@sjcrh/proteinpaint-client 2.211.0 → 2.212.0

package/dist/chunk-3CGMCYZB.js

@@ -1,237 +0,0 @@
-import {
-  DataPointInteractions,
-  axisstyle,
-  createLollipopFromGene,
-  drawHoverShapes,
-  showResultsTable,
-  table2col,
-  to_svg
-} from "./chunk-K7HFOAR7.js";
-import {
-  Menu
-} from "./chunk-7XZA2XR2.js";
-import {
-  icons
-} from "./chunk-6RRZRISL.js";
-import {
-  axisLeft
-} from "./chunk-Z2ZITHT4.js";
-import {
-  linear
-} from "./chunk-4OLM3KSB.js";
-import {
-  select_default
-} from "./chunk-I6Y4O3RR.js";
-
-// plots/manhattan/manhattan.ts
-var manhattanLayoutDefaults = {
-  plotWidth: 1e3,
-  plotHeight: 400,
-  pngDotRadius: 2,
-  yAxisX: 70,
-  yAxisY: 40,
-  yAxisSpace: 20,
-  xAxisLabelPad: 30,
-  yAxisPad: 5,
-  axisColor: "#545454",
-  showYAxisLine: true,
-  fontSize: 12,
-  showLegend: true,
-  legendItemWidth: 80,
-  legendDotRadius: 3,
-  legendRightOffset: 15,
-  legendTextOffset: 12,
-  legendVerticalOffset: 4,
-  legendFontSize: 12,
-  showInteractiveDots: true,
-  interactiveDotRadius: 2,
-  interactiveDotStrokeWidth: 1,
-  showDownload: true,
-  interactiveDotsCap: 5e3,
-  maxTooltipGenes: 5
-};
-function plotManhattan(div, data, settings, app, custom = {}) {
-  const handle = { points: [], highlight: () => {
-  } };
-  settings = {
-    ...settings
-  };
-  let interactivePoints = data.plotData.points;
-  if (data.plotData.points.length > settings.interactiveDotsCap) {
-    interactivePoints = data.plotData.points.sort((a, b) => Math.abs(b.y) - Math.abs(a.y)).slice(0, settings.interactiveDotsCap);
-  }
-  const signed = data.plotData.y_min < 0;
-  div.style("position", "relative");
-  const geneTip = new Menu({ padding: "" });
-  const svg = div.append("svg").attr("data-testid", "sjpp-manhattan").attr("width", settings.plotWidth + 2 * settings.pngDotRadius + settings.yAxisX + settings.yAxisSpace).attr("height", settings.plotHeight + 2 * settings.pngDotRadius + settings.yAxisY * 4);
-  const yPlot = linear().domain([data.plotData.y_min, data.plotData.y_max]).range([settings.plotHeight + 2 * settings.pngDotRadius, 0]);
-  const yPad = data.plotData.y_pad ?? settings.pngDotRadius;
-  const yAxisLow = signed ? data.plotData.y_min + yPad : 0;
-  const yAxisScale = linear().domain([yAxisLow, data.plotData.y_max - yPad]).range([yPlot(yAxisLow), yPlot(data.plotData.y_max - yPad)]);
-  const axisG = svg.append("g").attr("transform", `translate(${settings.yAxisX + settings.yAxisSpace - settings.yAxisPad},${settings.yAxisY})`);
-  axisG.call(
-    axisLeft(yAxisScale).tickSizeOuter(0)
-    // removes top/bottom cap lines for clean look
-  );
-  axisstyle({
-    axis: axisG,
-    color: settings.axisColor,
-    fontsize: settings.fontSize + 2,
-    showline: settings.showYAxisLine
-  });
-  svg.append("text").attr("x", -((settings.plotHeight + 2 * settings.pngDotRadius) / 2) - settings.yAxisY).attr("y", settings.yAxisX / 2).attr("transform", "rotate(-90)").attr("text-anchor", "middle").attr("font-size", `${settings.fontSize + 4}px`).attr("fill", "black").text((custom.yAxisLabel ?? "-log\u2081\u2080(q-value)") + (data.plotData.has_capped_points ? " [capped]" : ""));
-  svg.append("image").attr("transform", `translate(${settings.yAxisX + settings.yAxisSpace},${settings.yAxisY})`).attr("width", settings.plotWidth + 2 * settings.pngDotRadius).attr("height", settings.plotHeight + 2 * settings.pngDotRadius).attr("href", `data:image/png;base64,${data.pngImg || data.png}`);
