTIONARY_TERM } from '#shared/terms.js'\n\n// Given a clusterId, return all its children clusterIds\nexport function getAllChildrenClusterIds(clickedClusterId, left) {\n\tconst mergedClusters = left\n\t\t? this.hierClusterData.clustering.row.mergedClusters\n\t\t: this.hierClusterData.clustering.col.mergedClusters\n\tconst children = mergedClusters.get(clickedClusterId).childrenClusters || []\n\tlet allChildren = [...children]\n\tfor (const child of children) {\n\t\tallChildren = allChildren.concat(this.getAllChildrenClusterIds(child, left))\n\t}\n\treturn allChildren\n}\n\nexport function addSelectedSamplesOptions(clickedSampleNames, event) {\n\tconst l = this.settings.matrix.controlLabels\n\tconst ss = this.opts.allow2selectSamples\n\tconst optionArr = [\n\t\t{\n\t\t\tlabel: 'Zoom in',\n\t\t\tcallback: () => {\n\t\t\t\tthis.triggerZoomBranch(this, clickedSampleNames)\n\t\t\t}\n\t\t},\n\t\t{\n\t\t\tlabel: `List ${clickedSampleNames.length} ${l.samples}`,\n\t\t\tcallback: () => this.showTable4selectedSamples(clickedSampleNames)\n\t\t}\n\t]\n\n\t// when allow2selectSamples presents\n\tif (ss) {\n\t\toptionArr.push({\n\t\t\tlabel: ss.buttonText || `Select ${l.samples}`,\n\t\t\tcallback: async () => {\n\t\t\t\t// convert ids of selected samples based on\n\t\t\t\t// attributes defined in allow2selectSamples\n\t\t\t\tconst samples = clickedSampleNames.map(c => this.data.samples[c])\n\t\t\t\tss.callback({\n\t\t\t\t\tsamples: await this.app.vocabApi.convertSampleId(samples, ss.attributes),\n\t\t\t\t\tsource: ss.defaultSelectionLabel || `Selected ${l.samples} from gene expression`\n\t\t\t\t})\n\t\t\t}\n\t\t})\n\t} else {\n\t\tif (this.state.nav && this.state.nav.header_mode !== 'hidden') {\n\t\t\tconst samples = clickedSampleNames.map(c => this.sampleOrder.find(s => s.row.sample == c).row)\n\t\t\tfor (const s of samples) {\n\t\t\t\tif (!s.sampleId) s.sampleId = s.sample\n\t\t\t}\n\t\t\toptionArr.push({\n\t\t\t\tlabel: 'Add to a group',\n\t\t\t\tcallback: async () => {\n\t\t\t\t\tconst group = {\n\t\t\t\t\t\tname: 'Group',\n\t\t\t\t\t\titems: samples\n\t\t\t\t\t}\n\t\t\t\t\tthis.addGroup(group)\n\t\t\t\t}\n\t\t\t})\n\t\t}\n\t}\n\n\tthis.mouseout()\n\tthis.dom.tip.hide()\n\tthis.dom.dendroClickMenu.d.selectAll('*').remove()\n\tthis.dom.dendroClickMenu.d\n\t\t.selectAll('div')\n\t\t.data(optionArr)\n\t\t.enter()\n\t\t.append('div')\n\t\t.attr('class', 'sja_menuoption')\n\t\t.style('border-radius', '0px')\n\t\t.html(d => d.label)\n\t\t.attr('data-testid', d => `hierCluster_dendro_menu_${d.label.split(' ')[0]}`)\n\t\t.on('click', event => {\n\t\t\tthis.dom.dendroClickMenu.d.selectAll('*').remove()\n\t\t\tevent.target.__data__.callback()\n\t\t})\n\tthis.dom.dendroClickMenu.show(event.clientX, event.clientY)\n}\n\nexport function addSelectedRowsOptions(clickedRowNames, event) {\n\t// TODO to support other hierCluster types\n\tconst rowType =\n\t\tthis.config.dataType == 'geneExpression'\n\t\t\t? 'genes'\n\t\t\t: this.config.dataType == 'metaboliteIntensity'\n\t\t\t? 'metabolites'\n\t\t\t: this.config.dataType == 'proteomeAbundance'\n\t\t\t? 