@sjcrh/proteinpaint-client 2.200.0 → 2.202.0

package/dist/chunk-MKPU5TWN.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../termsetting/handlers/NumericDensity.ts"],
+  "sourcesContent": ["import type { TermSetting } from '../TermSetting.ts'\nimport type { NumRegularBin, NumCustomBins, NumCont, NumSpline } from '#tw'\nimport type { NumericBin } from '#types'\nimport { violinRenderer } from '#dom'\nimport { select, pointer, type BaseType } from 'd3-selection'\nimport { scaleLinear, drag as d3drag } from 'd3'\nimport { getValueConversionFactor } from '#shared/helpers.js'\n//import { get_bin_label, get_bin_range_equation } from '#shared/termdb.bins.js'\n\nexport type BoundaryOpts = {\n\tvalues: BoundaryValue[]\n\tcallback: (d: DraggedLineData, value: number) => void\n}\n\nexport type BoundaryValue = {\n\tx: number\n\tisDraggable: boolean\n\tmovesWithLineIndex?: number\n\tisLastVisibleLine?: boolean\n}\n\nexport type LineData = BoundaryValue & {\n\tscaledX: number\n\tindex: number\n}\n\nexport type DraggedLineData = LineData & {\n\tdraggedX?: number\n\tstart?: number\n\tend?: number\n}\n\nexport class NumericDensity {\n\ttermsetting: TermSetting\n\topts: any // TODO\n\ttw: NumRegularBin | NumCustomBins | NumCont | NumSpline\n\n\tdom: {\n\t\t[name: string]: any\n\t} = {}\n\t// WeakMap allows deletion of value when the object/DOM key is deleted,\n\t// so better for avoiding memory leak\n\tvrByDiv: WeakMap<HTMLElement, any> = new WeakMap()\n\tvr!: violinRenderer\n\tdensity_data!: any\n\tranges: NumericBin[] = []\n\tno_density_data = false\n\tbrushes: any[] = []\n\txscale!: any\n\tplot_size: {\n\t\twidth: number\n\t\theight: number\n\t\txpad: number\n\t\typad: number\n\t\tradius: number\n\t} = {\n\t\twidth: 500,\n\t\theight: 100,\n\t\txpad: 10,\n\t\typad: 20,\n\t\tradius: 8\n\t}\n\n\tconstructor(opts) {\n\t\tthis.opts = opts\n\t\tthis.termsetting = opts.termsetting\n\t\tthis.tw = opts.termsetting.tw\n\t}\n\n\t/* the boundary values exchanged with the bin/knot editors, and the domain of this.xscale, are in\n\tthe term's user-facing unit; density_data is in the unit the values are stored in. only the two\n\tgetters below cross that line, to put the plot's endpoints in the same unit as those values.\n\n\tthey multiply instead of calling toUserUnit(), which rounds: rounding is right for a number shown\n\tin an input, but a rounded domain endpoint distorts every scaled x by up to half of the last shown\n\tdigit, and collapses the domain outright when the converted range is smaller than that (a stored\n\trange of under 2 days at scaleFactor=1/365.25). it would also disagree with violinRenderer, whose\n\taxis this plot's lines overlay and which scales its own domain unrounded */\n\tget scaleFactor() {\n\t\treturn getValueConversionFactor(this.tw.term)\n\t}\n\n\tget displayMin() {\n\t\treturn this.density_data.min * this.scaleFactor\n\t}\n\n\tget displayMax() {\n\t\treturn this.density_data.max * this.scaleFactor\n\t}\n\n\tasync setData() {\n\t\t//if (this.density_data) return this.density_data\n\t\tconst self = this.termsetting\n\t\tconst d = await self.vocabApi.getViolinBox(\n\t\t\t{\n\t\t\t\tplotType: 'violin',\n\t\t\t\ttw: { type: self.tw.type, term: self.term, q: self.q },\n\t\t\t\tsvgw: this.plot_size.width,\n\t\t\t\tradius: this.plot_size.radius,\n\t\t\t\tfilter: self.filter\n\t\t\t},\n\t\t\tself.opts.getBodyParams?.()\n\t\t)\n\t\tif (d.error) throw d\n\t\tthis.density_data = d\n\t\treturn this.density_data\n\t}\n\n\tasync showViolin(div, boundaryOpts?) {\n\t\tawait this.setData()\n\n\t\tif (!this.vrByDiv.has(div)) {\n\t\t\tdiv.style('padding', '5px').selectAll('*').remove()\n\t\t\tconst loadingDiv = div\n\t\t\t\t.append('div')\n\t\t\t\t.style('padding', '10px')\n\t\t\t\t.style('text-align', 'center')\n\t\t\t\t.html('Getting distribution data ...