@sjcrh/proteinpaint-client 2.206.1 → 2.207.0

package/dist/chunk-GH5EQCLQ.js

@@ -0,0 +1,379 @@
+import {
+  SPANSELECTOR,
+  renderLabelSpans,
+  trackLabelSpanData
+} from "./chunk-C2MCQZWH.js";
+import {
+  fillTermWrapper,
+  termsettingInit
+} from "./chunk-NQDF3U2C.js";
+import {
+  isNumericTerm
+} from "./chunk-HZ3TCGBK.js";
+import {
+  select_default
+} from "./chunk-I6Y4O3RR.js";
+
+// plots/matrix/matrix.renderers.js
+function setRenderers(self) {
+  self.render = function() {
+    const s = self.settings.matrix;
+    const l = self.layout;
+    const d = self.dimensions;
+    const duration = self.dom.svg.attr("width") ? s.duration : 0;
+    self.dom.clipRect.attr("x", d.xOffset - 1).attr("y", 0).attr("width", d.mainw + 3).attr("height", d.mainh + 500);
+    self.renderSerieses(s, l, d, duration);
+    self.renderLabels(s, l, d, duration);
+    self.renderDivideByLabel(s, l, d, duration);
+    self.dom.colBeam.attr("width", d.dx).attr("height", d.mainh).style("stroke", s.beamStroke);
+    self.dom.rowBeam.attr("width", d.zoomedMainW).attr("height", s.rowh).style("stroke", s.beamStroke);
+  };
+  self.renderSerieses = function(s, l, d, duration) {
+    if (self.prevUseCanvas != s.useCanvas) {
+      self.dom.seriesesG.selectAll("g").remove();
+    }
+    if (s.useCanvas) {
+      const _g = self.dom.seriesesG.selectAll("g");
+      const g = (
+        /*(_g.size() && _g) ||*/
+        self.dom.seriesesG.append("g").datum(this.serieses)
+      );
+      self.renderCanvas(this.serieses, g, d, s, _g, duration);
+    } else {
+      self.dom.seriesesG.attr("transform", `translate(${d.xOffset + d.seriesXoffset},${d.yOffset})`);
+      const sg = self.dom.seriesesG.selectAll(".sjpp-mass-series-g").data(this.serieses, (series) => series.tw.$id);
+      sg.exit().remove();
+      sg.each(self.renderSeries);
+      sg.enter().append("g").attr("class", "sjpp-mass-series-g").style("opacity", 1e-3).each(self.renderSeries);
+      self.mouseout();
+    }
+    self.prevUseCanvas = s.useCanvas;
+  };
+  self.renderSeries = async function(series) {
+    const s = self.settings.matrix;
+    const d = self.dimensions;
+    const g = select_default(this);
+    const duration = g.attr("transform") ? s.duration : 0;
+    g.attr("transform", `translate(${series.x},${series.y})`).style("opacity", 1);
+    const last = series.cells[series.cells.length - 1];
+    const height = series.y + last?.y + s.rowh;
+    const rects = g.selectAll("rect").data(series.cells, (cell) => cell.sample + ";;" + cell.tw.$id + ";;" + cell.valueIndex);
+    rects.exit().remove();
+    rects.each(self.renderCell);
+    rects.enter().append("rect").each(self.renderCell);
+  };
+  self.renderCanvas = async function(serieses, g, d, s, _g, duration) {
+    const pxr = window.devicePixelRatio <= 1 ? 1 : window.devicePixelRatio;
+    g.selectAll("*").remove();
+    const width = d.imgW;
+    const height = self.dimensions.mainh;
+    const canvas = window.OffscreenCanvas ? new OffscreenCanvas(width * pxr, height * pxr) : (
+      // TODO: no need to support older browser versions???
