@sjcrh/proteinpaint-client 2.208.0 → 2.210.0

package/dist/chunk-I25LKYC4.js

@@ -0,0 +1,379 @@
+import {
+  SPANSELECTOR,
+  renderLabelSpans,
+  trackLabelSpanData
+} from "./chunk-C2MCQZWH.js";
+import {
+  fillTermWrapper,
+  termsettingInit
+} from "./chunk-55FABQU2.js";
+import {
+  isNumericTerm
+} from "./chunk-KIAMLQ7S.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.$id);
+      sg.exit().remove();
+      sg.each(self.renderSeries);
+      sg.enter().append("g").attr("class", "sjpp-mass-series-g").attr("data-testid", (d2) => `sjpp-mass-series-g-${d2.tw.term.name}`).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.$id](cell.key) : getRectFill(cell);
+    const s = self.settings.matrix;
+    const rect = select_default(this).attr("x", cell.x || 0).attr("y", cell.y || 0).attr("width", cell.width || self.dimensions.colw).attr("height", "height" in cell ? Math.max(0, cell.height) : s.rowh).attr("shape-rendering", "crispEdges").attr("fill", cell.fill);
+    if (cell.border) {
+      rect.attr("stroke", "white").attr("stroke-width", 0.8);
+    }
+  };
+  self.renderLabels = function(s, l, d, duration) {
+    const relatedSamplesByAncestorId = /* @__PURE__ */ new Map();
+    for (const direction of ["top", "btm", "left", "right"]) {
+      let renderLabel2 = function(lab) {
+        const g = select_default(this);
+        g.attr("transform", side.attr.labelGTransform);
+        if (!g.select(":scope>text").size()) g.append("text");
+        const showContAxis = !side.isGroup && lab.grp?.type !== "hierCluster" && lab.tw?.q?.mode == "continuous";
+        const labelText = side.label(lab);
+        const text = g.select(":scope>text").attr("fill", "#000").attr("data-testid", `sjpp-matrix-label-${direction}`).style("display", side.display || "");
+        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-I25LKYC4.js.map

package/dist/chunk-I25LKYC4.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/matrix/matrix.renderers.js"],
+  "sourcesContent": ["import { select } from 'd3-selection'\nimport { fillTermWrapper, termsettingInit } from '#termsetting'\nimport { isNumericTerm } from '#shared/terms.js'\nimport { trackLabelSpanData, renderLabelSpans, SPANSELECTOR } from './matrix.labelSpans.ts'\n\nexport function setRenderers(self) {\n\tself.render = function () {\n\t\tconst s = self.settings.matrix\n\t\tconst l = self.layout\n\t\tconst d = self.dimensions\n\t\tconst duration = self.dom.svg.attr('width') ? s.duration : 0\n\n\t\tself.dom.clipRect\n\t\t\t.attr('x', d.xOffset - 1)\n\t\t\t.attr('y', 0)\n\t\t\t.attr('width', d.mainw + 3)\n\t\t\t// add 500 so that the column labels are not clipped\n\t\t\t.attr('height', d.mainh + 500)\n\n\t\t// const x = self.type == 'hierCluster' ? self.settings.hierCluster.xDendrogramHeight : 0\n\t\t// const y = self.type == 'hierCluster' ? self.settings.hierCluster.yDendrogramHeight : 0\n\t\t// self.dom.mainG\n\t\t// \t.attr('transform', `translate(${x},${y})`)\n\n\t\tself.renderSerieses(s, l, d, duration)\n\t\tself.renderLabels(s, l, d, duration)\n\t\tself.renderDivideByLabel(s, l, d, duration)\n\n\t\tself.dom.colBeam.attr('width', d.dx).attr('height', d.mainh).style('stroke', s.beamStroke)\n\n\t\tself.dom.rowBeam.attr('width', d.zoomedMainW).attr('height', s.rowh).style('stroke', s.beamStroke)\n\t}\n\n\tself.renderSerieses = function (s, l, d, duration) {\n\t\tif (self.prevUseCanvas != s.useCanvas) {\n\t\t\tself.dom.seriesesG.selectAll('g').remove()\n\t\t}\n\t\tif (s.useCanvas) {\n\t\t\tconst _g = self.dom.seriesesG.selectAll('g')\n\t\t\tconst g = /*(_g.size() && _g) ||*/ self.dom.seriesesG.append('g').datum(this.serieses)\n\t\t\tself.renderCanvas(this.serieses, g, d, s, _g, duration)\n\t\t} else {\n\t\t\tself.dom.seriesesG\n\t\t\t\t//.transition()\n\t\t\t\t//.duration(duration)\n\t\t\t\t.attr('transform', `translate(${d.xOffset + d.seriesXoffset},${d.yOffset})`)\n\n\t\t\tconst sg = self.dom.seriesesG.selectAll('.sjpp-mass-series-g').data(this.serieses, series => series.tw.$id)\n\t\t\tsg.exit().remove()\n\t\t\tsg.each(self.renderSeries)\n\t\t\tsg.enter()\n\t\t\t\t.append('g')\n\t\t\t\t.attr('class', 'sjpp-mass-series-g')\n\t\t\t\t.attr('data-testid', d => `sjpp-mass-series-g-${d.tw.term.name}`)\n\t\t\t\t.style('opacity', 0.001)\n\t\t\t\t.each(self.renderSeries)\n\t\t\t// need to reset imgBox and beam highlighters after rendering to avoid misaligned beam highlighters\n\t\t\tself.mouseout()\n\t\t}\n\t\tself.prevUseCanvas = s.useCanvas\n\t}\n\n\tself.renderSeries = async function (series) {\n\t\tconst s = self.settings.matrix\n\t\tconst d = self.dimensions\n\t\tconst g = select(this)\n\t\tconst duration = g.attr('transform') ? s.duration : 0\n\n\t\tg //.transition()\n\t\t\t//.duration(duration)\n\t\t\t.attr('transform', `translate(${series.x},${series.y})`)\n\t\t\t.style('opacity', 1)\n\t\tconst last = series.cells[series.cells.length - 1]\n\t\tconst height = series.y + last?.y + s.rowh\n\n\t\tconst rects = g\n\t\t\t.selectAll('rect')\n\t\t\t.data(series.cells, cell => cell.sample + ';;' + cell.tw.$id + ';;' + cell.valueIndex)\n\t\trects.exit().remove()\n\t\trects.each(self.renderCell)\n\t\trects.enter().append('rect').each(self.renderCell)\n\t}\n\n\tself.renderCanvas = async function (serieses, g, d, s, _g, duration) {\n\t\tconst pxr = window.devicePixelRatio <= 1 ? 1 : window.devicePixelRatio\n\t\t// TODO: may not need to remove the image???\n\t\tg.selectAll('*').remove()\n\t\tconst width = d.imgW\n\t\tconst height = self.dimensions.mainh\n\t\tconst canvas = window.OffscreenCanvas\n\t\t\t? new OffscreenCanvas(width * pxr, height * pxr)\n\t\t\t: // TODO: no need to support older browser versions???\n\t\t\t  self.dom.holder\n\t\t\t\t\t.append('canvas')\n\t\t\t\t\t.attr('width', pxr * width)\n\t\t\t\t\t.attr('height', pxr * height)\n\t\t\t\t\t.style('opacity', 0)\n\t\t\t\t\t.node()\n\t\tconst ctx = canvas.getContext('2d')\n\t\tctx.imageSmoothingEnabled = false\n\t\tctx.imageSmoothingQuality = 'high'\n\t\t//ctx.lineWidth = 0.5\n\t\t//ctx.setTransform(pxr, 0, 0, pxr, 0, 0)\n\t\tctx.scale(pxr, pxr)\n\t\tfor (const series of serieses) {\n\t\t\tfor (const cell of series.cells) {\n\t\t\t\tself.renderCellWithCanvas(ctx, cell, series, s, d, series.y)\n\t\t\t}\n\t\t}\n\n\t\tif (window.OffscreenCanvas) {\n\t\t\tconst reader = new FileReader()\n\t\t\treader.addEventListener(\n\t\t\t\t'load',\n\t\t\t\t() => {\n\t\t\t\t\t// remove a previously rendered image, if applicable, right before replacing it\n\t\t\t\t\t// so that there will be no flicker on update\n\t\t\t\t\t_g?.remove()\n\t\t\t\t\tself.dom.seriesesG\n\t\t\t\t\t\t//.transition()\n\t\t\t\t\t\t//.duration(duration)\n\t\t\t\t\t\t.attr('transform', `translate(${d.xOffset + d.seriesXoffset},${d.yOffset})`)\n\n\t\t\t\t\tg.selectAll('image').remove()\n\t\t\t\t\tg.append('image')\n\t\t\t\t\t\t.attr('xlink:href', reader.result)\n\t\t\t\t\t\t.attr('x', d.xMin) //d.seriesXoffset + d.xMin) //d.xMin) // + d.xOffset) //d.seriesXoffset - d.xMin)\n\t\t\t\t\t\t.attr('width', width)\n\t\t\t\t\t\t.attr('height', height)\n\t\t\t\t},\n\t\t\t\tfalse\n\t\t\t)\n\t\t\tconst blob = await canvas.convertToBlob({ quality: 1 })\n\t\t\tconst dataURL = reader.readAsDataURL(blob)\n\t\t} else {\n\t\t\t_g?.remove()\n\t\t\tself.dom.seriesesG\n\t\t\t\t//.transition()\n\t\t\t\t//.duration(duration)\n\t\t\t\t.attr('transform', `translate(${d.xOffset + d.seriesXoffset},${d.yOffset})`)\n\n\t\t\tconst dataURL = canvas.toDataURL()\n\t\t\tconst ratio = window.devicePixelRatio * window.devicePixelRatio\n\t\t\tg.append('image').attr('width', width).attr('height', height).attr('xlink:href', dataURL)\n\t\t\tif (!window.OffscreenCanvas) canvas.remove()\n\t\t}\n\t\t// need to reset imgBox and beam highlighters after rendering to avoid misaligned beam highlighters\n\t\tself.mouseout()\n\t}\n\n\tself.renderCellWithCanvas = function (ctx, cell, series, s, d, _y) {\n\t\tif (!cell.fill)\n\t\t\tcell.fill = cell.$id in self.colorScaleByTermId ? self.colorScaleByTermId[cell.$id](cell.key) : getRectFill(cell)\n\t\tconst x = cell.x ? cell.x - d.xMin : 0\n\t\tconst y = _y ? _y + cell.y : cell.y || 0\n\t\tconst width = s.useMinPixelWidth ? Math.max(cell.width || d.colw, d.pxw) : cell.width || d.colw\n\t\tconst height = 'height' in cell ? cell.height : s.rowh\n\t\tctx.fillStyle = cell.fill\n\t\tctx.fillRect(x, y, width, height)\n\n\t\tconst borderWidth = Math.min(width, height) * 0.1\n\t\tif (cell.border) {\n\t\t\t// Draw the border\n\t\t\tctx.lineWidth = borderWidth // Set border width, you can adjust this value\n\t\t\tctx.strokeStyle = 'white' // Set the border color, you can use any color\n\t\t\tctx.strokeRect(x, y, width, height) // Draw the border\n\t\t}\n\t}\n\n\tself.renderCell = function (cell) {\n\t\tif (!cell.fill)\n\t\t\tcell.fill = cell.$id in self.colorScaleByTermId ? self.colorScaleByTermId[cell.$id](cell.key) : getRectFill(cell)\n\t\tconst s = self.settings.matrix\n\t\tconst rect = select(this)\n\t\t\t//.transition()\n\t\t\t// TODO: use s.duration if there is a way to avoid any remaining glitchy transitions\n\t\t\t// using the cell index in the .data() bind function seems to fix glitches in split cells,\n\t\t\t// but cells with overriden values flashes during a transition\n\t\t\t//.duration(0) //'x' in cell ? s.duration : 0)\n\t\t\t.attr('x', cell.x || 0)\n\t\t\t.attr('y', cell.y || 0)\n\t\t\t.attr('width', cell.width || self.dimensions.colw)\n\t\t\t.attr('height', 'height' in cell ? Math.max(0, cell.height) : s.rowh)\n\t\t\t.attr('shape-rendering', 'crispEdges')\n\t\t\t.attr('fill', cell.fill)\n\t\tif (cell.border) {\n\t\t\trect.attr('stroke', 'white').attr('stroke-width', 0.8)\n\t\t}\n\t}\n\n\tself.renderLabels = function (s, l, d, duration) {\n\t\tconst relatedSamplesByAncestorId = new Map()\n\n\t\tfor (const direction of ['top', 'btm', 'left', 'right']) {\n\t\t\tconst side = l[direction]\n\t\t\tside.box\n\t\t\t\t.style('display', side.display || '')\n\t\t\t\t//.transition()\n\t\t\t\t//.duration(duration)\n\t\t\t\t.attr('transform', side.attr.boxTransform)\n\n\t\t\tconst labels = side.box.selectAll('.sjpp-matrix-label').data(side.data, side.key)\n\t\t\tlabels.exit().remove()\n\t\t\tlabels.each(renderLabel)\n\t\t\tlabels.enter().append('g').attr('class', 'sjpp-matrix-label').each(renderLabel)\n\n\t\t\t// unconditionally clear any previously rendered ancestor spans from this side box;\n\t\t\t// renderLabelSpans() below re-adds them only when applicable, so stale spans are\n\t\t\t// removed when the feature is disabled, the chart is transposed (sample labels move\n\t\t\t// to a different side box), or the chart is a hierCluster\n\t\t\tside.box.selectAll(SPANSELECTOR).remove()\n\n\t\t\t// ancestor spans are a matrix-only feature; hierCluster orders samples by the\n\t\t\t// dendrogram, not ancestry (see the chartType guards in matrix.groups/matrix.sort)\n\t\t\tif (self.config.chartType == 'matrix' && s.sortBySampleAncestry && side.prefix == 'sample')\n\t\t\t\trenderLabelSpans(relatedSamplesByAncestorId, side, d)\n\n\t\t\tfunction renderLabel(lab) {\n\t\t\t\tconst g = select(this)\n\t\t\t\t//const textduration = g.attr('transform') ? duration : 0\n\t\t\t\tg //.transition()\n\t\t\t\t\t//.duration(textduration)\n\t\t\t\t\t.attr('transform', side.attr.labelGTransform)\n\n\t\t\t\tif (!g.select(':scope>text').size()) g.append('text')\n\t\t\t\tconst showContAxis = !side.isGroup && lab.grp?.type !== 'hierCluster' && lab.tw?.q?.mode == 'continuous'\n\t\t\t\tconst labelText = side.label(lab)\n\t\t\t\t// added display style here because visibilility of these text elements were not being\n\t\t\t\t// properly received in webkit playwright\n\t\t\t\tconst text = g\n\t\t\t\t\t.select(':scope>text')\n\t\t\t\t\t.attr('fill', '#000')\n\t\t\t\t\t.attr('data-testid', `sjpp-matrix-label-${direction}`)\n\t\t\t\t\t.style('display', side.display || '')\n\n\t\t\t\tlet continuousBarHAdjust\n\t\t\t\tconst twSpecificSettings = self.config.settings.matrix.twSpecificSettings\n\t\t\t\tconst twSettingsBarH = twSpecificSettings[lab.tw?.$id]?.contBarH\n\t\t\t\tif (twSettingsBarH && s.barh) continuousBarHAdjust = (twSettingsBarH - s.barh) * 0.5\n\n\t\t\t\ttext\n\t\t\t\t\t//.transition()\n\t\t\t\t\t//.duration(textduration)\n\t\t\t\t\t.attr(\n\t\t\t\t\t\t'display',\n\t\t\t\t\t\tlab.grp?.type === 'hierCluster' && s.clusterRowh < 6\n\t\t\t\t\t\t\t? 'none'\n\t\t\t\t\t\t\t: side.attr.fontSize < 6 || labelText === 'configure'\n\t\t\t\t\t\t\t? 'none'\n\t\t\t\t\t\t\t: ''\n\t\t\t\t\t)\n\t\t\t\t\t.attr('font-size', lab.grp?.type === 'hierCluster' ? Math.max(4, s.clusterRowh - 4) : side.attr.fontSize)\n\t\t\t\t\t.attr('text-anchor', side.attr.labelAnchor)\n\t\t\t\t\t.attr(\n\t\t\t\t\t\t'transform',\n\t\t\t\t\t\tside.attr.labelTransform + (continuousBarHAdjust ? ` translate(0,${continuousBarHAdjust})` : '')\n\t\t\t\t\t)\n\t\t\t\t\t.attr('cursor', 'pointer')\n\t\t\t\t\t.attr(side.attr.textpos.coord, side.attr.textpos.factor * (showContAxis ? 30 : 0))\n\n\t\t\t\tif (!Array.isArray(labelText)) {\n\t\t\t\t\ttext.text(labelText)\n\t\t\t\t\ttext.attr(\n\t\t\t\t\t\t'y',\n\t\t\t\t\t\tlab.grp?.type !== 'hierCluster' && lab.tw?.q?.mode == 'continuous'\n\t\t\t\t\t\t\t? 10\n\t\t\t\t\t\t\t: lab.grp?.type === 'hierCluster'\n\t\t\t\t\t\t\t? 0.1 * s.clusterRowh\n\t\t\t\t\t\t\t: 0\n\t\t\t\t\t)\n\t\t\t\t\tif (lab.grp?.type !