<br/>')\n\n\t\t\tconst densityDiv = div.append('div')\n\t\t\tloadingDiv.remove()\n\t\t\tconst vr = new violinRenderer({\n\t\t\t\tholder: densityDiv,\n\t\t\t\trd: this.density_data,\n\t\t\t\twidth: this.plot_size.width,\n\t\t\t\theight: this.plot_size.height,\n\t\t\t\tradius: this.plot_size.radius,\n\t\t\t\t// axis ticks are labeled in the term's user-facing unit, e.g. years and not days\n\t\t\t\tscaleFactor: this.scaleFactor\n\t\t\t})\n\t\t\tthis.vrByDiv.set(div, vr)\n\t\t}\n\n\t\tthis.vr = this.vrByDiv.get(div)\n\t\tthis.dom.svg = this.vr.svg\n\t\tthis.vr.render()\n\t\tif (boundaryOpts) await this.setBinLines(boundaryOpts)\n\n\t\treturn this.density_data\n\t}\n\n\tasync setBinLines(boundaryOpts) {\n\t\tif (this.density_data.max == this.density_data.min) {\n\t\t\tthis.handleNoDensity()\n\t\t} else {\n\t\t\t// svg for range plot\n\t\t\t// const div = self.q.mode == 'spline' ? self.dom.knots_div : self.dom.bins_div\n\t\t\t//this.vr.render()\n\n\t\t\t// add binsize_g for termsetting lines\n\t\t\tif (this.dom.binsize_g) this.dom.binsize_g.selectAll('*').remove()\n\t\t\tthis.dom.binsize_g = this.dom.svg\n\t\t\t\t.append('g')\n\t\t\t\t.attr('transform', `translate(${this.plot_size.xpad}, ${this.plot_size.ypad})`)\n\t\t\t\t.attr('class', 'binsize_g')\n\n\t\t\t// boundary values come from the editors in the user-facing unit, so the domain is too\n\t\t\tconst maxvalue = this.displayMax\n\t\t\tconst minvalue = this.displayMin\n\n\t\t\tthis.xscale = scaleLinear()\n\t\t\t\t.domain([minvalue, maxvalue])\n\t\t\t\t.range([this.plot_size.xpad, this.plot_size.width + this.plot_size.xpad])\n\n\t\t\tthis.ranges = []\n\t\t\tthis.brushes = []\n\t\t\tthis.renderBinLines(boundaryOpts)\n\t\t}\n\t}\n\n\thandleNoDensity() {\n\t\tthis.no_density_data = true\n\t\tthis.ranges = []\n\t\tthis.brushes = []\n\t}\n\n\trenderBinLines(boundaryOpts: BoundaryOpts) {\n\t\t//this.boundaryOpts = boundaryOpts\n\t\tconst { plot_size, tw, xscale, scaleFactor } = this\n\t\tif (!this.density_data) throw `Missing .density_data [density.ts, renderBinLines()]`\n\t\tconst scaledMinX = Math.round(this.xscale(this.displayMin))\n\t\tconst scaledMaxX = Math.round(this.xscale(this.displayMax))\n\t\tconst lines: DraggedLineData[] = []\n\t\tfor (const [index, v] of boundaryOpts.values.entries()) {\n\t\t\tlines.push({ ...v, index, scaledX: Math.round(this.xscale(v.x)) })\n\t\t}\n\t\tconst lastVisibleLine = lines.find(l => l.isLastVisibleLine)\n\t\tconst lastVisibleScaledX = lastVisibleLine ? lastVisibleLine.scaledX : scaledMaxX\n\t\tconst dragger = d3drag().on('drag', onDrag).on('end', onDrag)\n\n\t\tthis.dom.binsize_g.selectAll('line').remove()\n\t\tthis.dom.binsize_g\n\t\t\t.selectAll('line')\n\t\t\t.data(lines)\n\t\t\t.enter()\n\t\t\t.append('line')\n\t\t\t.style('stroke', (d: LineData) => (d.isDraggable ? '#cc0000' : '#555'))\n\t\t\t.style('stroke-width', 1)\n\t\t\t.attr('x1', (d: LineData) => d.scaledX)\n\t\t\t.attr('y1', 0)\n\t\t\t.attr('x2', (d: LineData) => d.scaledX)\n\t\t\t.attr('y2', plot_size.height)\n\t\t\t.style('cursor', (d: LineData) => (d.isDraggable ? 'ew-resize' : ''))\n\t\t\t.attr('display', (d: LineData) => (!d.isDraggable && d.scaledX > lastVisibleScaledX ? 'none' : ''))\n\t\t\t.on('mouseover', function (this: SVGLineElement, _, d: LineData) {\n\t\t\t\tif (d.isDraggable) select(this).style('stroke-width', 3)\n\t\t\t})\n\t\t\t.on('mouseout', function (this: BaseType) {\n\t\t\t\tselect(this).style('stroke-width', 1)\n\t\t\t})\n\t\t\t.each(function (this: Element, d: LineData) {\n\t\t\t\tif (d.isDraggable) select(this).call(dragger)\n\t\t\t})\n\n\t\tconst lineElems = this.dom.binsize_g.node().querySelectorAll('line')\n\n\t\t/* the boundary value that a line at this x reports. a converted value is on a much smaller\n\t\tscale than what it was converted from (e.g. 70 years vs 25868 days), so rounding an integer\n\t\tterm to a whole number would make the line jump by a year at a time. round to 2 decimals in\n\t\tthat case instead */\n\t\tfunction toBoundaryValue(x: number): number {\n\t\t\tconst inverted = xscale.invert(x)\n\t\t\treturn Number(\n\t\t\t\tscaleFactor != 1 ? inverted.toFixed(2) : tw.term.type == 'integer' ? Math.round(inverted) : inverted.toFixed(3)\n\t\t\t)\n\t\t}\n\n\t\t// the boundary a line currently stands for, which is its dragged position once it has been moved\n\t\tfunction toLineValue(line: DraggedLineData): number {\n\t\t\treturn line.draggedX === undefined ? line.x : toBoundaryValue(line.draggedX)\n\t\t}\n\n\t\t/* the nearest draggable line on either side, if there is one. a boundary may not be dragged\n\t\tonto or past one of them: an editor addresses a boundary by the index its line had when the\n\t\tlines were rendered, so two boundaries that swap order make the next drag event overwrite