-  const xScale = linear().domain([-data.plotData.x_buffer, data.plotData.total_genome_length + data.plotData.x_buffer]).range([0, settings.plotWidth + 2 * settings.pngDotRadius]);
-  if (settings.showInteractiveDots && data.plotData.points && data.plotData.points.length > 0) {
-    const hoverLayer = svg.append("g").attr("transform", `translate(${settings.yAxisX + settings.yAxisSpace},${settings.yAxisY})`).style("pointer-events", "none");
-    const cover = select_default(svg.node().parentNode).append("div").style("position", "absolute").style("left", `${settings.yAxisX + settings.yAxisSpace}px`).style("top", `${settings.yAxisY}px`).style("width", `${settings.plotWidth + 2 * settings.pngDotRadius}px`).style("height", `${settings.plotHeight + 2 * settings.pngDotRadius}px`).style("pointer-events", "all");
-    const circlePath = (r) => `M${r},0 A${r},${r} 0 1,1 ${-r},0 A${r},${r} 0 1,1 ${r},0 Z`;
-    const linkedLayer = svg.append("g").attr("transform", `translate(${settings.yAxisX + settings.yAxisSpace},${settings.yAxisY})`).style("pointer-events", "none");
-    handle.points = interactivePoints;
-    handle.highlight = (dots) => drawHoverShapes(
-      linkedLayer,
-      dots.map((d) => ({
-        path: circlePath(settings.pngDotRadius + 2),
-        transform: `translate(${d.pixel_x},${d.pixel_y})`,
-        stroke: "black",
-        strokeWidth: 2
-      }))
-    );
-    const grin2Hover = (d, container) => {
-      const table = table2col({ holder: container.append("div"), margin: "10px" });
-      table.addRow("Gene", d.gene);
-      table.addRow("Position", `${d.chrom}:${d.start}-${d.end}`);
-      const [t1, t2] = table.addRow();
-      t1.text("Type");
-      t2.html(`<span style="color:${d.color}">\u25CF</span> ${d.type.charAt(0).toUpperCase() + d.type.slice(1)}`);
-      table.addRow("Q-value", d.q_value.toPrecision(3));
-      table.addRow("Subject count", d.nsubj);
-    };
-    const grin2Table = (dots) => ({
-      columns: [
-        { label: "Gene" },
-        { label: "Position" },
-        { label: "Type" },
-        { label: "Q-value", sortable: true },
-        { label: "Subject count", sortable: true }
-      ],
-      rows: dots.map((d) => [
-        { value: d.gene },
-        { value: `${d.chrom}:${d.start}-${d.end}` },
-        {
-          html: `<span style="color:${d.color}">\u25CF</span> ${d.type.charAt(0).toUpperCase() + d.type.slice(1)}`
-        },
-        { value: d.q_value.toPrecision(3) },
-        { value: d.nsubj }
-      ])
-    });
-    const interactions = new DataPointInteractions({
-      cover,
-      hoverLayer,
-      hoverTip: geneTip,
-      points: interactivePoints,
-      getX: (d) => d.pixel_x,
-      getY: (d) => d.pixel_y,
-      hitRadius: settings.pngDotRadius + 3,
-      toHoverSpec: (d) => ({
-        path: circlePath(settings.pngDotRadius),
-        transform: `translate(${d.pixel_x},${d.pixel_y})`,
-        fill: "none",
-        stroke: "black",
-        strokeWidth: settings.interactiveDotStrokeWidth
-      }),
-      maxTooltipRows: settings.maxTooltipGenes,
-      onHover: custom.onHover,
-      itemNoun: custom.itemNoun ?? "gene",
-      renderSingleHoverTooltip: custom.renderSingleHoverTooltip ?? grin2Hover,
-      buildMultiHitTableData: custom.buildMultiHitTableData ?? grin2Table,
-      // A caller with actions gets the module's standard click flow: an action menu for one
-      // dot, a pick-a-row menu for several. Without one, GRIN2's behaviour below.
