@sjcrh/proteinpaint-client 2.146.4-1 → 2.147.1

package/dist/chunk-PGNZXLHB.js

@@ -0,0 +1,468 @@
+import {
+  colorDelta,
+  getInterpolatedDomainRange,
+  removeOutliers
+} from "./chunk-5GYHGTRN.js";
+import {
+  dtcnv
+} from "./chunk-PAV653SV.js";
+import {
+  copyMerge
+} from "./chunk-SU6RBYZK.js";
+import {
+  Blues_default,
+  Reds_default
+} from "./chunk-PMZS3SHH.js";
+import {
+  axisBottom,
+  axisLeft,
+  axisRight,
+  axisTop
+} from "./chunk-LOZEKOES.js";
+import {
+  linear
+} from "./chunk-W2IWHXLL.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
+});
+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;
+  }
+  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 tentativeColw = Math.max(s.colwMin, Math.min(spacedColw, s.colwMax));
+    const noSpacedColw = (this.availContentWidth - totalColgspace) / this.sampleOrder.length;
+    const colwNoSpace = Math.max(s.colwMin, Math.min(noSpacedColw, s.colwMax));
+    if (colwNoSpace * s.zoomLevel < 2) {
+      this.computedSettings.colw = noSpacedColw;
+      this.computedSettings.colspace = 0;
+    } else {
+      this.computedSettings.colw = tentativeColw;
+      this.computedSettings.colspace = s.colspace;
+    }
+  }
+  const hch = this.state.config.settings.hierCluster?.yDendrogramHeight || 0;
+  const availHeight = 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 = [];
+    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;
+      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 = s.barh;
+      if (!("gap" in twSettings)) twSettings.contBarGap = 4;
+      const barh = twSettings.contBarH;
+      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 = (
+        // rangeSpansZero || t.counts.maxval <= 0
+        // 	? [t.counts.minval, t.counts.maxval]
+        // 	: [t.counts.maxval, t.counts.minval]
+        [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) {
+    this.cnvValues = removeOutliers(this.cnvValues);
+    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;
+    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}`
+            );
+          const 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,
+            stepSize: 100,
+            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,
+          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 = this.chartType !== "hierCluster" && 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 = 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-PGNZXLHB.js.map