+      self.dom.holder.append("canvas").attr("width", pxr * width).attr("height", pxr * height).style("opacity", 0).node()
+    );
+    const ctx = canvas.getContext("2d");
+    ctx.imageSmoothingEnabled = false;
+    ctx.imageSmoothingQuality = "high";
+    ctx.scale(pxr, pxr);
+    for (const series of serieses) {
+      for (const cell of series.cells) {
+        self.renderCellWithCanvas(ctx, cell, series, s, d, series.y);
+      }
+    }
+    if (window.OffscreenCanvas) {
+      const reader = new FileReader();
+      reader.addEventListener(
+        "load",
+        () => {
+          _g?.remove();
+          self.dom.seriesesG.attr("transform", `translate(${d.xOffset + d.seriesXoffset},${d.yOffset})`);
+          g.selectAll("image").remove();
+          g.append("image").attr("xlink:href", reader.result).attr("x", d.xMin).attr("width", width).attr("height", height);
+        },
+        false
+      );
+      const blob = await canvas.convertToBlob({ quality: 1 });
+      const dataURL = reader.readAsDataURL(blob);
+    } else {
+      _g?.remove();
+      self.dom.seriesesG.attr("transform", `translate(${d.xOffset + d.seriesXoffset},${d.yOffset})`);
+      const dataURL = canvas.toDataURL();
+      const ratio = window.devicePixelRatio * window.devicePixelRatio;
+      g.append("image").attr("width", width).attr("height", height).attr("xlink:href", dataURL);
+      if (!window.OffscreenCanvas) canvas.remove();
+    }
+    self.mouseout();
+  };
+  self.renderCellWithCanvas = function(ctx, cell, series, s, d, _y) {
+    if (!cell.fill)
+      cell.fill = cell.$id in self.colorScaleByTermId ? self.colorScaleByTermId[cell.$id](cell.key) : getRectFill(cell);
+    const x = cell.x ? cell.x - d.xMin : 0;
+    const y = _y ? _y + cell.y : cell.y || 0;
+    const width = s.useMinPixelWidth ? Math.max(cell.width || d.colw, d.pxw) : cell.width || d.colw;
+    const height = "height" in cell ? cell.height : s.rowh;
+    ctx.fillStyle = cell.fill;
+    ctx.fillRect(x, y, width, height);
+    const borderWidth = Math.min(width, height) * 0.1;
+    if (cell.border) {
+      ctx.lineWidth = borderWidth;
+      ctx.strokeStyle = "white";
+      ctx.strokeRect(x, y, width, height);
+    }
+  };
+  self.renderCell = function(cell) {
+    if (!cell.fill)
+      cell.fill = cell.$id in self.colorScaleByTermId ? self.colorScaleByTermId[cell.$id](cell.key) : getRectFill(cell);
+    const s = self.settings.matrix;
+    const rect = select_default(this).attr("x", cell.x || 0).attr("y", cell.y || 0).attr("width", cell.width || self.dimensions.colw).attr("height", "height" in cell ? Math.max(0, cell.height) : s.rowh).attr("shape-rendering", "crispEdges").attr("fill", cell.fill);
+    if (cell.border) {
+      rect.attr("stroke", "white").attr("stroke-width", 0.8);
+    }
+  };
+  self.renderLabels = function(s, l, d, duration) {
+    const relatedSamplesByAncestorId = /* @__PURE__ */ new Map();
+    for (const direction of ["top", "btm", "left", "right"]) {
+      let renderLabel2 = function(lab) {
+        const g = select_default(this);
+        g.attr("transform", side.attr.labelGTransform);
+        if (!g.select(":scope>text").size()) g.append("text");
+        const showContAxis = !side.isGroup && lab.grp?.type !== "hierCluster" && lab.tw?.q?.mode == "continuous";
+        const labelText = side.label(lab);
+        const text = g.select(":scope>text").attr("fill", "#000");
+        let continuousBarHAdjust;
+        const twSpecificSettings = self.config.settings.matrix.twSpecificSettings;
+        const twSettingsBarH = twSpecificSettings[lab.tw?.$id]?.contBarH;
+        if (twSettingsBarH && s.barh) continuousBarHAdjust = (twSettingsBarH - s.barh) * 0.5;
+        text.attr(
+          "display",
+          lab.grp?.type === "hierCluster" && s.clusterRowh < 6 ? "none" : side.attr.fontSize < 6 || labelText === "configure" ? "none" : ""