-      ...custom.getActions ? {
-        getActions: custom.getActions,
-        renderSingleHitInfo: custom.renderSingleHitInfo ?? custom.renderSingleHoverTooltip,
-        getRowKey: custom.getRowKey
-      } : {
-        // Manhattan single-click goes straight to a lollipop launch — no menu.
-        // Release hover-suppression immediately so the cursor's next move re-engages.
-        onSingleClick: (d, _event, ctx) => {
-          ctx.dismiss();
-          if (app && d.gene) createLollipopFromGene(d.gene, app);
-        },
-        // Manhattan multi-click shows showResultsTable directly with `app + clickMenu`
-        // so the table renders inline Matrix/Lollipop buttons. Reuses the module's
-        // clickMenu so its onHide cleanup (clear flag, clear hover) fires on dismiss.
-        // Content is built BEFORE show2 so Menu can measure the populated rect for
-        // its right-edge clamp — otherwise the wide table is placed at cursor+offsetX
-        // and extends off the right edge of the viewport.
-        onMultiClick: (dots, event, ctx) => {
-          if (!app) {
-            ctx.dismiss();
-            return;
-          }
-          ctx.clickMenu.clear();
-          const holder = ctx.clickMenu.d.append("div").style("margin", "10px");
-          showResultsTable({ tableDiv: holder, hits: dots, app, clickMenu: ctx.clickMenu });
-          ctx.clickMenu.show2(event.clientX, event.clientY);
-        }
-      }
-    });
-    interactions.attach();
-  }
-  if (data.plotData.chrom_data) {
-    const chromLabelY = settings.plotHeight + 2 * settings.pngDotRadius + settings.yAxisY + 10;
-    Object.entries(data.plotData.chrom_data).forEach(([chrom, chromData]) => {
-      const chromLabel = chrom.replace("chr", "");
-      if (chromLabel === "M") return;
-      const centerPos = settings.yAxisX + settings.yAxisSpace + xScale(chromData.center);
-      svg.append("text").attr("x", centerPos).attr("y", chromLabelY).attr("text-anchor", "middle").attr("font-size", `${settings.fontSize + 2}px`).text(chromLabel);
-    });
-  }
-  svg.append("text").attr("x", settings.yAxisX + settings.yAxisSpace + (settings.plotWidth + 2 * settings.pngDotRadius) / 2).attr("y", settings.plotHeight + 2 * settings.pngDotRadius + settings.yAxisY + settings.xAxisLabelPad).attr("text-anchor", "middle").attr("font-size", `${settings.fontSize + 4}px`).attr("fill", "black").text("Chromosomes");
-  const title = svg.append("text").attr("x", settings.yAxisX + settings.yAxisSpace).attr("y", settings.yAxisY / 2).attr("font-weight", "bold").attr("font-size", `${settings.fontSize + 2}px`).text(custom.title ?? "Manhattan Plot");
-  const titleWidth = title.node().getBBox?.().width || 100;
-  if (settings.showDownload) {
-    const downloadDiv = div.append("div").style("position", "absolute").style("top", "5px").style("left", `${settings.yAxisX + settings.yAxisSpace + titleWidth + 8}px`);
-    icons["download"](downloadDiv, {
-      width: 16,
-      height: 16,
-      title: "Download Manhattan plot",
-      handler: () => {
-        const svgNode = svg.node();
-        const clone = svgNode.cloneNode(true);
-        const bbox = svgNode.getBBox();
-        clone.setAttribute("width", bbox.width.toString());
-        clone.setAttribute("height", bbox.height.toString());
-        clone.setAttribute("viewBox", `${bbox.x} ${bbox.y} ${bbox.width} ${bbox.height}`);
-        to_svg(clone, `manhattan_plot_${(/* @__PURE__ */ new Date()).toISOString().replace(/[:.]/g, "-").slice(0, -5)}`, {