'proteins'\n\t\t\t: 'items'\n\n\tconst optionArr = [\n\t\t{\n\t\t\tlabel: `List ${clickedRowNames.length} ${rowType}`,\n\t\t\tcallback: () => this.showTable4selectedRows(clickedRowNames, rowType)\n\t\t}\n\t]\n\n\tif (this.config.dataType == 'geneExpression' && this.app.opts.genome.termdbs) {\n\t\t// when doing gene exp clustering and has genome-level geneset db, enable option for gene ORA analysis\n\t\t// gene ORA cutoffs queried from genome file\n\t\tconst minGeneCutoff = this.app.opts.genome.termdbs.msigdb.geneORAparam.minCutoff\n\t\tconst maxGeneCutoff = this.app.opts.genome.termdbs.msigdb.geneORAparam.maxCutoff\n\t\toptionArr.push({\n\t\t\tlabel: `Gene set overrepresentation analysis`,\n\t\t\tdisabled: clickedRowNames.length < minGeneCutoff || clickedRowNames.length > maxGeneCutoff,\n\t\t\tcallback: () => {\n\t\t\t\tif (clickedRowNames.length < minGeneCutoff || clickedRowNames.length > maxGeneCutoff) return\n\t\t\t\tthis.dom.dendroClickMenu.d.selectAll('*').remove()\n\t\t\t\tconst lst = []\n\t\t\t\tfor (const x of clickedRowNames) {\n\t\t\t\t\tconst j = this.terms?.find?.(t => t.tw.$id == x)\n\t\t\t\t\tif (j) {\n\t\t\t\t\t\tconst n = j.tw?.term?.gene\n\t\t\t\t\t\tif (n) lst.push(n)\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tconst config = {\n\t\t\t\t\tchartType: 'geneORA',\n\t\t\t\t\tgeneORAparams: {\n\t\t\t\t\t\tsample_genes: lst.join(','),\n\t\t\t\t\t\tgenome: this.app.vocabApi.opts.state.vocab.genome\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tthis.app.dispatch({\n\t\t\t\t\ttype: 'plot_create',\n\t\t\t\t\tconfig\n\t\t\t\t})\n\t\t\t}\n\t\t})\n\t}\n\n\tthis.mouseout()\n\tthis.dom.tip.hide()\n\tthis.dom.dendroClickMenu.d.selectAll('*').remove()\n\tthis.dom.dendroClickMenu.d\n\t\t.selectAll('div')\n\t\t.data(optionArr)\n\t\t.enter()\n\t\t.append('div')\n\t\t.attr('class', d => (d.disabled ? 'sja_menuoption_not_interactive' : 'sja_menuoption'))\n\t\t.style('opacity', d => (d.disabled ? 0.5 : 1))\n\t\t.style('border-radius', '0px')\n\t\t.html(d =>\n\t\t\td.disabled\n\t\t\t\t? `${d.label} <span style=\"font-size: 0.6em; display: block; margin-left: 2px; margin-top: 2px;\">Only available when 15 - 500 genes selected</span>`\n\t\t\t\t: d.label\n\t\t)\n\t\t.attr('data-testid', d => `hierCluster_dendro_menu_${d.label.split(' ')[0]}`)\n\t\t.on('click', event => {\n\t\t\tif (event.target.__data__?.callback) event.target.__data__.callback()\n\t\t})\n\tthis.dom.dendroClickMenu.show(event.clientX, event.clientY)\n}\n\n// zoom in matrix to the selected dendrogram branch\nexport function triggerZoomBranch(self, clickedSampleNames) {\n\tif (self.zoomArea) {\n\t\tself.zoomArea.remove()\n\t\tdelete self.zoomArea\n\t}\n\tconst c = {\n\t\tstartCell: self.serieses[0].cells.find(d => d.sample == clickedSampleNames[0]),\n\t\tendCell: self.serieses[0].cells.find(d => d.sample == clickedSampleNames[clickedSampleNames.length - 1])\n\t}\n\n\tconst s = self.settings.matrix\n\tconst d = self.dimensions\n\tconst start = c.startCell.totalIndex < c.endCell.totalIndex ? c.startCell : c.endCell\n\tconst zoomIndex = Math.floor(start.totalIndex + Math.abs(c.endCell.totalIndex - c.startCell.totalIndex) / 2)\n\tconst centerCell = self.sampleOrder[zoomIndex] // || self.getImgCell(event)\n\tconst colw = self.computedSettings.colw || self.settings.matrix.colw\n\tconst maxZoomLevel = s.colwMax / colw\n\tconst minZoomLevel = s.colwMin / colw\n\tconst tentativeZoomLevel = Math.max(\n\t\t1,\n\t\t((s.zoomLevel * d.mainw) / Math.max(c.endCell.x - c.startCell.x, 2 * d.colw)) * 0.7\n\t)\n\tconst zoomLevel = Math.max(minZoomLevel, Math.min(tentativeZoomLevel, maxZoomLevel))\n\t//const zoomCenter = centerCell.totalIndex * d.dx + (centerCell.grpIndex - 1) * s.colgspace + d.seriesXoffset\n\n\tself.app.dispatch({\n\t\ttype: 'plot_edit',\n\t\tid: self.id,\n\t\tconfig: {\n\t\t\tsettings: {\n\t\t\t\tmatrix: {\n\t\t\t\t\tzoomLevel,\n\t\t\t\t\tzoomCenterPct: 0.5,\n\t\t\t\t\t//zoomLevel < 1 && d.mainw >= d.zoomedMainW ? 