== 'hierCluster' && lab.tw?.q?.mode == 'continuous') text.attr('x', -20)\n\t\t\t\t} else {\n\t\t\t\t\t// this is required because labelText in the if-condition is not wrapped in tspan,\n\t\t\t\t\t// so the text.selectAll('tspan') below will not remove previous label\n\t\t\t\t\ttext.text('')\n\n\t\t\t\t\tconst tspan = text.selectAll('tspan').data(labelText)\n\t\t\t\t\t//tspan.exit().remove()\n\t\t\t\t\t//tspan.attr('dx', getTspanDx).attr('font-size', getTspanFontSize).text(getTspanText)\n\t\t\t\t\ttspan\n\t\t\t\t\t\t.enter()\n\t\t\t\t\t\t.append('tspan')\n\t\t\t\t\t\t.attr('class', getTspanCls)\n\t\t\t\t\t\t.attr('dx', getTspanDx)\n\t\t\t\t\t\t.attr('font-size', getTspanFontSize)\n\t\t\t\t\t\t.text(getTspanText)\n\t\t\t\t}\n\n\t\t\t\ttext\n\t\t\t\t\t.on('mouseover', labelText === 'configure' ? () => text.attr('opacity', 0.5) : null)\n\t\t\t\t\t.on('mouseout', labelText === 'configure' ? () => text.attr('opacity', 0) : null)\n\n\t\t\t\tconst hasAxis = g.select('.sjpp-matrix-cell-axis').size() && true\n\t\t\t\tif (showContAxis && labelText) {\n\t\t\t\t\tif (!hasAxis) {\n\t\t\t\t\t\tg.append('g').attr('class', 'sjpp-matrix-cell-axis').attr('shape-rendering', 'crispEdges')\n\t\t\t\t\t}\n\t\t\t\t\tconst axisg = g.select('.sjpp-matrix-cell-axis')\n\t\t\t\t\taxisg.selectAll('*').remove()\n\t\t\t\t\tconst domain = [lab.counts.maxval, lab.counts.minval]\n\t\t\t\t\tif (s.transpose) domain.reverse()\n\n\t\t\t\t\tconst twSpecificSettings = self.config.settings.matrix.twSpecificSettings\n\t\t\t\t\tconst twSettings = twSpecificSettings[lab.tw.$id]\n\t\t\t\t\tconst x = !s.transpose ? 0 : twSettings.contBarGap - 1 - lab.labelOffset\n\t\t\t\t\tconst y = !s.transpose ? twSettings.contBarGap - 1 - lab.labelOffset : 0\n\t\t\t\t\taxisg\n\t\t\t\t\t\t.attr('shape-rendering', 'crispEdges')\n\t\t\t\t\t\t.attr('transform', `translate(${x},${y})`)\n\t\t\t\t\t\t.call(side.attr.axisFxn(lab.scales.full.domain(lab.scales.tickValues)).tickValues(lab.scales.tickValues))\n\t\t\t\t} else if (hasAxis) {\n\t\t\t\t\tg.select('.sjpp-matrix-cell-axis').remove()\n\t\t\t\t}\n\n\t\t\t\t// only track ancestry span data (which does a per-label getBBox) when the\n\t\t\t\t// feature is enabled and applicable; matches the renderLabelSpans() guard\n\t\t\t\t// above, so a disabled plot (or a hierCluster) does no DOM measurement here\n\t\t\t\tif (self.config.chartType == 'matrix' && s.sortBySampleAncestry && side.prefix == 'sample')\n\t\t\t\t\ttrackLabelSpanData(lab, side, direction, text, relatedSamplesByAncestorId)\n\t\t\t}\n\n\t\t\tfunction getTspanCls(d) {\n\t\t\t\treturn d.cls\n\t\t\t}\n\t\t\tfunction getTspanDx(d) {\n\t\t\t\treturn d.dx\n\t\t\t}\n\t\t\tfunction getTspanFontSize(d) {\n\t\t\t\treturn d.fontSize || side.attr.fontSize\n\t\t\t}\n\t\t\tfunction getTspanText(d) {\n\t\t\t\treturn d.text\n\t\t\t}\n\t\t}\n\t}\n\n\tself.colLabelGTransform = (lab, grpIndex) => {\n\t\tconst s = self.settings.matrix\n\t\tconst d = self.dimensions\n\t\tlab.labelOffset = 0.8 * d.colw\n\t\tconst x = lab.grpIndex * s.colgspace + lab.totalIndex * d.dx + lab.labelOffset + lab.totalHtAdjustments\n\t\tconst y = 0 //lab.tw?.q?.mode == 'continuous' ? -30 : 0\n\t\treturn `translate(${x + d.seriesXoffset},${y})`\n\t}\n\n\tself.colGrpLabelGTransform = (lab, grpIndex) => {\n\t\tconst s = self.settings.matrix\n\t\tconst d = self.dimensions\n\t\tconst len = (lab.processedLst || lab.grp.lst).length\n\t\tconst x =\n\t\t\tlab.grpIndex * s.colgspace +\n\t\t\tlab.prevGrpTotalIndex * d.dx +\n\t\t\t(len * d.dx) / 2 +\n\t\t\ts.grpLabelFontSize / 2 +\n\t\t\tlab.totalHtAdjustments\n\t\treturn `translate(${x + d.seriesXoffset},0)`\n\t}\n\n\tself.rowLabelGTransform = (lab, grpIndex) => {\n\t\tconst s = self.settings.matrix\n\t\tconst d = self.dimensions\n\t\tconst x = 0 // lab.tw?.q?.mode == 'continuous' ? -30 : 0\n\t\tlab.labelOffset = 0.7 * (lab.grp.type == 'hierCluster' ? s.clusterRowh : s.rowh)\n\t\tconst y = lab.grpIndex * s.rowgspace + lab.totalIndex * d.dy + lab.labelOffset + lab.totalHtAdjustments\n\t\treturn `translate(${x},${y})`\n\t}\n\n\tself.rowGrpLabelGTransform = (lab, grpIndex) => {\n\t\tconst s = self.settings.matrix\n\t\tconst d = self.dimensions\n\t\tconst len = (lab.processedLst || lab.grp.lst).length\n\t\tconst x = lab.tw?.q?.mode == 'continuous' ? 20 : 0\n\t\tconst y =\n\t\t\tlab.grpIndex * s.rowgspace +\n\t\t\tlab.prevGrpTotalIndex * d.dy +\n\t\t\t(len * d.dy) / 2 +\n\t\t\ts.grpLabelFontSize / 2 +\n\t\t\tlab.totalHtAdjustments\n\t\treturn `translate(${x},${y})`\n\t}\n\n\tself.rowAxisGTransform = (lab, grpIndex) => {\n\t\tconst s = self.settings.matrix\n\t\tconst d = self.dimensions\n\t\tconst x = 0 // lab.tw?.q?.mode == 'continuous' ? -30 : 0\n\t\tconst y = lab.grpIndex * s.rowgspace + lab.totalIndex * d.dy + 0.7 * s.rowh + lab.totalHtAdjustments\n\t\treturn `translate(${x},${y})`\n\t}\n\n\tself.renderDivideByLabel = async (s, l, d) => {\n\t\tself.dom.mainG.selectAll('.sjpp-matrix-divide-by-label').remove()\n\t\tif (!self.config.divideBy) return\n\t\tconst name = self.config.divideBy?.term.name || ''\n\t\tconst text = name.length <= s.rowlabelmaxchars ? name : name.slice(0, s.rowlabelmaxchars) + '\u2026'\n\t\tconst sides = !s.transpose ? [l.left, l.right] : [l.top, l.bottom]\n\t\tconst box = sides.find(d => !d.isGroup)?.box\n\t\tconst y = (s.collabelpos == 'top' ? d.mainh + s.collabelmaxchars : -s.collabelmaxchars) + 8\n\t\tconst anchor = s.rowlabelpos == 'left' ? 'end' : 'start'\n\t\tconst cl = s.controlLabels\n\n\t\tconst gNote = box.append('g').attr('class', 'sjpp-matrix-divide-by-label').attr('transform', `translate(0, ${y})`)\n\n\t\tgNote\n\t\t\t.append('text')\n\t\t\t.attr('text-anchor', anchor)\n\t\t\t.attr('font-style', 'italic')\n\t\t\t.attr('y', -20)\n\t\t\t.text(`${cl.Samples} grouped by`)\n\n\t\tconst g = box\n\t\t\t.datum({ tw: self.config.divideBy })\n\t\t\t.append('g')\n\t\t\t.attr('class', 'sjpp-matrix-divide-by-label')\n\t\t\t.attr('transform', `translate(0, ${y})`)\n\t\t\t.on('click', (event, d) => {\n\t\t\t\tpill.showMenu(event, textElem.node())\n\t\t\t})\n\n\t\tconst textElem = g.append('text').attr('text-anchor', anchor).attr('font-weight', 600).text(text)\n\n\t\tg.append('title').text(`${cl.Samples} are grouped by this gene or variable. Click to edit.`)\n\n\t\tconst customMenuOptions = []\n\t\tconst tvsKey = isNumericTerm(self.config.divideBy.term) ? 