+        ).attr("font-size", lab.grp?.type === "hierCluster" ? Math.max(4, s.clusterRowh - 4) : side.attr.fontSize).attr("text-anchor", side.attr.labelAnchor).attr(
+          "transform",
+          side.attr.labelTransform + (continuousBarHAdjust ? ` translate(0,${continuousBarHAdjust})` : "")
+        ).attr("cursor", "pointer").attr(side.attr.textpos.coord, side.attr.textpos.factor * (showContAxis ? 30 : 0));
+        if (!Array.isArray(labelText)) {
+          text.text(labelText);
+          text.attr(
+            "y",
+            lab.grp?.type !== "hierCluster" && lab.tw?.q?.mode == "continuous" ? 10 : lab.grp?.type === "hierCluster" ? 0.1 * s.clusterRowh : 0
+          );
+          if (lab.grp?.type !== "hierCluster" && lab.tw?.q?.mode == "continuous") text.attr("x", -20);
+        } else {
+          text.text("");
+          const tspan = text.selectAll("tspan").data(labelText);
+          tspan.enter().append("tspan").attr("class", getTspanCls2).attr("dx", getTspanDx2).attr("font-size", getTspanFontSize2).text(getTspanText2);
+        }
+        text.on("mouseover", labelText === "configure" ? () => text.attr("opacity", 0.5) : null).on("mouseout", labelText === "configure" ? () => text.attr("opacity", 0) : null);
+        const hasAxis = g.select(".sjpp-matrix-cell-axis").size() && true;
+        if (showContAxis && labelText) {
+          if (!hasAxis) {
+            g.append("g").attr("class", "sjpp-matrix-cell-axis").attr("shape-rendering", "crispEdges");
+          }
+          const axisg = g.select(".sjpp-matrix-cell-axis");
+          axisg.selectAll("*").remove();
+          const domain = [lab.counts.maxval, lab.counts.minval];
+          if (s.transpose) domain.reverse();
+          const twSpecificSettings2 = self.config.settings.matrix.twSpecificSettings;
+          const twSettings = twSpecificSettings2[lab.tw.$id];
+          const x = !s.transpose ? 0 : twSettings.contBarGap - 1 - lab.labelOffset;
+          const y = !s.transpose ? twSettings.contBarGap - 1 - lab.labelOffset : 0;
+          axisg.attr("shape-rendering", "crispEdges").attr("transform", `translate(${x},${y})`).call(side.attr.axisFxn(lab.scales.full.domain(lab.scales.tickValues)).tickValues(lab.scales.tickValues));
+        } else if (hasAxis) {
+          g.select(".sjpp-matrix-cell-axis").remove();
+        }
+        if (self.config.chartType == "matrix" && s.sortBySampleAncestry && side.prefix == "sample")
+          trackLabelSpanData(lab, side, direction, text, relatedSamplesByAncestorId);
+      }, getTspanCls2 = function(d2) {
+        return d2.cls;
+      }, getTspanDx2 = function(d2) {
+        return d2.dx;
+      }, getTspanFontSize2 = function(d2) {
+        return d2.fontSize || side.attr.fontSize;
+      }, getTspanText2 = function(d2) {
+        return d2.text;
+      };
+      var renderLabel = renderLabel2, getTspanCls = getTspanCls2, getTspanDx = getTspanDx2, getTspanFontSize = getTspanFontSize2, getTspanText = getTspanText2;
+      const side = l[direction];
+      side.box.style("display", side.display || "").attr("transform", side.attr.boxTransform);
+      const labels = side.box.selectAll(".sjpp-matrix-label").data(side.data, side.key);
+      labels.exit().remove();
+      labels.each(renderLabel2);
+      labels.enter().append("g").attr("class", "sjpp-matrix-label").each(renderLabel2);
+      side.box.selectAll(SPANSELECTOR).remove();
+      if (self.config.chartType == "matrix" && s.sortBySampleAncestry && side.prefix == "sample")
+        renderLabelSpans(relatedSamplesByAncestorId, side, d);
+    }
+  };
+  self.colLabelGTransform = (lab, grpIndex) => {
+    const s = self.settings.matrix;
+    const d = self.dimensions;
+    lab.labelOffset = 0.8 * d.colw;
+    const x = lab.grpIndex * s.colgspace + lab.totalIndex * d.dx + lab.labelOffset + lab.totalHtAdjustments;
+    const y = 0;
+    return `translate(${x + d.seriesXoffset},${y})`;
+  };
+  self.colGrpLabelGTransform = (lab, grpIndex) => {
+    const s = self.settings.matrix;