0.5 : zoomCenter / d.mainw,\n\t\t\t\t\tzoomIndex,\n\t\t\t\t\tzoomGrpIndex: centerCell.grpIndex\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t})\n\tself.resetInteractions()\n}\n\n// show the list of clicked samples as a table\nexport function showTable4selectedSamples(clickedSampleNames) {\n\tconst templates = this.state.termdbConfig.urlTemplates\n\tconst rows = templates?.sample\n\t\t? clickedSampleNames.map(c => [\n\t\t\t\t{ value: this.hierClusterData.bySampleId[c].label, url: `${templates.sample.base}${c}` }\n\t\t  ])\n\t\t: clickedSampleNames.map(c => [{ value: this.hierClusterData.bySampleId[c].label }])\n\n\tconst columns = [{ label: this.settings.matrix.controlLabels.Sample }]\n\n\trenderTable({\n\t\trows,\n\t\tcolumns,\n\t\tdiv: this.dom.dendroClickMenu.clear().d.append('div').style('margin', '10px'),\n\t\tshowLines: true,\n\t\tmaxHeight: '35vh',\n\t\tresize: true\n\t})\n}\n\n// show the list of clicked samples as a table\nexport function showTable4selectedRows(clickedRowNames, rowType) {\n\t// clickedRowNames is array of tw.$id\n\tconst templates = this.state.termdbConfig.urlTemplates\n\n\tconst rows = []\n\tif (templates?.gene && this.config.dataType == 'geneExpression' && this.hierClusterData.byTermId) {\n\t\t// show gene names with templated url\n\t\tfor (const i of clickedRowNames) {\n\t\t\tconst genesymbol = this.terms.find(t => t.tw?.$id == i)?.tw?.term?.gene\n\t\t\tif (!genesymbol) continue\n\t\t\t// FIXME hardcoded to assume gencode\n\t\t\tconst gencode = this.hierClusterData.byTermId[i]?.gencodeId\n\t\t\tif (gencode) {\n\t\t\t\trows.push([{ value: genesymbol, url: `${templates.gene.base}${gencode}` }])\n\t\t\t} else {\n\t\t\t\trows.push([{ value: genesymbol }])\n\t\t\t}\n\t\t}\n\t} else {\n\t\tfor (const i of clickedRowNames) {\n\t\t\tconst tw = this.terms.find(t => t.tw?.$id == i)?.tw\n\t\t\tif (!tw) continue\n\t\t\t// item name can be either gene or not gene (will use term.name)\n\t\t\tconst n = tw.term?.gene || tw.term?.name\n\t\t\tif (!n) continue\n\t\t\trows.push([{ value: n }])\n\t\t}\n\t}\n\n\tconst div = this.dom.dendroClickMenu.clear().d.append('div').style('margin', '10px')\n\n\t// Create a button to copy names in the table\n\tconst buttonDiv = div.append('div').style('padding', '5px')\n\tconst copyButton = buttonDiv\n\t\t.append('button')\n\t\t.html(`Copy ${rowType}`)\n\t\t.attr('class', '.sja_menu_div button')\n\t\t.style('margin-top', '2px')\n\t\t.style('padding', '5px')\n\t\t.on('click', () => {\n\t\t\tconst geneNames = rows.map(row => row[0].value).join('\\n')\n\t\t\tnavigator.clipboard.writeText(geneNames).then(() => {}, console.warn)\n\t\t\tcopyButton.html(`Copy ${rowType}&nbsp;&check;`)\n\t\t})\n\trenderTable({\n\t\trows,\n\t\tcolumns: [{ label: rowType }],\n\t\tdiv: div.append('div'),\n\t\tshowLines: true,\n\t\tmaxHeight: '35vh',\n\t\tresize: true\n\t})\n}\n\n// upon clicking, find the corresponding clicked clusterId from this.hierClusterData.clustering.col.mergedClusters\nexport function