'ranges' : 'values'\n\t\tif (\n\t\t\tself.config.legendValueFilter.lst?.find(\n\t\t\t\tl => l.legendGrpName == self.config.divideBy.term.id || l.legendGrpName == self.config.divideBy.term.name\n\t\t\t)?.tvs[tvsKey]?.length\n\t\t) {\n\t\t\tcustomMenuOptions.push({ label: `Show filtered ${cl.samples}`, callback: self.showDeletedSampleGroups })\n\t\t}\n\n\t\tconst pill = await termsettingInit({\n\t\t\tmenuOptions: '{edit,replace,remove}',\n\t\t\t//numericEditMenuVersion: opts.numericEditMenuVersion,\n\n\t\t\tcustomMenuOptions, //custom menu options other than menuOptions\n\t\t\tvocabApi: self.app.vocabApi,\n\t\t\tvocab: self.state.vocab,\n\t\t\t//activeCohort: opts.state?.activeCohort,\n\t\t\tholder: g,\n\t\t\tdebug: self.opts.debug,\n\t\t\tusecase: { target: 'matrix' },\n\t\t\tgetBodyParams: () => {\n\t\t\t\tconst currentGeneNames = self.termOrder\n\t\t\t\t\t.filter(t => t.tw.term.type === 'geneVariant')\n\t\t\t\t\t.map(t =>\n\t\t\t\t\t\tt.tw.term.chr ? `${t.tw.term.chr}:${t.tw.term.start}-${t.tw.term.stop}` : t.tw.term.gene || t.tw.term.name\n\t\t\t\t\t) // TODO term.gene replaces term.name\n\t\t\t\tif (currentGeneNames.length) return { currentGeneNames }\n\t\t\t\treturn {}\n\t\t\t},\n\t\t\tcallback: async tw => {\n\t\t\t\t// showing \"processing data ...\"\" before pill is set\n\t\t\t\tif (self.dom.loadingDiv && self.dom.svg) {\n\t\t\t\t\tself.dom.loadingDiv.selectAll('*').remove()\n\t\t\t\t\tself.dom.loadingDiv.html('').style('display', '').style('position', 'relative').style('left', '45%')\n\t\t\t\t\tself.dom.loadingDiv.html('Processing data ...')\n\t\t\t\t\tself.dom.svg.style('opacity', 0.1).style('pointer-events', 'none')\n\t\t\t\t}\n\t\t\t\t// data is object with only one needed attribute: q, never is null\n\t\t\t\tif (tw && !tw.q) throw 'data.q{} missing from pill callback'\n\t\t\t\tif (tw?.term && isNumericTerm(tw.term)) {\n\t\t\t\t\t// any numeric term should be discrete when used as divideBy term\n\t\t\t\t\t// tw is missing when dividedBy term deleted\n\t\t\t\t\ttw.q = { ...tw.q, mode: 'discrete' }\n\t\t\t\t}\n\t\t\t\tif (tw) await fillTermWrapper(tw, self.app.vocabApi)\n\t\t\t\tawait pill.main(tw ? tw : { term: null, q: null })\n\t\t\t\tbox.datum({ tw })\n\t\t\t\tself.app.dispatch({\n\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\tid: self.id,\n\t\t\t\t\tconfig: {\n\t\t\t\t\t\tdivideBy: tw,\n\t\t\t\t\t\tlegendValueFilter: self.mayRemoveTvsEntry(self.config.divideBy)\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t\t}\n\t\t})\n\t\tconst arg = {\n\t\t\tterm: self.config.divideBy.term,\n\t\t\tq: self.config.divideBy.q\n\t\t}\n\t\tif (self.config.divideBy.$id) arg.$id = self.config.divideBy.$id\n\t\tpill.main(arg)\n\t}\n\n\tself.adjustSvgDimensions = async function (prevTranspose) {\n\t\tconst s = self.settings.matrix\n\t\tconst hc = self.settings.hierCluster || {}\n\t\tconst l = self.layout\n\t\tconst hcHeight = !hc.yDendrogramHeight ? 0 : hc.yDendrogramHeight + (l.top.display === 'none' ? 0 : 10)\n\t\tconst hcWidth = hc.xDendrogramHeight || 0\n\t\tconst d = self.dimensions\n\t\tconst duration = self.dom.svg.attr('width') ? s.duration : 0\n\n\t\t// wait for labels to render; when transposing, must wait for\n\t\t// the label rotation to end before measuring the label height and width\n\t\tawait sleep(prevTranspose == s.transpose ? duration : s.duration)\n\n\t\t// these are the label boxes\n\t\tconst topBox = l.top.box.node().getBBox()\n\t\tconst btmBox = l.btm.box.node().getBBox()\n\t\tconst leftBox = l.left.box.node().getBBox()\n\t\tconst rtBox = l.right.box.node().getBBox()\n\t\tconst legendBox = self.dom.legendG.node().getBBox()\n\t\tconst seriesBox = self.dom.seriesesG.node().getBBox()\n\n\t\td.extraWidth = leftBox.width + rtBox.width + s.margin.left + s.margin.right + s.rowlabelgap * 2\n\t\td.extraHeight = topBox.height + btmBox.height + s.margin.top + s.margin.bottom + s.collabelgap * 2\n\t\td.svgw = d.mainw + d.extraWidth + hcWidth\n\t\td.svgh = d.mainh + d.extraHeight + legendBox.height + 20 + s.scrollHeight + hcHeight\n\t\tself.dom.svg\n\t\t\t//.transition()\n\t\t\t//.duration(duration)\n\t\t\t.attr('width', d.svgw)\n\t\t\t.attr('height', d.svgh)\n\n\t\t//calculate the max gene label\n\t\tlet maxLabelWidth = self.type == 'hierCluster' ? 