+    const d = self.dimensions;
+    const len = (lab.processedLst || lab.grp.lst).length;
+    const x = lab.grpIndex * s.colgspace + lab.prevGrpTotalIndex * d.dx + len * d.dx / 2 + s.grpLabelFontSize / 2 + lab.totalHtAdjustments;
+    return `translate(${x + d.seriesXoffset},0)`;
+  };
+  self.rowLabelGTransform = (lab, grpIndex) => {
+    const s = self.settings.matrix;
+    const d = self.dimensions;
+    const x = 0;
+    lab.labelOffset = 0.7 * (lab.grp.type == "hierCluster" ? s.clusterRowh : s.rowh);
+    const y = lab.grpIndex * s.rowgspace + lab.totalIndex * d.dy + lab.labelOffset + lab.totalHtAdjustments;
+    return `translate(${x},${y})`;
+  };
+  self.rowGrpLabelGTransform = (lab, grpIndex) => {
+    const s = self.settings.matrix;
+    const d = self.dimensions;
+    const len = (lab.processedLst || lab.grp.lst).length;
+    const x = lab.tw?.q?.mode == "continuous" ? 20 : 0;
+    const y = lab.grpIndex * s.rowgspace + lab.prevGrpTotalIndex * d.dy + len * d.dy / 2 + s.grpLabelFontSize / 2 + lab.totalHtAdjustments;
+    return `translate(${x},${y})`;
+  };
+  self.rowAxisGTransform = (lab, grpIndex) => {
+    const s = self.settings.matrix;
+    const d = self.dimensions;
+    const x = 0;
+    const y = lab.grpIndex * s.rowgspace + lab.totalIndex * d.dy + 0.7 * s.rowh + lab.totalHtAdjustments;
+    return `translate(${x},${y})`;
+  };
+  self.renderDivideByLabel = async (s, l, d) => {
+    self.dom.mainG.selectAll(".sjpp-matrix-divide-by-label").remove();
+    if (!self.config.divideBy) return;
+    const name = self.config.divideBy?.term.name || "";
+    const text = name.length <= s.rowlabelmaxchars ? name : name.slice(0, s.rowlabelmaxchars) + "\u2026";
+    const sides = !s.transpose ? [l.left, l.right] : [l.top, l.bottom];
+    const box = sides.find((d2) => !d2.isGroup)?.box;
+    const y = (s.collabelpos == "top" ? d.mainh + s.collabelmaxchars : -s.collabelmaxchars) + 8;
+    const anchor = s.rowlabelpos == "left" ? "end" : "start";
+    const cl = s.controlLabels;
+    const gNote = box.append("g").attr("class", "sjpp-matrix-divide-by-label").attr("transform", `translate(0, ${y})`);
+    gNote.append("text").attr("text-anchor", anchor).attr("font-style", "italic").attr("y", -20).text(`${cl.Samples} grouped by`);
+    const g = box.datum({ tw: self.config.divideBy }).append("g").attr("class", "sjpp-matrix-divide-by-label").attr("transform", `translate(0, ${y})`).on("click", (event, d2) => {
+      pill.showMenu(event, textElem.node());
+    });
+    const textElem = g.append("text").attr("text-anchor", anchor).attr("font-weight", 600).text(text);
+    g.append("title").text(`${cl.Samples} are grouped by this gene or variable. Click to edit.`);
+    const customMenuOptions = [];
+    const tvsKey = isNumericTerm(self.config.divideBy.term) ? "ranges" : "values";
+    if (self.config.legendValueFilter.lst?.find(
+      (l2) => l2.legendGrpName == self.config.divideBy.term.id || l2.legendGrpName == self.config.divideBy.term.name
+    )?.tvs[tvsKey]?.length) {
+      customMenuOptions.push({ label: `Show filtered ${cl.samples}`, callback: self.showDeletedSampleGroups });
+    }
+    const pill = await termsettingInit({
+      menuOptions: "{edit,replace,remove}",
+      //numericEditMenuVersion: opts.numericEditMenuVersion,
+      customMenuOptions,
+      //custom menu options other than menuOptions
+      vocabApi: self.app.vocabApi,
+      vocab: self.state.vocab,
+      //activeCohort: opts.state?.activeCohort,
+      holder: g,
+      debug: self.opts.debug,
+      usecase: { target: "matrix" },
+      getBodyParams: () => {
+        const currentGeneNames = self.termOrder.filter((t) => t.tw.term.type === "geneVariant").map(
+          (t) => t.tw.term.chr ? `${t.tw.term.chr}:${t.tw.term.start}-${t.tw.term.stop}` : t.tw.term.gene || t.tw.term.name
+        );
+        if (currentGeneNames.length) return { currentGeneNames };
+        return {};