getClusterFromTopDendrogram(event) {\n\t// Need imgBox to find the position of event relative to dendrogram\n\tif (event.target.tagName == 'image') this.imgBox = event.target.getBoundingClientRect()\n\telse return\n\n\tconst y = event.clientY - this.imgBox.y - event.target.clientTop\n\tconst xMin = this.dimensions.xMin\n\tconst x = event.clientX - this.imgBox.x - event.target.clientLeft + xMin\n\n\tfor (const [clusterId, cluster] of this.hierClusterData.clustering.col.mergedClusters) {\n\t\tconst { x1, y1, x2, y2, clusterY } = cluster.clusterPosition\n\t\tif (\n\t\t\t(x1 <= x && x <= x2 && clusterY - 5 < y && y < clusterY + 5) ||\n\t\t\t(clusterY <= y && y <= y1 && x1 - 5 < x && x < x1 + 5) ||\n\t\t\t(clusterY <= y && y <= y2 && x2 - 5 < x && x < x2 + 5)\n\t\t) {\n\t\t\treturn clusterId\n\t\t}\n\t}\n}\n\n// upon clicking, find the corresponding clicked clusterId from this.hierClusterData.clustering.row.mergedClusters\nexport function getClusterFromLeftDendrogram(event) {\n\t// Need imgBox to find the position of event relative to dendrogram\n\tif (event.target.tagName == 'image') this.imgBox = event.target.getBoundingClientRect()\n\telse return\n\n\tconst y = event.clientY - this.imgBox.y - event.target.clientTop\n\tconst xMin = this.dimensions.xMin\n\tconst x = event.clientX - this.imgBox.x - event.target.clientLeft + xMin\n\n\tfor (const [clusterId, cluster] of this.hierClusterData.clustering.row.mergedClusters) {\n\t\tconst { x1, y1, x2, y2, clusterX } = cluster.clusterPosition\n\t\tif (\n\t\t\t(y1 <= y && y <= y2 && clusterX - 5 < x && x < clusterX + 5) ||\n\t\t\t(clusterX <= x && x <= x1 && y1 - 5 < y && y < y1 + 5) ||\n\t\t\t(clusterX <= x && x <= x2 && y2 - 5 < y && y < y2 + 5)\n\t\t) {\n\t\t\treturn clusterId\n\t\t}\n\t}\n}\n\nexport function setClusteringBtn(holder, callback) {\n\tconst cl = this.config.settings.matrix.controlLabels\n\tconst dataType = this.config.dataType\n\tconst clusterRowLabel =\n\t\tdataType == 'geneExpression'\n\t\t\t? 'Genes'\n\t\t\t: dataType == 'metaboliteIntensity'\n\t\t\t? 'Metabolites'\n\t\t\t: dataType == 'proteomeAbundance'\n\t\t\t? 'Proteins'\n\t\t\t: dataType == 'numericDictTerm'\n\t\t\t? 'Variables'\n\t\t\t: 'Rows'\n\tconst cluteringButtonLabel =\n\t\tdataType == 'geneExpression'\n\t\t\t? 'Gene Expression Clustering'\n\t\t\t: dataType == 'metaboliteIntensity'\n\t\t\t? 'Metabolite Intensity Clustering'\n\t\t\t: dataType == 'proteomeAbundance'\n\t\t\t? 'Protein Abundance Clustering'\n\t\t\t: 'Clustering'\n\tholder\n\t\t.append('button')\n\t\t//.property('disabled', d => d.disabled)\n\t\t.datum({\n\t\t\tlabel: cluteringButtonLabel,\n\t\t\tgetCount: () => this.hcTermGroup?.lst.length || 0,\n\t\t\tshowCount:\n\t\t\t\tdataType == METABOLITE_INTENSITY || dataType == PROTEOME_ABUNDANCE || dataType == NUMERIC_DICTIONARY_TERM\n\t\t\t\t\t? 'append'\n\t\t\t\t\t: 'hide',\n\t\t\trows: [\n\t\t\t\t{\n\t\t\t\t\tlabel: `Cluster ${cl.Samples}`,\n\t\t\t\t\ttitle: `Option to enable ${cl.samples} clustering, instead of enabling ${cl.samples} sorting.