@sjcrh/proteinpaint-client 2.217.0 → 2.218.0

package/dist/chunk-WU3YXPRE.js

@@ -1,217 +0,0 @@
-import {
-  DATermTypes,
-  DMRCATE_DEFAULTS
-} from "./chunk-NNDKYTUV.js";
-import {
-  dofetch3
-} from "./chunk-BIJOXCLN.js";
-import {
-  DMR_SCAN_ELEMENT_TYPE
-} from "./chunk-ZPWBYHNE.js";
-import {
-  rgb
-} from "./chunk-Q5RDQNIT.js";
-
-// plots/volcano/colors.ts
-function getGroupColors(config) {
-  const groups = config?.samplelst?.groups;
-  const termValues = config?.tw?.term?.values;
-  const rawDown = termValues?.[groups?.[0]?.name]?.color || "red";
-  const rawUp = termValues?.[groups?.[1]?.name]?.color || "blue";
-  return {
-    controlColor: toHex(rawDown, "red"),
-    caseColor: toHex(rawUp, "blue")
-  };
-}
-function toHex(color, fallback) {
-  const c = rgb(color || fallback);
-  return c.displayable() ? c.formatHex() : rgb(fallback).formatHex();
-}
-
-// plots/volcano/model/VolcanoModel.ts
-var VolcanoModel = class {
-  /** TODO: This model is used in both the volcano and gsea.
-   * In the future, create base model in DA and use specific
-   * classes for the volcano and gsea. */
-  constructor(plot, termType) {
-    this.plot = plot;
-    this.app = plot.app;
-    this.termType = termType;
-  }
-  /** May use mapper instead as more termTypes are added */
-  async getData(config, settings) {
-    this.config = config;
-    this.settings = settings;
-    if (this.termType === DATermTypes.GENE_EXPRESSION) {
-      const body = await this.getGERequestBody();
-      const response = await dofetch3("termdb/DE", { body, signal: this.plot.api?.getAbortSignal() });
-      if (response && !response.error) response.daRequest = body;
-      return response;
-    }
-    if (this.termType === DATermTypes.DNA_METHYLATION) {
-      const body = await this.getDMRequestBody();
-      const response = await dofetch3("termdb/diffMeth", { body, signal: this.plot.api?.getAbortSignal() });
-      if (response && !response.error) response.daRequest = body;
-      return response;
-    }
-    if (this.termType === DATermTypes.SINGLECELL_CELLTYPE) {
-      const body = await this.getSCCTRequestBody();
-      return await dofetch3("termdb/singlecellDEgenes", { body, signal: this.plot.api?.getAbortSignal() });
-    }
-    if (this.termType === DATermTypes.PROTEOME_DAP) {
-      const body = this.getDapRequestBody();
-      return await dofetch3("termdb/dapVolcano", { body, signal: this.plot.api?.getAbortSignal() });
-    }
-    if (this.termType === DATermTypes.SINGLECELL_GENE_EXPRESSION) {
-    }
-    throw new Error(`Volcano plot does not support route for termType='${this.termType}'`);
-  }
-  //Gene expression
-  async getGERequestBody() {
-    await this.getOtherSamples(this.config.samplelst);
-    const state = this.app.getState();
-    const body = {
-      kind: "DE",
-      genome: this.app.vocabApi.vocab.genome,
-      dslabel: this.app.vocabApi.vocab.dslabel,
-      method: this.settings.method,
-      min_count: this.settings.minCount,
-      min_total_count: this.settings.minTotalCount,
-      samplelst: this.config.samplelst,
-      filter: state.termfilter.filter,
-      filter0: state.termfilter.filter0,
-      cpm_cutoff: this.settings.cpmCutoff,
-      volcanoRender: this.getVolcanoRender()
-    };
-    const pseudobulk = this.config.tw?.pseudobulk;
-    if (pseudobulk) body.pseudobulk = pseudobulk;
-    this.addConfounderTw(body);
-    return body;
-  }
-  //DNA methylation
-  async getDMRequestBody() {
-    await this.getOtherSamples(this.config.samplelst);
-    const state = this.app.getState();
-    const body = {
-      kind: "DM",
-      genome: this.app.vocabApi.vocab.genome,
-      dslabel: this.app.vocabApi.vocab.dslabel,
-      samplelst: this.config.samplelst,