+      },
+      callback: async (tw) => {
+        if (self.dom.loadingDiv && self.dom.svg) {
+          self.dom.loadingDiv.selectAll("*").remove();
+          self.dom.loadingDiv.html("").style("display", "").style("position", "relative").style("left", "45%");
+          self.dom.loadingDiv.html("Processing data ...");
+          self.dom.svg.style("opacity", 0.1).style("pointer-events", "none");
+        }
+        if (tw && !tw.q) throw "data.q{} missing from pill callback";
+        if (tw?.term && isNumericTerm(tw.term)) {
+          tw.q = { ...tw.q, mode: "discrete" };
+        }
+        if (tw) await fillTermWrapper(tw, self.app.vocabApi);
+        await pill.main(tw ? tw : { term: null, q: null });
+        box.datum({ tw });
+        self.app.dispatch({
+          type: "plot_edit",
+          id: self.id,
+          config: {
+            divideBy: tw,
+            legendValueFilter: self.mayRemoveTvsEntry(self.config.divideBy)
+          }
+        });
+      }
+    });
+    const arg = {
+      term: self.config.divideBy.term,
+      q: self.config.divideBy.q
+    };
+    if (self.config.divideBy.$id) arg.$id = self.config.divideBy.$id;
+    pill.main(arg);
+  };
+  self.adjustSvgDimensions = async function(prevTranspose) {
+    const s = self.settings.matrix;
+    const hc = self.settings.hierCluster || {};
+    const l = self.layout;
+    const hcHeight = !hc.yDendrogramHeight ? 0 : hc.yDendrogramHeight + (l.top.display === "none" ? 0 : 10);
+    const hcWidth = hc.xDendrogramHeight || 0;
+    const d = self.dimensions;
+    const duration = self.dom.svg.attr("width") ? s.duration : 0;
+    await sleep(prevTranspose == s.transpose ? duration : s.duration);
+    const topBox = l.top.box.node().getBBox();
+    const btmBox = l.btm.box.node().getBBox();
+    const leftBox = l.left.box.node().getBBox();
+    const rtBox = l.right.box.node().getBBox();
+    const legendBox = self.dom.legendG.node().getBBox();
+    const seriesBox = self.dom.seriesesG.node().getBBox();
+    d.extraWidth = leftBox.width + rtBox.width + s.margin.left + s.margin.right + s.rowlabelgap * 2;
+    d.extraHeight = topBox.height + btmBox.height + s.margin.top + s.margin.bottom + s.collabelgap * 2;
+    d.svgw = d.mainw + d.extraWidth + hcWidth;
+    d.svgh = d.mainh + d.extraHeight + legendBox.height + 20 + s.scrollHeight + hcHeight;
+    self.dom.svg.attr("width", d.svgw).attr("height", d.svgh);
+    let maxLabelWidth = self.type == "hierCluster" ? 0 : leftBox.width, maxLabelNumChars = 0;
+    if (hc.xDendrogramHeight) {
+      self.dom.termLabelG.selectAll(".sjpp-matrix-label").each(function(d2) {
+        if (d2.grp.type !== "hierCluster") return;
+        const box = this.getBBox();
+        if (box.width > maxLabelWidth) {
+          maxLabelWidth = box.width;
+          maxLabelNumChars = d2.label.length;
+        }
+      });
+    }
+    const x = -l.left.offset + hcWidth + maxLabelWidth;
+    const xAdjust = !hc.xDendrogramHeight ? 0 : Math.max(leftBox.width - (hc.xDendrogramHeight + maxLabelWidth), 0);
+    const y = (l.top.display == "none" ? 0 : topBox.height) - l.top.offset + hcHeight;
+    self.dom.mainG.attr("transform", `translate(${x + xAdjust},${y})`);
+    self.dom.clipRect.attr("y", -y).attr("height", d.mainh + 500 + y);
+    const legendX = d.xOffset + (s.transpose ? 20 : 0);
+    const legendY = d.yOffset + d.mainh + s.collabelgap + (l.btm.display == "none" ? 0 : btmBox.height) + 20;
+    self.dom.legendG.attr("transform", `translate(${legendX},${legendY})`);
+    if (hc.xDendrogramHeight) {
+      const dendroX = maxLabelWidth + xAdjust - l.left.offset + d.xOffset - d.dx / 2;
+      self.dom.hcClipRect.attr("x", dendroX + hcWidth + d.dx / 2).attr("y", 0).attr("width", d.mainw + 3).attr("height", d.mainh + hc.yDendrogramHeight + 500);
+      self.topDendroX = dendroX + d.seriesXoffset;
+      self.dom.topDendrogram.attr("transform", `translate(${self.topDendroX}, 0)`);