`,\n\t\t\t\t\ttype: 'checkbox',\n\t\t\t\t\tchartType: 'hierCluster',\n\t\t\t\t\tsettingsKey: 'clusterSamples',\n\t\t\t\t\tboxLabel: `Cluster ${cl.Samples} (Disable ${cl.Samples} Sorting)`,\n\t\t\t\t\tcallback: checked => {\n\t\t\t\t\t\tif (!checked) {\n\t\t\t\t\t\t\tthis.config.settings.hierCluster.yDendrogramHeight = 0\n\t\t\t\t\t\t\tthis.config.settings.hierCluster.clusterSamples = false\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\tthis.config.divideBy = null\n\t\t\t\t\t\t\tthis.config.settings.hierCluster.yDendrogramHeight = 200\n\t\t\t\t\t\t\tthis.config.settings.hierCluster.clusterSamples = true\n\t\t\t\t\t\t}\n\t\t\t\t\t\tthis.app.dispatch({\n\t\t\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\t\t\tid: this.id,\n\t\t\t\t\t\t\tconfig: this.config\n\t\t\t\t\t\t})\n\t\t\t\t\t}\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\tlabel: `Cluster ${clusterRowLabel}`,\n\t\t\t\t\ttitle: `Option to enable ${clusterRowLabel} clustering, instead of enabling ${clusterRowLabel} sorting.`,\n\t\t\t\t\ttype: 'checkbox',\n\t\t\t\t\tchartType: 'hierCluster',\n\t\t\t\t\tsettingsKey: 'clusterRows',\n\t\t\t\t\tboxLabel: `Cluster ${clusterRowLabel} (Disable ${clusterRowLabel} Sorting)`,\n\t\t\t\t\tcallback: checked => {\n\t\t\t\t\t\tif (!checked) {\n\t\t\t\t\t\t\tthis.config.settings.hierCluster.clusterRows = false\n\t\t\t\t\t\t\tthis.config.settings.hierCluster.sortClusterRows = 'asListed'\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\tthis.config.settings.hierCluster.clusterRows = true\n\t\t\t\t\t\t\tthis.config.settings.hierCluster.sortClusterRows = undefined\n\t\t\t\t\t\t}\n\t\t\t\t\t\tthis.app.dispatch({\n\t\t\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\t\t\tid: this.id,\n\t\t\t\t\t\t\tconfig: this.config\n\t\t\t\t\t\t})\n\t\t\t\t\t}\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\tlabel: `Sort ${clusterRowLabel}`,\n\t\t\t\t\ttitle: `Set how to order the ${clusterRowLabel} as rows`,\n\t\t\t\t\ttype: 'radio',\n\t\t\t\t\tchartType: 'hierCluster',\n\t\t\t\t\tsettingsKey: 'sortClusterRows',\n\t\t\t\t\toptions: [\n\t\t\t\t\t\t{ label: `By input ${clusterRowLabel} order`, value: 'asListed' },\n\t\t\t\t\t\t{ label: `By ${clusterRowLabel} name`, value: 'byName' }\n\t\t\t\t\t],\n\t\t\t\t\tstyles: { padding: 0, 'padding-right': '10px', margin: 0, display: 'inline-block' },\n\t\t\t\t\tgetDisplayStyle(plot) {\n\t\t\t\t\t\treturn plot.settings.hierCluster.clusterRows ? 'none' : 'table-row'\n\t\t\t\t\t}\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\tlabel: 'Z-score Transformation',\n\t\t\t\t\ttitle: `Option to do Z-score transformation`,\n\t\t\t\t\ttype: 'checkbox',\n\t\t\t\t\tchartType: 'hierCluster',\n\t\t\t\t\tsettingsKey: 'zScoreTransformation',\n\t\t\t\t\tboxLabel: `Perform Z-score Transformation`,\n\t\t\t\t\tcallback: checked => {\n\t\t\t\t\t\tif (!checked) {\n\t\t\t\t\t\t\tthis.config.settings.hierCluster.zScoreTransformation = false\n\t\t\t\t\t\t\tthis.config.settings.hierCluster.colorScale = 'whiteRed'\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\tthis.config.settings.hierCluster.zScoreTransformation = true\n\t\t\t\t\t\t\tthis.config.settings.hierCluster.colorScale = 'blueWhiteRed'\n\t\t\t\t\t\t}\n\t\t\t\t\t\tthis.app.dispatch({\n\t\t\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\t\t\tid: this.id,\n\t\t\t\t\t\t\tconfig: this.config\n\t\t\t\t\t\t})\n\t\t\t\t\t}\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\tlabel: `Clustering Method`,\n\t\t\t\t\ttitle: `Sets which clustering method to use`,\n\t\t\t\t\ttype: 'radio',\n\t\t\t\t\tchartType: 'hierCluster',\n\t\t\t\t\tsettingsKey: 'clusterMethod',\n\t\t\t\t\toptions: clusterMethodLst\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\tlabel: `Distance Method`,\n\t\t\t\t\ttitle: `Sets which distance method to use for clustering`,\n\t\t\t\t\ttype: 'radio',\n\t\t\t\t\tchartType: 'hierCluster',\n\t\t\t\t\tsettingsKey: 'distanceMethod',\n\t\t\t\t\toptions: distanceMethodLst\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\tlabel: `Column Dendrogram Height`,\n\t\t\t\t\ttitle: `The maximum height to render the column dendrogram`,\n\t\t\t\t\ttype: 'number',\n\t\t\t\t\tchartType: 'hierCluster',\n\t\t\t\t\tsettingsKey: 'yDendrogramHeight',\n\t\t\t\t\tgetDisplayStyle(plot) {\n\t\t\t\t\t\treturn plot.settings.hierCluster.clusterSamples ? 'table-row' : 'none'\n\t\t\t\t\t}\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\tlabel: `Row Dendrogram Width`,\n\t\t\t\t\ttitle: `The maximum width to render the row dendrogram`,\n\t\t\t\t\ttype: 'number',\n\t\t\t\t\tchartType: 'hierCluster',\n\t\t\t\t\tsettingsKey: 'xDendrogramHeight',\n\t\t\t\t\tgetDisplayStyle(plot) {\n\t\t\t\t\t\treturn plot.settings.hierCluster.clusterRows ? 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+  "names": ["event", "d"]
+}

package/dist/chunk-HUBO743S.js

@@ -0,0 +1,82 @@
+import {
+  Menu
+} from "./chunk-HYOEWQ5P.js";
+import {
+  select_default
+} from "./chunk-I6Y4O3RR.js";
+
+// plots/matrix/matrix.dom.js
+function setMatrixDom(opts) {
+  const holder = opts.controls ? opts.holder : opts.holder.append("div");
+  holder.style("position", "relative");
+  const controls = this.opts.controls || holder.append("div");
+  const errorDiv = holder.append("div");
+  const loadingDiv = holder.append("div").style("position", "relative").style("top", this.opts.controls ? 0 : "50px").style("left", "50px");
+  const errdiv = holder.append("div").attr("class", "sja_errorbar").style("display", "none");
+  const warningDiv = holder.append("div").attr("class", "sja_errorbar").style("display", "none");
+  const svg = holder.append("svg").attr("data-testid", "sjpp-matrix-svg").style("margin", "20px").style("overflow", "visible").on("mousemove.label", this.svgMousemove).on("mouseup.label", this.svgMouseup);
+  this.seriesClipId = `sjpp_clip_${this.id}`;
+  const mainG = svg.append("g").attr("class", "sjpp-matrix-maing").on("mouseover", this.showCellInfo).on("mousemove", this.showCellInfo).on("mouseout", this.mouseout);
+  const rectsG = mainG.append("g").attr("clip-path", `url(#${this.seriesClipId})`);
+  const sampleLabelsPG = mainG.append("g");
+  const termLabelsPG = mainG.append("g");
+  const tip = new Menu({ padding: "5px" });
+  this.dom = {
+    header: opts.header,
+    holder,
+    contentNode: opts.holder.node().closest(".sjpp-output-sandbox-content") || opts.holder.node().parentNode,
+    errdiv,
+    warningDiv,
+    controls,
+    errorDiv,
+    loadingDiv,
+    svg,
+    clipRect: svg.append("defs").append("clipPath").attr("id", this.seriesClipId).attr("clipPathUnits", "userSpaceOnUse").append("rect").attr("display", "block"),
+    mainG,
+    cluster: rectsG.append("g").attr("class", "sjpp-matrix-cluster-g").on("mousedown", this.seriesesGMousedown).on("mousemove", this.seriesesGMousemove),
+    //.on('mouseup', this.seriesesGMouseup),
+    seriesesG: rectsG.append("g").attr("class", "sjpp-matrix-serieses-g").attr("data-testid", "sjpp_matrix_mainG_serieses").on("mousedown", this.seriesesGMousedown),