the\n\t\twrong one, and two boundaries of the same value are merged into a single one, leaving the\n\t\teditor with fewer boundaries than the plot has lines */\n\t\tfunction getNeighbors(d: DraggedLineData): [DraggedLineData | undefined, DraggedLineData | undefined] {\n\t\t\tconst x = d.draggedX ?? d.scaledX\n\t\t\tlet lower, upper\n\t\t\tfor (const line of lines) {\n\t\t\t\tif (line.index === d.index || !line.isDraggable) continue\n\t\t\t\tconst lineX = line.draggedX ?? line.scaledX\n\t\t\t\tif (lineX <= x) {\n\t\t\t\t\tif (!lower || lineX > (lower.draggedX ?? lower.scaledX)) lower = line\n\t\t\t\t} else if (!upper || lineX < (upper.draggedX ?? upper.scaledX)) upper = line\n\t\t\t}\n\t\t\treturn [lower, upper]\n\t\t}\n\n\t\tfunction onDrag(this: any, event: PointerEvent, _d: any) {\n\t\t\tconst d = _d as DraggedLineData\n\t\t\tconst [lower, upper] = getNeighbors(d)\n\t\t\t/* a line follows the pointer but stops at the edge of the plot and at its neighboring\n\t\t\tlines. clamping rather than ignoring an out of bounds drag keeps a line draggable when it\n\t\t\tstarts outside those limits, as a boundary kept from a wider cohort does: its line is\n\t\t\tdrawn past the edge of the plot, where every pointer position is out of bounds */\n\t\t\tconst lowerX = Math.max(scaledMinX, lower ? lower.draggedX ?? lower.scaledX : scaledMinX)\n\t\t\tconst upperX = Math.min(scaledMaxX, upper ? upper.draggedX ?? upper.scaledX : scaledMaxX)\n\t\t\tif (upperX - lowerX < 2) return // no room to drag between the limits\n\t\t\tconst draggedX = Math.min(Math.max(pointer(event, this)[0], lowerX + 1), upperX - 1)\n\t\t\tconst value = toBoundaryValue(draggedX)\n\t\t\t/* the rounded value may still land on a neighboring boundary a pixel or two away. the\n\t\t\tedges of the plot are not boundaries, so only a neighboring line is compared */\n\t\t\tif (lower && value === toLineValue(lower)) return\n\t\t\tif (upper && value === toLineValue(upper)) return\n\n\t\t\td.draggedX = draggedX\n\t\t\tselect(this).attr('x1', d.draggedX).attr('y1', 0).attr('x2', d.draggedX).attr('y2', plot_size.height)\n\n\t\t\tconst lastVisibleScaledX = lastVisibleLine?.draggedX ?? lastVisibleLine?.scaledX ?? scaledMaxX\n\n\t\t\tconst xOffset = d.draggedX - d.scaledX\n\t\t\tif (xOffset) {\n\t\t\t\tfor (const elem of lineElems) {\n\t\t\t\t\tconst c = elem.__data__\n\t\t\t\t\tif (c.movesWithLineIndex !== d.index) continue\n\t\t\t\t\tc.draggedX = c.scaledX + xOffset\n\t\t\t\t\tselect(elem)\n\t\t\t\t\t\t.attr('x1', c.draggedX)\n\t\t\t\t\t\t.attr('x2', c.draggedX)\n\t\t\t\t\t\t.style('display', c.draggedX >= lastVisibleScaledX ? 'none' : '')\n\t\t\t\t}\n\t\t\t\tboundaryOpts.callback(d, value)\n\t\t\t}\n\t\t}\n\t}\n\n\tdestroy() {\n\t\tfor (const [k, v] of Object.entries(this.dom)) {\n\t\t\tdelete this.dom[k]\n\t\t\tif (typeof v.remove == 'function') v.remove()\n\t\t}\n\t}\n}\n"],
+  "mappings": 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+  "names": ["lastVisibleScaledX"]
+}

package/dist/chunk-NIZTWHGT.js

@@ -0,0 +1,514 @@
+import {
+  colorDelta,
+  getInterpolatedDomainRange,
+  removeOutliers
+} from "./chunk-73PFJ2VF.js";
+import {
+  copyMerge
+} from "./chunk-H6INPPUC.js";
+import {
+  dtcnv
+} from "./chunk-GEQUQ3GG.js";
+import {
+  Blues_default,
+  Reds_default
+} from "./chunk-2KXLYFAO.js";
+import {
+  axisBottom,
+  axisLeft,
+  axisRight,
+  axisTop
+} from "./chunk-LOZEKOES.js";
+import {
+  linear
+} from "./chunk-UJELJXJG.js";
+import {
+  roundValueAuto
+} from "./chunk-TLT4YIG3.js";
+import {
+  __export
+} from "./chunk-HFNDKYVF.js";
+
+// plots/matrix/matrix.layout.js
+var matrix_layout_exports = {};
+__export(matrix_layout_exports, {
+  getMaxGrpLabelWidth: () => getMaxGrpLabelWidth,
+  setAutoDimensions: () => setAutoDimensions,
+  setLabelsAndScales: () => setLabelsAndScales,
+  setLayout: () => setLayout
+});
+var MINCOLWSPACED = 7;
+function setAutoDimensions(xOffset) {
+  const m = this.state.config.settings.matrix;
+  if (!this.autoDimensions) this.autoDimensions = /* @__PURE__ */ new Set();
+  if (!m.colw) this.autoDimensions.add("colw");
+  else this.autoDimensions.delete("colw");
+  if (!m.rowh) this.autoDimensions.add("rowh");
+  else this.autoDimensions.delete("rowh");
+  const s = this.settings.matrix;
+  this.computedSettings = {