+      const y2 = l.top.display == "none" ? 0 : topBox.height + s.collabelgap;
+      self.dom.leftDendrogram.attr("transform", `translate(${dendroX - maxLabelWidth - 10}, ${y2})`);
+    }
+  };
+}
+function getRectFill(d) {
+  if (d.fill) return d.fill;
+  const cls = d.class || Array.isArray(d.values) && d.values[0].class;
+  if (!cls) console.log;
+  return cls ? mclass[cls].color : "#555";
+}
+function sleep(ms) {
+  return new Promise((resolve) => setTimeout(resolve, ms));
+}
+
+export {
+  setRenderers
+};
+//# sourceMappingURL=chunk-GH5EQCLQ.js.map

package/dist/chunk-GIBTGABW.js

@@ -0,0 +1,263 @@
+import {
+  Matrix
+} from "./chunk-7WL4LROG.js";
+import {
+  hierCluster_renderers_exports
+} from "./chunk-BXM6PRTG.js";
+import {
+  hierCluster_interactivity_exports
+} from "./chunk-BH55L7RJ.js";
+import {
+  filterJoin,
+  getNormalRoot
+} from "./chunk-NQDF3U2C.js";
+import {
+  clusterMethodLst,
+  distanceMethodLst,
+  dofetch3
+} from "./chunk-GRVO7RW4.js";
+import {
+  TermTypes2Dt,
+  dictionaryNumericTypes
+} from "./chunk-HZ3TCGBK.js";
+import {
+  colorScaleMap
+} from "./chunk-IZUYLFOX.js";
+import {
+  deepEqual,
+  getCompInit
+} from "./chunk-WINIL2KN.js";
+import {
+  extent,
+  linear
+} from "./chunk-4OLM3KSB.js";
+
+// plots/matrix/hierCluster.js
+var HierCluster = class _HierCluster extends Matrix {
+  static type = "hierCluster";
+  constructor(opts) {
+    super(opts);
+    this.type = _HierCluster.type;
+    this.chartType = _HierCluster.type;
+  }
+  async init(appState) {
+    await super.init(appState);
+    this.maySetSandboxHeader(appState);
+    this.hcClipId = this.seriesClipId + "-hc";
+    this.dom.hcClipRect = this.dom.svg.select("defs").append("clipPath").attr("id", this.hcClipId).attr("clipPathUnits", "userSpaceOnUse").append("rect").attr("display", "block");
+    this.dom.topDendrogram = this.dom.svg.insert("g", "g").attr("clip-path", `url(#${this.hcClipId})`).append("g").attr("class", "sjpp-matrix-dendrogram").attr("data-testid", "hierCluster_top_dendrogram").on("click", (event) => {
+      const clickedClusterId = this.getClusterFromTopDendrogram(event);
+      if (clickedClusterId) {
+        this.clickedClusterIds = this.getAllChildrenClusterIds(clickedClusterId);
+        this.clickedClusterIds.push(clickedClusterId);
+        const clickedCluster = this.hierClusterData.clustering.col.mergedClusters.get(clickedClusterId);
+        const clickedClusterSampleNames = clickedCluster.children.map((c) => c.name);
+        this.addSelectedSamplesOptions(clickedClusterSampleNames, event);
+      } else {
+        delete this.clickedClusterIds;
+      }
+      if (this.clickedLeftClusterIds) {
+        delete this.clickedLeftClusterIds;
+        this.plotDendrogramHclust();
+      } else this.plotDendrogramHclust("top");
+    });
+    this.dom.leftDendrogram = this.dom.svg.insert("g", "g").attr("class", "sjpp-matrix-dendrogram").attr("data-testid", "hierCluster_left_dendrogram").on("click", (event) => {
+      const clickedLeftClusterId = this.getClusterFromLeftDendrogram(event);
+      if (clickedLeftClusterId) {
+        this.clickedLeftClusterIds = this.getAllChildrenClusterIds(clickedLeftClusterId, true);
+        this.clickedLeftClusterIds.push(clickedLeftClusterId);
+        const clickedLeftCluster = this.hierClusterData.clustering.row.mergedClusters.get(clickedLeftClusterId);
+        const clickedLeftClusterRowsNames = clickedLeftCluster.children.map((c) => c.name);
+        this.addSelectedRowsOptions(clickedLeftClusterRowsNames, event);
+      } else {
+        delete this.clickedLeftClusterIds;
+      }
+      if (this.clickedClusterIds) {
+        delete this.clickedClusterIds;
+        this.plotDendrogramHclust();
+      } else this.plotDendrogramHclust("left");
+    });
+  }
+  async setHierClusterData(_data = {}) {
+    this.prevServerData = this.currServerData;
+    const [d, twlst] = await this.requestData({});
+    if (d.error) throw d.error;