-      filter: state.termfilter.filter,
-      filter0: state.termfilter.filter0,
-      min_samples_per_group: this.settings.minSamplesPerGroup,
-      exclude_sex_chr: this.settings.excludeSexChr,
-      /* Omitted rather than sent as 'promoter' when it is the default, so a request
-      from a promoter-only dataset is byte-identical to what this client sent before
-      the element picker existed. The server resolves an absent element_type to
-      'promoter'. This does NOT preserve cache keys -- the key object gained the
-      field server-side, so every pre-existing dm/ entry is orphaned on deploy
-      regardless of what the client sends. */
-      ...this.settings.elementType && this.settings.elementType != "promoter" ? { element_type: this.settings.elementType } : {},
-      // the scan's own knobs; the server ignores them for any other element type
-      ...this.settings.elementType == DMR_SCAN_ELEMENT_TYPE ? {
-        scan: {
-          ...this.settings.scanChromosome ? { chromosome: this.settings.scanChromosome } : {},
-          backgroundCorrection: !!this.settings.backgroundCorrection,
-          minCpgs: this.settings.minCpgs,
-          profileBinBp: this.settings.profileBinBp,
-          // only when changed: an explicit default would orphan every cached scan
-          ...this.settings.lambda != DMRCATE_DEFAULTS.lambda ? { lambda: this.settings.lambda } : {},
-          ...this.settings.C != DMRCATE_DEFAULTS.C ? { C: this.settings.C } : {},
-          ...this.settings.fdrCutoff != DMRCATE_DEFAULTS.fdrCutoff ? { fdrCutoff: this.settings.fdrCutoff } : {}
-        }
-      } : {},
-      volcanoRender: this.getVolcanoRender()
-    };
-    if (this.settings.elementType != DMR_SCAN_ELEMENT_TYPE) this.addConfounderTw(body);
-    return body;
-  }
-  /** Parameters telling the server to run the `volcano` Rust renderer and return a
-   * volcano PNG + top-significant rows instead of the full dot list. */
-  getVolcanoRender() {
-    const dotRadius = Math.max(this.settings.width, this.settings.height) / 80;
-    const { caseColor, controlColor } = getGroupColors(this.config);
-    const useDeltaBeta = this.termType === DATermTypes.DNA_METHYLATION && this.settings.xAxis == "delta_beta";
-    return {
-      significanceThresholds: {
-        pValueCutoff: this.settings.pValue,
-        pValueType: this.settings.pValueType,
-        foldChangeCutoff: useDeltaBeta ? this.settings.deltaBetaCutoff : this.settings.foldChangeCutoff
-      },
-      ...useDeltaBeta ? { xField: "delta_beta" } : {},
-      // Tied to the delta-beta axis: the control that sets it is only offered for
-      // methylation, and centering a log2 fold-change axis is a different conversation.
-      ...useDeltaBeta && this.settings.centerDeltaBeta ? { centerX: true } : {},
-      pixelWidth: this.settings.width,
-      pixelHeight: this.settings.height,
-      colorSignificant: toHex(this.settings.defaultSignColor, "red"),
-      colorSignificantUp: caseColor,
-      colorSignificantDown: controlColor,
-      colorNonsignificant: toHex(this.settings.defaultNonSignColor, "black"),
-      dotRadius,
-      maxInteractiveDots: this.settings.maxInteractiveDots,
-      // Render the PNG at device-pixel resolution so it stays sharp on
-      // retina screens. The server reports the plot extent in CSS-space,
-      // so SVG overlay coords are unaffected.
-      //
-      // Oversample by 2× so the PNG also stays sharp when the user
-      // *zooms in after* the initial render (the captured DPR is frozen
-      // at fetch time — bigger headroom = more tolerable post-render
-      // zoom before pixelation appears). The server clamp keeps the
-      // bitmap memory bounded.