+    useCanvas: this.sampleOrder.length > m.svgCanvasSwitch
+  };
+  if (s.availContentWidth) {
+    this.availContentWidth = s.availContentWidth;
+  } else {
+    let boundingWidth = this.dom.contentNode.getBoundingClientRect().width;
+    if (boundingWidth < 600) {
+      boundingWidth = window.document.body.clientWidth;
+    }
+    const maxGrpLabelWidth = this.getMaxGrpLabelWidth();
+    const padding = Math.max(65, maxGrpLabelWidth);
+    const hcw = this.state.config.settings.hierCluster?.xDendrogramHeight || 0;
+    this.availContentWidth = boundingWidth - padding - s.margin.right - xOffset - hcw;
+  }
+  let colwSpaced, colwNoSpace;
+  if (this.autoDimensions.has("colw")) {
+    const totalColgspace = s.colgspace * Math.max(0, this.visibleSampleGrps.size - 1);
+    const tentativeGaps = this.sampleOrder.length * s.colspace + totalColgspace;
+    const spacedColw = (this.availContentWidth - tentativeGaps) / this.sampleOrder.length;
+    const constrainedMINCOLWSPACED = Math.max(s.colwMin, Math.min(MINCOLWSPACED, s.colwMax));
+    colwSpaced = Math.max(constrainedMINCOLWSPACED, Math.min(spacedColw, s.colwMax));
+    const noSpacedColw = (this.availContentWidth - totalColgspace) / this.sampleOrder.length;
+    colwNoSpace = Math.max(s.colwMin, Math.min(noSpacedColw, s.colwMax));
+    this.computedSettings.colw = colwSpaced <= MINCOLWSPACED ? colwNoSpace : colwSpaced;
+    this.computedSettings.zoomMin = s.colwMin / this.computedSettings.colw;
+    this.computedSettings.zoomMax = s.colwMax / this.computedSettings.colw;
+  } else {
+    colwSpaced = m.colw;
+    colNoSpace = m.colw;
+    this.computedSettings.colw = m.colw;
+    this.computedSettings.zoomMin = s.colwMin / m.colw;
+    this.computedSettings.zoomMax = s.colwMax / m.colw;
+  }
+  const { colw } = this.computedSettings;
+  this.computedSettings.colspace = colw === colwNoSpace && colwSpaced < colwNoSpace || colw * s.zoomLevel < MINCOLWSPACED ? 0 : s.colspace;
+  const hch = this.state.config.settings.hierCluster?.yDendrogramHeight || 0;
+  const availHeight = s.availContentHeight || screen.availHeight - hch;
+  this.computedSettings.clusterRowh = Math.min(
+    s.rowhMax,
+    Math.max(s.rowhMin, Math.floor(availHeight / this.numClusterTerms))
+  );
+  copyMerge(this.settings.matrix, this.computedSettings);
+}
+function getMaxGrpLabelWidth() {
+  const s = this.settings.matrix;
+  const g = this.dom.svg.append("g").attr("opacity", 0.01);
+  let maxWidth = 0;
+  for (const grp of this.termGroups) {
+    const grpLabel = !grp.name ? "" : grp.name.length <= s.termGrpLabelMaxChars ? grp.name : grp.name.slice(0, s.termGrpLabelMaxChars) + "\u2026";
+    const text = g.append("text").text(grpLabel).attr("font-size", 12);
+    const box = text.node().getBBox();
+    if (maxWidth < box.width) maxWidth = box.width;
+  }
+  g.remove();
+  return maxWidth;
+}
+function setLabelsAndScales() {
+  const s = this.settings.matrix;
+  this.cnvValues = [];
+  const ht = s.transpose ? s.colw : s.rowh;
+  const grpTotals = {};
+  const processedLabels = { sampleGrpByName: {}, termGrpByName: {} };
+  let totalHtAdjustments = 0;
+  for (const t of this.termOrder) {
+    const countedSamples = /* @__PURE__ */ new Set();
+    t.counts = { samples: 0, hits: 0 };
+    const renderedContinuousVs = [];
+    let hasMixedValues = false;
+    if (t.tw.term.type == "termCollection") {
+      t.counts.minval = 0;
+      t.counts.maxval = 0;
+    }
+    t.counts.subGroupCounts = {};
+    for (const group of this.sampleGroups) {
+      t.counts.subGroupCounts[group.name] = {
+        samplesTotal: 0,
+        // number of counted (not Blank or WT) samples
+        classes: {}
+        // number of each class
+      };
+      if (t.tw.term.type == "geneVariant") {
+        t.counts.subGroupCounts[group.name].samplesNotTested = 0;
+      }
+    }
+    if (!processedLabels.termGrpByName[t.grp.name || ""]) {
+      const name = t.grp.name || "";
+      t.grp.label = name.length <= s.termGrpLabelMaxChars ? name : name.slice(0, s.termGrpLabelMaxChars) + "\u2026";
+      processedLabels.termGrpByName[name] = t.grp.label;
+    }
+    for (const sample of this.sampleOrder) {
+      if (countedSamples.has(sample.row.sample)) continue;
+      const name = sample.grp.name || "";