-          apply_dom_styles: true
-        });
-      }
-    });
-  }
-  const mutationTypes = [...new Set(data.plotData.points.map((p) => p.type).filter(Boolean))];
-  const legendData = custom.legend?.map((l) => ({ type: l.label, color: l.color, hollow: l.hollow })) ?? mutationTypes.map((type) => {
-    const point = data.plotData.points.find((p) => p.type === type);
-    return {
-      type: String(type).charAt(0).toUpperCase() + String(type).slice(1),
-      color: point?.color
-    };
-  });
-  if (settings.showLegend && legendData.length > 0) {
-    const legendY = settings.yAxisY / 2;
-    const totalWidth = legendData.length * settings.legendItemWidth;
-    const legendX = settings.yAxisX + settings.yAxisSpace + (settings.plotWidth + 2 * settings.pngDotRadius) - totalWidth - settings.legendRightOffset;
-    legendData.forEach((item, i) => {
-      const x = legendX + i * settings.legendItemWidth;
-      svg.append("circle").attr("cx", x + 8).attr("cy", legendY).attr("r", settings.legendDotRadius).attr("fill", item.hollow ? "none" : item.color).attr("stroke", item.hollow ? item.color : "none");
-      svg.append("text").attr("x", x + 8 + settings.legendTextOffset).attr("y", legendY + settings.legendVerticalOffset).attr("font-size", `${settings.legendFontSize + 2}px`).text(item.type);
-    });
-  }
-  return handle;
-}
-
-export {
-  manhattanLayoutDefaults,
-  plotManhattan
-};
-//# sourceMappingURL=chunk-3CGMCYZB.js.map

package/dist/chunk-3I4DBVLM.js

@@ -1,55 +0,0 @@
-import {
-  colorinframe
-} from "./chunk-K7HFOAR7.js";
-import {
-  IN_frame,
-  OUT_frame
-} from "./chunk-57Z4VYLM.js";
-
-// src/spliceevent.phrase.js
-function spliceevent_phrase_default(evt) {
-  const htmls = [];
-  if (evt.isaltexon || evt.isskipexon) {
-    const exonstart = Math.min(...evt.skippedexon);
-    const exonstop = Math.max(...evt.skippedexon);
-    htmls.push(
-      '<div style="display:inline-block">' + (exonstart == exonstop ? "exon " + (exonstart + 1) : "exons " + (exonstart + 1) + "-" + (exonstop + 1)) + " " + (evt.isaltexon ? "alternative usage" : "skipping") + "</div>"
-    );
-    if (evt.isaltexon) {
-      htmls.push(
-        "<div class=sja_tinylogo_body>" + evt.gmB.isoform + ", " + evt.gmA.isoform + "</div><div class=sja_tinylogo_head>ISOFORMS</div>"
-      );
-    } else {
-      htmls.push("<div class=sja_tinylogo_body>" + evt.gm.isoform + "</div><div class=sja_tinylogo_head>ISOFORM</div>");
-    }
-    if (evt.junctionB.data) {
-      htmls.push(
-        "<div class=sja_tinylogo_body>" + evt.junctionB.data.length + "</div><div class=sja_tinylogo_head>SAMPLE" + (evt.junctionB.data.length > 1 ? "S" : "") + "</div>"
-      );
-    }
-    htmls.push("<div class=sja_tinylogo_body>" + evt.percentage + " %</div><div class=sja_tinylogo_head>PERCENT</div>");
-    if (evt.framenocheck) {
-      if (evt.utr3) {
-        htmls.push(`<div class=sja_tinylogo_body style="background-color:#ededed">3' UTR</div>`);
-      } else if (evt.utr5) {
-        htmls.push(`<div class=sja_tinylogo_body style="background-color:#ededed">5' UTR</div>`);
-      }
-    } else if (evt.frame == IN_frame) {
-      htmls.push(
-        '<div class=sja_tinylogo_body style="background-color:' + colorinframe + ';color:white">IN</div><div class=sja_tinylogo_head>FRAME</div>'
-      );
-    } else if (evt.frame == OUT_frame) {
-      htmls.push("<div class=sja_tinylogo_body>OUT</div><div class=sja_tinylogo_head>FRAME</div>");
-    } else {
-      htmls.push("<div class=sja_tinylogo_body>?</div><div class=sja_tinylogo_head>FRAME</div>");
