@sjcrh/proteinpaint-client 2.193.0 → 2.195.0

package/dist/chunk-BOO4W7WD.js

@@ -1,482 +0,0 @@
-import {
-  renderTable
-} from "./chunk-L7VDSIM7.js";
-import {
-  clusterMethodLst,
-  distanceMethodLst
-} from "./chunk-6G4YOMWW.js";
-import {
-  METABOLITE_INTENSITY,
-  NUMERIC_DICTIONARY_TERM,
-  PROTEOME_ABUNDANCE
-} from "./chunk-IVXCWCKS.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-BOO4W7WD.js.map

package/dist/chunk-BOO4W7WD.js.map

@@ -1,7 +0,0 @@
-{
-  "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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