+      if (!(name in processedLabels.sampleGrpByName)) {
+        sample.grp.label = name.length <= s.sampleGrpLabelMaxChars ? name : name.slice(0, s.sampleGrpLabelMaxChars) + "\u2026";
+        if (this.config.divideBy) sample.grp.label += ` (${sample.grp.lst.length})`;
+        processedLabels.sampleGrpByName[name] = sample.grp.label;
+      }
+      const sampleName = sample.row._ref_.label || "";
+      sample.label = sampleName.length <= s.collabelmaxchars ? sampleName : sampleName.slice(0, s.collabelmaxchars) + "\u2026";
+      const anno = sample.row[t.tw.$id];
+      if (!anno) continue;
+      if (t.tw.term.type == "termCollection" && anno.hasMixedValues) {
+        hasMixedValues = true;
+      }
+      if (t.tw.term.type == "termCollection" && anno.values) {
+        for (const val of anno.values) {
+          const pct = val.value;
+          if (pct > 0) {
+            const cumSum = val.pre_val_sum + pct;
+            if (!("maxval" in t.counts) || t.counts.maxval < cumSum) {
+              t.counts.maxval = cumSum;
+            }
+          } else if (pct < 0) {
+            const cumSum = val.pre_val_sum + pct;
+            if (!("minval" in t.counts) || t.counts.minval > cumSum) {
+              t.counts.minval = cumSum;
+            }
+          }
+        }
+      }
+      const { filteredValues, countedValues, renderedValues } = this.classifyValues(
+        anno,
+        t.tw,
+        t.grp,
+        this.settings.matrix,
+        sample.row
+      );
+      anno.filteredValues = filteredValues;
+      anno.countedValues = countedValues;
+      anno.renderedValues = renderedValues;
+      if (anno.countedValues?.length) {
+        t.counts.samples += 1;
+        t.counts.hits += anno.countedValues.length;
+        if (t.tw.q?.mode == "continuous") {
+          const v = anno.value;
+          if (!t.tw.term.values?.[v]?.uncomputable) {
+            if (!("minval" in t.counts) || t.counts.minval > v) t.counts.minval = v;
+            if (!("maxval" in t.counts) || t.counts.maxval < v) t.counts.maxval = v;
+          }
+        }
+        if (t.tw.term.type == "geneVariant" && anno.values) {
+          for (const val of anno.values) {
+            if (val.dt == dtcnv && "value" in val && !s.ignoreCnvValues) {
+              const v = val.value;
+              this.cnvValues.push(v);
+            }
+          }
+        }
+      }
+      if (t.tw.q?.mode == "continuous" && renderedValues?.length && t.grp.type != "hierCluster") {
+        renderedContinuousVs.push(
+          t.tw.term.valueConversion ? t.tw.term.valueConversion.scaleFactor * (renderedValues[0].value || renderedValues[0]) : renderedValues[0].value || renderedValues[0]
+        );
+      }
+      const subGroup = t.counts.subGroupCounts?.[sample.grp.name];
+      const countedValuesNoSkip = anno.filteredValues.filter((v) => {
+        if (t.tw.term.type == "geneVariant") {
+          if (v.class == "WT" || v.class == "Blank") return false;
+        }
+        return true;
+      });
+      if (countedValuesNoSkip.length) {
+        if (t.tw.term.type == "geneVariant") {
+          let sampleCounted = false;
+          for (const countedValue of countedValuesNoSkip) {
+            if (s.geneVariantCountSamplesSkipMclass.includes(countedValue.class)) {
+              if (!subGroup.notTestedClasses) subGroup.notTestedClasses = {};
+              if (!(countedValue.class in subGroup.notTestedClasses)) subGroup.notTestedClasses[countedValue.class] = 1;
+              else subGroup.notTestedClasses[countedValue.class] += 1;
+            } else if (!(countedValue.class in subGroup.classes)) {
+              if (!sampleCounted) {
+                subGroup.samplesTotal += 1;
+                sampleCounted = true;
+              }
+              subGroup.classes[countedValue.class] = 1;
+            } else {
+              if (!sampleCounted) {
+                subGroup.samplesTotal += 1;
+                sampleCounted = true;
+              }
+              subGroup.classes[countedValue.class] += 1;
+            }
+          }
+        } else {
+          subGroup.samplesTotal += 1;
+          for (const countedValue of countedValuesNoSkip) {
+            if (!(countedValue in subGroup.classes)) subGroup.classes[countedValue] = 1;
+            else subGroup.classes[countedValue] += 1;