+    this.currServerData = structuredClone(d);
+    if (!deepEqual(this.prevServerData, this.currServerData)) {
+      delete this.clickedClusterIds;
+      delete this.clickedLeftClusterIds;
+    }
+    const s = this.settings.hierCluster;
+    if (!d.clustering) {
+      if (d.gene) {
+        throw `Cannot do clustering: data is only available for 1 gene (${d.gene}). Try again by adding more genes.`;
+      }
+    }
+    this.hierClusterData = d;
+    const c = this.hierClusterData.clustering;
+    this.setHierColorScale(c);
+    const samples = {};
+    for (const [i, column] of c.col.order.entries()) {
+      samples[column.name] = { sample: column.name };
+      for (const [j, row] of c.row.order.entries()) {
+        const tw = twlst.find((tw2) => tw2.$id === row.name || tw2.id === row.name);
+        const value = c.matrix[j][i];
+        samples[column.name][tw.$id] = {
+          key: tw.term.name,
+          values: [
+            {
+              sample: column.name,
+              dt: TermTypes2Dt[this.state.config.dataType],
+              label: s.termGroupName,
+              // gene: tw.term.name,
+              // chr: tw.term.chr,
+              // pos: `${tw.term.start}-${tw.term.stop}`,
+              value
+              // the color will be computed in matrix.cells, so that
+              // it can get updated even when there are no nonsetting state diff
+            }
+          ]
+        };
+      }
+    }
+    this.hcTermNameOrder = this.settings.hierCluster.sortClusterRows == "asListed" ? twlst.map((t) => t.term.name) : this.settings.hierCluster.sortClusterRows == "byName" ? twlst.map((t) => t.term.name).sort() : dictionaryNumericTypes.has(this.config.dataType) ? c.row.order.map((row) => twlst.find((t) => t.$id == row.name || t.term.id == row.name)?.term.name) : c.row.order.map((row) => twlst.find((t) => t.$id == row.name)?.term.name);
+    if (this.hcTermNameOrder.includes(void 0)) throw `unable to map row.name to term.name`;
+    this.hcTermSorter = (a, b) => {
+      const i = this.hcTermNameOrder.indexOf(a.tw.term.name);
+      const j = this.hcTermNameOrder.indexOf(b.tw.term.name);
+      if (i == -1 && j == -1) return 0;
+      if (i == -1) return 1;
+      if (j == -1) return -1;
+      return i - j;
+    };
+    this.hcSampleNameOrder = c.col.order.map((col) => col.name);
+    this.hcSampleSorter = (a, b) => {
+      const i = this.hcSampleNameOrder.indexOf(a.sample);
+      const j = this.hcSampleNameOrder.indexOf(b.sample);
+      if (i == -1 && j == -1) return 0;
+      if (i == -1) return 1;
+      if (j == -1) return -1;
+      return i - j;
+    };
+    const byTermId = {};
+    for (const tw of twlst) {
+      if (d.byTermId?.[tw.term.name]) byTermId[tw.$id] = d.byTermId[tw.term.name];
+    }
+    this.hierClusterSamples = {
+      refs: { byTermId, bySampleId: d.bySampleId },
+      lst: c.col.order.map((c2) => samples[c2.name]),
+      samples,
+      removedHierClusterTerms: d.removedHierClusterTerms
+    };
+  }
+  async requestData() {
+    const body = this.currRequestOpts?.hierCluster || this.getHCRequestBody(this.state);
+    const twlst = this.hcTermGroup.lst;
+    const data = await dofetch3("termdb/cluster", { body, signal: this.api.getAbortSignal?.() });
+    return [data, twlst];
+  }
+  getHCRequestBody(state) {
+    this.hcTermGroup = this.config.termgroups.find((grp) => grp.type == "hierCluster") || this.termOrder?.find((t) => t.grp.type == "hierCluster")?.grp;
+    const s = state.config.settings.hierCluster;
+    const dictionaryLegendFilter = {
+      type: "tvslst",
+      in: true,
+      join: "and",
+      lst: state.config.legendValueFilter.lst.filter((f) => !f.tvs.legendFilterType)
+    };
+    const terms = this.getClusterRowTermsAsParameter();
+    if (!terms.length) throw "no data";
+    if (!clusterMethodLst.find((i) => i.value == s.clusterMethod)) throw "Invalid cluster method";