-      devicePixelRatio: (typeof window !== "undefined" ? window.devicePixelRatio : 1) * 2
-    };
-  }
-  //This is a workaround until the server can accept an arr of confounder tws
-  addConfounderTw(body) {
-    const confounders = this.config?.confounderTws;
-    if (confounders?.length) {
-      body.tw = this.config.confounderTws[0];
-      if (confounders.length > 1) body.tw2 = this.config.confounderTws[1];
-    }
-  }
-  //Single cell cell type
-  getSCCTRequestBody() {
-    const body = {
-      genome: this.app.vocabApi.vocab.genome,
-      dslabel: this.app.vocabApi.vocab.dslabel,
-      sample: this.config.sample,
-      termId: this.config.termId,
-      categoryName: this.config.categoryName,
-      volcanoRender: this.getVolcanoRender()
-    };
-    return body;
-  }
-  getDapRequestBody() {
-    const { organism, assay, cohort } = this.config.proteomeDetails;
-    return {
-      genome: this.app.vocabApi.vocab.genome,
-      dslabel: this.app.vocabApi.vocab.dslabel,
-      organism,
-      assay,
-      cohort,
-      volcanoRender: this.getVolcanoRender()
-    };
-  }
-  /** retrieve the sampleId/sampleName for samples in
-   * the "others" group instead of using {in: false} */
-  async getOtherSamples(samplelst) {
-    const othersSamplesGroup = samplelst.groups.find((g) => !g.in);
-    if (!othersSamplesGroup) return;
-    const state = this.app.getState();
-    const samplesGroup = samplelst.groups.find((g) => g.in);
-    othersSamplesGroup.values = [];
-    for (const s of await this.plot.vocabApi.getFilteredSampleList(state.termfilter.filter)) {
-      if (!samplesGroup.values.some((i) => i.sampleId == s.id)) {
-        othersSamplesGroup.values.push({ sampleId: s.id, sample: s.name });
-      }
-    }
-    othersSamplesGroup.in = true;
-  }
-};
-
-export {
-  getGroupColors,
-  VolcanoModel
-};
-//# sourceMappingURL=chunk-WU3YXPRE.js.map

package/dist/chunk-X2HWRISK.js

@@ -1,480 +0,0 @@
-import {
-  renderTable
-} from "./chunk-NNDKYTUV.js";
-import {
-  clusterMethodLst,
-  distanceMethodLst
-} from "./chunk-BIJOXCLN.js";
-import {
-  termType2label
-} from "./chunk-AMW5LCUB.js";
-import {
-  select_default
-} from "./chunk-I6Y4O3RR.js";
-import {
-  __export
-} from "./chunk-HS5PO5ZQ.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.settings.matrix.controlLabels.terms;
-  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 ${rowType}&nbsp;&check;`);
-  });
-  renderTable({
-    rows,
-    columns: [{ label: rowType }],
-    div: div.append("div"),
-    showLines: true,
-    maxHeight: "35vh",
-    resize: true
-  });
-}
-function getClusterFromTopDendrogram(event) {
-  if (event.target.tagName == "image") this.imgBox = event.target.getBoundingClientRect();
-  else return;
-  const y = event.clientY - this.imgBox.y - event.target.clientTop;
-  const xMin = this.dimensions.xMin;
-  const x = event.clientX - this.imgBox.x - event.target.clientLeft + xMin;
-  for (const [clusterId, cluster] of this.hierClusterData.clustering.col.mergedClusters) {
-    const { x1, y1, x2, y2, clusterY } = cluster.clusterPosition;
-    if (x1 <= x && x <= x2 && clusterY - 5 < y && y < clusterY + 5 || clusterY <= y && y <= y1 && x1 - 5 < x && x < x1 + 5 || clusterY <= y && y <= y2 && x2 - 5 < x && x < x2 + 5) {
-      return clusterId;
-    }
-  }
-}
-function getClusterFromLeftDendrogram(event) {
-  if (event.target.tagName == "image") this.imgBox = event.target.getBoundingClientRect();
-  else return;
-  const y = event.clientY - this.imgBox.y - event.target.clientTop;
-  const xMin = this.dimensions.xMin;
-  const x = event.clientX - this.imgBox.x - event.target.clientLeft + xMin;
-  for (const [clusterId, cluster] of this.hierClusterData.clustering.row.mergedClusters) {
-    const { x1, y1, x2, y2, clusterX } = cluster.clusterPosition;
-    if (y1 <= y && y <= y2 && clusterX - 5 < x && x < clusterX + 5 || clusterX <= x && x <= x1 && y1 - 5 < y && y < y1 + 5 || clusterX <= x && x <= x2 && y2 - 5 < y && y < y2 + 5) {
-      return clusterId;
-    }
-  }
-}
-function setClusteringBtn(holder, callback) {
-  const cl = this.config.settings.matrix.controlLabels;
-  const dataType = this.config.dataType;
-  const clusterRowLabel = cl.Terms;
-  const cluteringButtonLabel = `${termType2label(dataType)} Clustering`;
-  holder.append("button").datum({
-    label: cluteringButtonLabel,
-    getCount: () => this.hcTermGroup?.lst.length || 0,
-    showCount: "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 !== "geneExpression") {
-    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-X2HWRISK.js.map