+          }
+        }
+      }
+      if (anno.filteredValues?.length && t.tw.term.type == "geneVariant") {
+        const notTested = anno.filteredValues.every((v) => v.class == "Blank");
+        if (notTested) {
+          subGroup.samplesNotTested += 1;
+        }
+      }
+    }
+    if (t.tw.label) {
+      t.label = t.tw.label;
+    } else if (t.grp.type == "hierCluster") {
+      t.label = t.tw.term.gene || t.tw.term.name;
+    } else {
+      t.label = t.tw.term.name;
+    }
+    if (t.label.length > s.rowlabelmaxchars) t.label = t.label.slice(0, s.rowlabelmaxchars - 1) + "\u2026";
+    const termGroupName = this.config?.settings.hierCluster?.termGroupName;
+    if (s.samplecount4gene && t.tw.term.type.startsWith("gene") && (!termGroupName || t.grp.name !== termGroupName)) {
+      const count = s.samplecount4gene === "abs" ? t.counts.samples : (100 * t.counts.samples / this.sampleOrder.length).toFixed(1) + "%";
+      t.label = `${t.label} (${count})`;
+    }
+    const twSpecificSettings = this.config.settings.matrix.twSpecificSettings;
+    if (!twSpecificSettings[t.tw.$id]) twSpecificSettings[t.tw.$id] = {};
+    const twSettings = twSpecificSettings[t.tw.$id];
+    if (t.grp.type !== "hierCluster" && t.tw.q?.mode == "continuous") {
+      const vc = t.tw.term.valueConversion;
+      if (vc) {
+        t.counts.minval *= vc.scaleFactor;
+        t.counts.maxval *= vc.scaleFactor;
+      }
+      if (renderedContinuousVs.length && t.tw.q.convert2ZScore) {
+        const mean = renderedContinuousVs.reduce((acc, val) => acc + val, 0) / renderedContinuousVs.length;
+        const std = Math.sqrt(
+          renderedContinuousVs.reduce((acc, val) => acc + Math.pow(val - mean, 2), 0) / renderedContinuousVs.length
+        );
+        t.mean = mean;
+        t.std = std;
+        t.counts.minval = (t.counts.minval - mean) / std;
+        t.counts.maxval = (t.counts.maxval - mean) / std;
+      }
+      if (!twSettings.contBarH) twSettings.contBarH = t.tw.term.type == "termCollection" ? 150 : s.barh;
+      if (!("gap" in twSettings)) twSettings.contBarGap = 4;
+      const barh = twSettings.contBarH;
+      if (t.tw.term.type == "termCollection") {
+        if (!("minval" in t.counts)) t.counts.minval = 0;
+        if (!("maxval" in t.counts)) t.counts.maxval = 0;
+      }
+      const absMin = Math.abs(t.counts.minval);
+      const rangeSpansZero = t.counts.minval < 0 && t.counts.maxval > 0;
+      const ratio = t.counts.minval >= 0 ? 1 : t.counts.maxval / (absMin + t.counts.maxval);
+      t.counts.posMaxHt = ratio * barh;
+      const tickValues = [t.counts.maxval, t.counts.minval];
+      t.scales = {
+        tickValues,
+        full: linear().domain(tickValues).range([1, barh])
+      };
+      if (t.counts.maxval >= 0) {
+        const domainMin = rangeSpansZero ? 0 : t.counts.minval;
+        t.scales.pos = linear().domain([domainMin, t.counts.maxval]).range([1, t.counts.posMaxHt]);
+      }
+      if (t.counts.minval < 0) {
+        const domainMax = rangeSpansZero ? 0 : t.counts.maxval;
+        t.scales.neg = linear().domain([domainMax, t.counts.minval]).range([1, barh - t.counts.posMaxHt]);
+      }
+    }
+    t.totalHtAdjustments = totalHtAdjustments;
+    t.rowHt = t.grp.type == "hierCluster" ? s.clusterRowh : twSettings.contBarH && t.tw.q?.mode == "continuous" ? twSettings.contBarH + 2 * twSettings.contBarGap : ht;
+    const adjustment = t.rowHt - ht - (t.grp.type == "hierCluster" ? s.rowspace : 0);
+    totalHtAdjustments += adjustment;
+    t.cumulativeAdjustment = totalHtAdjustments;
+    if (!(t.visibleGrpIndex in grpTotals)) grpTotals[t.visibleGrpIndex] = { htAdjustment: 0 };
+    grpTotals[t.visibleGrpIndex].htAdjustment += adjustment;
+    t.grpTotals = grpTotals[t.visibleGrpIndex];
+  }
+  let cnvLegendDomainRange;
+  if (this.cnvValues.length) {
+    if (s.cnvValues.cutoffMode == "fixed") {
+      this.cnvValues = this.cnvValues.filter((v) => v >= s.cnvValues.min && v <= s.cnvValues.max).sort((a, b) => a - b);
+      if (this.cnvValues[0] != s.cnvValues.min) this.cnvValues.unshift(s.cnvValues.min);
+      if (this.cnvValues[this.cnvValues.length - 1] != s.cnvValues.max) this.cnvValues.push(s.cnvValues.max);