+    if (!distanceMethodLst.find((i) => i.value == s.distanceMethod)) throw "Invalid distance method";
+    const body = {
+      genome: state.vocab.genome,
+      dslabel: state.vocab.dslabel,
+      dataType: state.config.dataType,
+      clusterMethod: s.clusterMethod,
+      distanceMethod: s.distanceMethod,
+      zScoreTransformation: s.zScoreTransformation,
+      terms,
+      filter: getNormalRoot(filterJoin([state.filter, dictionaryLegendFilter])),
+      filter0: state.filter0
+    };
+    if (state.config.dataType == "proteomeAbundance") {
+      body.proteomeDetails = {
+        organism: state.config.proteomeDetails?.organism,
+        assay: state.config.proteomeDetails?.assay,
+        cohort: state.config.proteomeDetails?.cohort
+      };
+    }
+    return body;
+  }
+  combineData() {
+    if (!this.hierClusterSamples) return;
+    const d = this.data;
+    const removedHierClusterTerms = this.hierClusterSamples.removedHierClusterTerms;
+    const samples = {};
+    const lst = [];
+    for (const sampleId in this.hierClusterSamples.samples) {
+      const s = this.hierClusterSamples.samples[sampleId];
+      samples[sampleId] = s;
+      lst.push(s);
+      if (sampleId in d.samples) Object.assign(s, d.samples[sampleId]);
+      const _ref_ = this.hierClusterSamples.refs.bySampleId[sampleId] || {};
+      if (!s._ref_) s._ref_ = _ref_;
+      else Object.assign(s._ref_, _ref_);
+    }
+    const t = this.hierClusterSamples.refs.byTermId;
+    for (const $id of Object.keys(t)) {
+      d.refs.byTermId[$id] = Object.assign({}, d.refs.byTermId[$id] || {}, t[$id]);
+    }
+    this.data = { samples, lst, refs: d.refs, removedHierClusterTerms };
+  }
+  setHierColorScale(c) {
+    const hc = this.settings.hierCluster;
+    const scale = linear(colorScaleMap[hc.colorScale].domain, colorScaleMap[hc.colorScale].range).clamp(true);
+    const globalMinMaxes = [];
+    for (const row of c.matrix) {
+      globalMinMaxes.push(...extent(row));
+    }
+    const absMax = Math.min(hc.zScoreCap, Math.max(...extent(globalMinMaxes).map(Math.abs)));
+    const [min, max] = hc.zScoreTransformation ? [-absMax, absMax] : [Math.min(...globalMinMaxes), Math.max(...globalMinMaxes)];
+    this.hierClusterValues = { scale, min, max };
+  }
+  getValueColor(value) {
+    const hc = this.settings.hierCluster;
+    if (hc.zScoreTransformation) {
+      const zScoreCap = this.settings.hierCluster.zScoreCap;
+      return this.hierClusterValues.scale((value - -zScoreCap) / (zScoreCap * 2));
+    } else {
+      return this.hierClusterValues.scale(value / this.hierClusterValues.max);
+    }
+  }
+  /* returns list of gene terms as request parameter, e.g. {gene,chr,start,stop}
+  	request parameter only need term but not tw, as it will simply fetch continuous sample values on terms without transform
+  
+  	use of this function is unfortunate because:
+  		the incomplete migration of {name} to {gene} for gene-based term
+  		geneset edit ui is hardcoded to return {name}
+  		existing plot states contain {name}
+  
+  	!!! migration instruction !!!
+  	- term.name is for display only, if a term is gene-based, it has term.gene=str
+  	- a geneVariant term can be based on a genomic range (and not a gene), in that case it won't have term.gene and cannot be used where gene is expected, e.g. gene-based clustering analysis
+  
+  	*/
+  getClusterRowTermsAsParameter() {
+    const lst = this.hcTermGroup.lst.map(this.opts.app.vocabApi.getTwMinCopy);
+    lst.sort((a, b) => a.term.name < b.term.name ? -1 : 1);
+    return lst;
+  }
+};
+for (const methods of [hierCluster_renderers_exports, hierCluster_interactivity_exports]) {
+  for (const methodName in methods) HierCluster.prototype[methodName] = methods[methodName];
+}
+var hierClusterInit = getCompInit(HierCluster);
+var componentInit = hierClusterInit;
+
+export {
+  HierCluster,
+  hierClusterInit,
+  componentInit
+};
+//# sourceMappingURL=chunk-GIBTGABW.js.map