0 : leftBox.width,\n\t\t\tmaxLabelNumChars = 0\n\t\tif (hc.xDendrogramHeight) {\n\t\t\tself.dom.termLabelG.selectAll('.sjpp-matrix-label').each(function (d) {\n\t\t\t\tif (d.grp.type !== 'hierCluster') return\n\t\t\t\t// TODO: may enable this optimization to only detect the label box width\n\t\t\t\t//       if the text length difference is likely to affect the width\n\t\t\t\t//       DOM measurements like getBBox() may affect performance if there are lots of labels\n\t\t\t\t// if (d.label.length < maxLabelNumChars - 10) return\n\t\t\t\tconst box = this.getBBox()\n\t\t\t\tif (box.width > maxLabelWidth) {\n\t\t\t\t\tmaxLabelWidth = box.width\n\t\t\t\t\tmaxLabelNumChars = d.label.length\n\t\t\t\t}\n\t\t\t})\n\t\t}\n\n\t\t// note: two leftBox.width terms cancels to zero\n\t\tconst x = -l.left.offset + hcWidth + maxLabelWidth\n\t\t// with hierCluster:\n\t\t// in case the term dendrograms + max term label width is less than the leftBox.width of all row labels,\n\t\t// then the mainG and top/left dendrograms must be offset have an additional offset based on the difference\n\t\tconst xAdjust = !hc.xDendrogramHeight ? 0 : Math.max(leftBox.width - (hc.xDendrogramHeight + maxLabelWidth), 0)\n\t\tconst y = (l.top.display == 'none' ? 0 : topBox.height) - l.top.offset + hcHeight\n\t\tself.dom.mainG\n\t\t\t//.transition()\n\t\t\t//.duration(duration)\n\t\t\t.attr('transform', `translate(${x + xAdjust},${y})`)\n\n\t\tself.dom.clipRect\n\t\t\t// the cliprect has to be moved upwards, plus increased height to that adjustment value,\n\t\t\t// in order to display all characters of every column/group label\n\t\t\t.attr('y', -y)\n\t\t\t// add 500 so that the column labels are not clipped\n\t\t\t.attr('height', d.mainh + 500 + y)\n\n\t\t// this position is based on layout.btm.attr.boxTransform, plus box height and margins\n\t\tconst legendX = d.xOffset + (s.transpose ? 20 : 0)\n\t\tconst legendY = d.yOffset + d.mainh + s.collabelgap + (l.btm.display == 'none' ? 0 : btmBox.height) + 20\n\n\t\tself.dom.legendG\n\t\t\t//.transition()\n\t\t\t//.duration(duration)\n\t\t\t.attr('transform', `translate(${legendX},${legendY})`)\n\n\t\tif (hc.xDendrogramHeight) {\n\t\t\tconst dendroX = maxLabelWidth + xAdjust - l.left.offset + d.xOffset - d.dx / 2\n\t\t\tself.dom.hcClipRect\n\t\t\t\t.attr('x', dendroX + hcWidth + d.dx / 2)\n\t\t\t\t.attr('y', 0)\n\t\t\t\t.attr('width', d.mainw + 3)\n\t\t\t\t// add 500 so that the column labels are not clipped\n\t\t\t\t.attr('height', d.mainh + hc.yDendrogramHeight + 500)\n\n\t\t\t// for easy reference when scrolling interactively\n\t\t\tself.topDendroX = dendroX + d.seriesXoffset\n\t\t\tself.dom.topDendrogram.attr('transform', `translate(${self.topDendroX}, 0)`)\n\t\t\tconst y = l.top.display == 'none' ? 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+  "names": ["d", "renderLabel", "getTspanCls", "getTspanDx", "getTspanFontSize", "getTspanText", "twSpecificSettings", "l", "y"]
+}