+    } else if (s.cnvValues.cutoffMode == "percentile" || s.cnvValues.cutoffMode == "auto") {
+      let maxPercentile = s.cnvValues.cutoffMode == "auto" ? s.cnvValues.defaultPercentile : s.cnvValues.percentile;
+      maxPercentile = maxPercentile / 100;
+      const minPercentile = roundValueAuto(1 - maxPercentile);
+      this.cnvValues = removeOutliers(this.cnvValues, { minPercentile, maxPercentile, baseValue: 0 });
+    } else throw new Error(`Invalid cnvValues cutoffMode: ${s.cnvValues.cutoffMode}`);
+    const minLoss = this.cnvValues[0] <= 0 ? this.cnvValues[0] : void 0;
+    const maxGain = this.cnvValues[this.cnvValues.length - 1] >= 0 ? this.cnvValues[this.cnvValues.length - 1] : void 0;
+    let maxLoss, minGain, absMax;
+    for (const n of this.cnvValues) {
+      if (n < 0) maxLoss = n;
+      if (!minGain && n > 0) {
+        minGain = n;
+        break;
+      }
+    }
+    for (const t of this.termOrder) {
+      if (t.tw.term.type == "geneVariant") {
+        if (!cnvLegendDomainRange) {
+          const loss0color = Blues_default(0);
+          const gain0color = Reds_default(0);
+          const colorDiff = colorDelta(loss0color, gain0color);
+          if (minLoss !== void 0 && maxGain !== void 0 && colorDiff > 25)
+            console.warn(
+              `CNV loss and gain do not have the same middle color for value=0'${loss0color}' vs '${gain0color}', color difference=${colorDiff}`
+            );
+          absMax = minLoss !== void 0 && maxGain !== void 0 ? Math.max(Math.abs(minLoss), maxGain) : minLoss !== void 0 ? Math.abs(minLoss) : maxGain;
+          cnvLegendDomainRange = getInterpolatedDomainRange({
+            absMin: 0,
+            absMax,
+            totalNumSteps: 10,
+            negInterpolator: minLoss !== void 0 && Blues_default,
+            posInterpolator: maxGain !== void 0 && Reds_default,
+            // force this middleColor to white, knowing that interpolateBlues and interpolateReds,
+            // as hardcoded above and below, share similar white colors for their minimum abs values
+            middleColor: "white"
+          });
+        }
+        t.scales = {
+          loss: Blues_default,
+          gain: Reds_default,
+          maxLoss,
+          maxGain,
+          minLoss,
+          minGain,
+          absMax,
+          legend: cnvLegendDomainRange
+        };
+      }
+    }
+  }
+}
+function setLayout() {
+  const s = this.settings.matrix;
+  const [col, row] = !s.transpose ? ["sample", "term"] : ["term", "sample"];
+  const [_t_, _b_] = s.collabelpos == "top" ? ["", "Grp"] : ["Grp", ""];
+  const [_l_, _r_] = s.rowlabelpos == "left" ? ["", "Grp"] : ["Grp", ""];
+  const top = col + _t_;
+  const btm = col + _b_;
+  const left = row + _l_;
+  const right = row + _r_;
+  this.samples = this.sampleOrder;
+  this.sampleGrps = this.sampleOrder.filter((s2) => s2.index === 0);
+  this.terms = this.termOrder;
+  this.termGrps = this.termOrder.filter((t) => t.index === 0);
+  const layout = {};
+  const sides = { top, btm, left, right };
+  for (const direction in sides) {
+    const d = sides[direction];
+    const Direction = direction[0].toUpperCase() + direction.slice(1);
+    layout[direction] = {
+      prefix: d,
+      data: this[`${d}s`],
+      offset: s[`${d}LabelOffset`],
+      box: this.dom[`${d}LabelG`],
+      key: this[`${d}Key`],
+      label: this[`${d}Label`],
+      render: this[`render${Direction}Label`],
+      isGroup: sides[direction].includes("Grp")
+    };
+  }
+  const yOffset = layout.top.offset + s.margin.top + s.scrollHeight;
+  const xOffset = layout.left.offset + s.margin.left;
+  this.setAutoDimensions(xOffset);
+  this.setLabelsAndScales();
+  const colw = Math.max(s.colwMin, Math.min(s.colwMax, s.colw * s.zoomLevel));
+  const dx = colw + s.colspace;
+  const nx = this[`${col}s`].length;
+  const dy = s.rowh + s.rowspace;
+  const ny = this[`${row}s`].length;
+  const mainwByColDimensions = nx * (colw + s.colspace) + this[`${col}Grps`].length * s.colgspace + (this[`${col}s`].slice(-1)[0]?.totalHtAdjustments || 0);
+  const mainw = Math.min(mainwByColDimensions, this.availContentWidth);
+  const lastRow = this[`${row}s`].slice(-1)[0];
+  const mainh = ny * dy + (this[`${row}Grps`].length - 1) * s.rowgspace + (lastRow?.cumulativeAdjustment || 0);