+    //.on('mousemove', this.seriesesGMousemove)
+    //.on('mouseup', this.seriesesGMouseup),
+    highlightBeamG: rectsG.append("g").attr("class", "sjpp-matrix-highlight-beam"),
+    sampleLabelsPG,
+    sampleGrpLabelG: sampleLabelsPG.append("g").attr("class", "sjpp-matrix-series-group-label-g").on("click", this.showSampleGroupMenu).on("mousedown.sjppMatrixLabelText", this.enableTextHighlight).on("mouseup.sjppMatrixLabelText", this.disableTextHighlight),
+    sampleLabelG: sampleLabelsPG.append("g").attr("class", "sjpp-matrix-series-label-g").on("click", (event) => this.mouseclick(event)),
+    /* // TODO: sample label drag to move
+    	.on('mouseover', this.sampleLabelMouseover)
+    	.on('mouseout', this.sampleLabelMouseout)
+    	.on('mousedown', this.sampleLabelMousedown)
+    	.on('mousemove', this.sampleLabelMousemove)
+    	.on('mouseup', this.sampleLabelMouseup)*/
+    termLabelsPG,
+    termGrpLabelG: termLabelsPG.append("g").attr("class", "sjpp-matrix-term-group-label-g").on("mouseover", this.termGrpLabelMouseover).on("mouseout", this.termGrpLabelMouseout).on("mousedown", this.termGrpLabelMousedown).on("mousemove", this.termGrpLabelMousemove).on("mouseup", this.termGrpLabelMouseup).on("mousedown.sjppMatrixLabelText", this.enableTextHighlight).on("mouseup.sjppMatrixLabelText", this.disableTextHighlight),
+    termLabelG: termLabelsPG.append("g").attr("class", "sjpp-matrix-term-label-g").on("mouseover", this.termLabelMouseover).on("mouseout", this.termLabelMouseout).on("mousedown", this.termLabelMousedown).on("mousemove", this.termLabelMousemove).on("mouseup", this.termLabelMouseup).on("mousedown.sjppMatrixLabelText", this.enableTextHighlight).on("mouseup.sjppMatrixLabelText", this.disableTextHighlight),
+    scroll: mainG.append("g"),
+    //legendDiv: holder.append('div').style('margin', '5px 5px 15px 50px'),
+    legendG: mainG.append("g").attr("class", "sjpp-matrix-legend-g").on("mouseover", this.legendLabelMouseover).on("mouseout", this.legendLabelMouseout).on("mouseup", this.legendLabelMouseup),
+    // !!! Do NOT use self.dom.tip.clear(), since it will also get rid of menutop and menubody
+    tip,
+    menutop: tip.d.append("div"),
+    menubody: tip.d.append("div"),
+    clickMenu: new Menu({ padding: "0px" }),
+    brushMenu: new Menu({ padding: "0px" }),
+    dendroClickMenu: new Menu({ padding: "0px" }),
+    legendMenu: new Menu({ padding: "0px" }),
+    matrixCellHoverOver: new Menu({ padding: "0px" })
+  };
+  this.dom.colBeam = this.dom.highlightBeamG.append("rect").style("display", "none").style("stroke-width", "0.5px").style("fill", "transparent").style("pointer-events", "none");
+  this.dom.rowBeam = this.dom.highlightBeamG.append("rect").style("display", "none").style("stroke-width", "0.5px").style("fill", "transparent").style("pointer-events", "none");
+  this.dom.tip.onHide = () => {
+    this.lastActiveLabel = this.activeLabel;
+    delete this.activeLabel;
+  };
+  select_default("body").on(`mousedown.matrixZoom-${this.id}`, this.resetInteractions);
+  window.onscroll = this.delayedMouseoutHandler;
+  const contentDiv = this.dom.holder.node().closest(".sjpp-output-sandbox-content");
+  if (contentDiv) contentDiv.onscroll = this.delayedMouseoutHandler;
+}
+
+export {
+  setMatrixDom
+};
+//# sourceMappingURL=chunk-HUBO743S.js.map