+  const colLabelFontSize = Math.min(
+    Math.max(colw + s.colspace - 2 * s.collabelpad - s.colspace, s.minLabelFontSize),
+    s.maxLabelFontSize
+  );
+  const topFontSize = _t_ == "Grp" ? s.grpLabelFontSize : colLabelFontSize;
+  layout.top.attr = {
+    boxTransform: `translate(${xOffset}, ${yOffset - s.collabelgap})`,
+    adjustBoxTransform: (dx2) => layout.top.box.attr("transform", `translate(${xOffset + dx2}, ${yOffset - s.collabelgap})`),
+    labelTransform: "rotate(-90)",
+    labelAnchor: "start",
+    labelGY: 0,
+    labelGTransform: this[`col${_t_}LabelGTransform`],
+    fontSize: topFontSize,
+    textpos: { coord: "y", factor: -1 },
+    axisFxn: axisTop
+  };
+  if (layout.top.prefix == "sample")
+    layout.top.display = s.sampleLabelsToggle !== "hide" && colw >= s.minLabelFontSize ? "" : "none";
+  const btmFontSize = _b_ == "Grp" ? s.grpLabelFontSize : colLabelFontSize;
+  layout.btm.attr = {
+    boxTransform: `translate(${xOffset}, ${yOffset + mainh + s.collabelgap})`,
+    adjustBoxTransform: (dx2) => layout.btm.box.attr("transform", `translate(${xOffset + dx2}, ${yOffset + mainh + s.collabelgap})`),
+    labelTransform: "rotate(-90)",
+    labelAnchor: "end",
+    labelGY: 0,
+    labelGTransform: this[`col${_b_}LabelGTransform`],
+    fontSize: btmFontSize,
+    textpos: { coord: "y", factor: 1 },
+    axisFxn: axisBottom
+  };
+  if (layout.btm.prefix == "sample")
+    layout.btm.display = s.sampleLabelsToggle !== "hide" && colw >= s.minLabelFontSize ? "" : "none";
+  const leftFontSize = _l_ == "Grp" ? s.grpLabelFontSize : Math.max(s.rowh + s.rowspace - 2 * s.rowlabelpad - s.rowspace, s.minLabelFontSize);
+  layout.left.attr = {
+    boxTransform: `translate(${xOffset - s.rowlabelgap}, ${yOffset})`,
+    labelTransform: "",
+    labelAnchor: "end",
+    labelGX: 0,
+    labelGTransform: this[`row${_l_}LabelGTransform`],
+    fontSize: leftFontSize,
+    textpos: { coord: "x", factor: -1 },
+    axisFxn: axisLeft
+  };
+  const rtFontSize = _r_ == "Grp" ? s.grpLabelFontSize : Math.max(s.rowh + s.rowspace - 2 * s.rowlabelpad, s.minLabelFontSize);
+  layout.right.attr = {
+    boxTransform: `translate(${xOffset + mainw + s.rowlabelgap}, ${yOffset})`,
+    labelTransform: "",
+    labelAnchor: "start",
+    labelGX: 0,
+    labelGTransform: this[`row${_r_}LabelGTransform`],
+    fontSize: rtFontSize,
+    textpos: { coord: "x", factor: 1 },
+    axisFxn: axisRight
+  };
+  this.dom.sampleLabelsPG.attr("clip-path", s.transpose ? "" : `url(#${this.seriesClipId})`);
+  this.dom.termLabelsPG.attr("clip-path", s.transpose ? `url(#${this.seriesClipId})` : "");
+  this.layout = layout;
+  if (!s.zoomCenterPct) {
+    s.zoomCenterPct = 0.5;
+    s.zoomIndex = Math.round(s.zoomCenterPct * mainw / dx);
+    s.zoomGrpIndex = this.sampleOrder[s.zoomIndex]?.grpIndex || 0;
+  }
+  const zoomCenter = s.zoomCenterPct * mainw;
+  const centerCellX = s.zoomIndex * dx + s.zoomGrpIndex * s.colgspace;
+  const zoomedMainW = Math.max(0, nx * dx + (this[`${col}Grps`].length - 1) * s.colgspace);
+  const seriesXoffset = s.zoomLevel <= 1 && mainw >= zoomedMainW ? 0 : Math.max(zoomCenter - centerCellX, mainw - zoomedMainW);
+  const imgW = (s.imgWMax > zoomedMainW ? zoomedMainW : s.imgWMax) - 1e-7;
+  const halfImgW = 0.5 * imgW;
+  const unwantedRightOvershoot = Math.max(0, centerCellX + halfImgW - zoomedMainW);
+  const imgLeftMin = Math.max(0, centerCellX - Math.min(halfImgW, imgW) - unwantedRightOvershoot);
+  const xMin = s.zoomLevel <= 1 && mainw >= zoomedMainW ? 0 : imgLeftMin;
+  const xMax = imgW + xMin;
+  this.dimensions = {
+    xMin,
+    xMax,
+    dx,
+    dy,
+    xOffset,
+    yOffset,
+    mainw,
+    mainh,
+    colw,
+    zoomedMainW,
+    seriesXoffset: seriesXoffset > 0 ? 0 : seriesXoffset,
+    maxMainW: Math.max(mainwByColDimensions, this.availContentWidth),
+    imgW,
+    // recompute the resolvable "pixel width", in case the pixel ratio changes
+    // when moving the browser window to a different monitor,
+    // will be used to sharpen canvas shapes that are smaller than this pixel width
+    pxw: 1 / window.devicePixelRatio
+  };
+}
+
+export {
+  setAutoDimensions,
+  getMaxGrpLabelWidth,
+  setLabelsAndScales,
+  setLayout,
+  matrix_layout_exports
+};
+//# sourceMappingURL=chunk-NIZTWHGT.js.map