-    }
-  } else {
-    return "unknown event type!!";
-  }
-  return htmls.join(" ");
-}
-
-export {
-  spliceevent_phrase_default
-};
-//# sourceMappingURL=chunk-3I4DBVLM.js.map

package/dist/chunk-42VFF74T.js

@@ -1,397 +0,0 @@
-import {
-  CNVkey2order
-} from "./chunk-SPFK5XZH.js";
-import {
-  TermTypes,
-  colorScaleMap,
-  dtcnv,
-  dtfusionrna,
-  dtgeneexpression,
-  dtsnvindel,
-  dtsv
-} from "./chunk-57Z4VYLM.js";
-import {
-  convertUnits
-} from "./chunk-W5J3LTYS.js";
-
-// plots/matrix/matrix.cells.js
-function setNumericCellProps(cell, tw, anno, value, s, t, self, width, height, dx, dy, i) {
-  const key = anno.key;
-  const values = tw.term.values || {};
-  cell.label = "label" in anno ? anno.label : values[key]?.label ? values[key].label : key;
-  cell.fill = self.config.settings.matrix.twSpecificSettings?.[tw.$id]?.[key]?.color || anno.color || values[anno.key]?.color || self.data.refs.byTermId?.[tw.$id]?.bins?.find((b) => anno.key == b.name)?.color;
-  cell.order = t.ref.bins ? t.ref.bins.findIndex((bin) => bin.name == key) : 0;
-  if (tw.q?.mode == "continuous") {
-    const twSpecificSettings = self.config.settings.matrix.twSpecificSettings;
-    if (!twSpecificSettings[tw.$id]) twSpecificSettings[tw.$id] = {};
-    const twSettings = twSpecificSettings[tw.$id];
-    if (!twSettings.contBarH) twSettings.contBarH = s.barh;
-    if (!("gap" in twSettings)) twSettings.contBarGap = 4;
-    const specialValue = tw.term.values?.[cell.key];
-    if (specialValue?.uncomputable) {
-      cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
-      cell.y = height * i;
-      cell.height = twSettings.contBarH;
-      cell.fill = "transparent";
-      const group = tw.legend?.group || tw.$id;
-      return;
-    }
-    cell.fill = self.config.settings.matrix.twSpecificSettings?.[tw.$id]?.contBarColor || "#555";
-    if (s.transpose) {
-      cell.height = t.scale(cell.key);
-      cell.x = twSettings.contBarGap;
-    } else {
-      const vc = cell.term.valueConversion;
-      let renderV = vc ? cell.key * vc.scaleFactor : cell.key;
-      if (tw.q.convert2ZScore) {
-        renderV = (renderV - t.mean) / t.std;
-        cell.fill = renderV > 0 ? "#FF6666" : "#6666FF";
-        cell.zscoreLabel = ` (Z-score: ${renderV.toFixed(2)})`;
-      }
-      cell.label = "label" in anno ? anno.label : values[key]?.label ? values[key].label : tw.term.unit ? `${cell.key.toFixed(2)} ${tw.term.unit}` : cell.key.toFixed(2);
-      cell.height = renderV >= 0 ? t.scales.pos(renderV) : t.scales.neg(renderV);
-      cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
-      cell.y = renderV >= 0 ? t.counts.posMaxHt + twSettings.contBarGap - cell.height : t.counts.posMaxHt + twSettings.contBarGap;
-      cell.convertedValueLabel = !vc ? "" : convertUnits(cell.key, vc.fromUnit, vc.toUnit, vc.scaleFactor);
-    }
-  } else {
-    cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
-    cell.y = height * i;
-    const group = tw.legend?.group || tw.$id;
-    return { ref: t.ref, group, value: key, entry: { key, label: cell.label, fill: cell.fill } };
-  }
-}
-function setSurvivalCellProps(cell, tw, anno, value, s, t, self, width, height, dx, dy, i) {
-  const key = tw.q?.mode == "continuous" ? anno.value : anno.key;
-  cell.key = key;
-  cell.label = tw.q?.mode == "continuous" ? tw.term.unit ? `${key} ${tw.term.unit}` : key : tw.term.values?.[key].label ? tw.term.values?.[key].label : "Exit code: " + key;
-  cell.fill = self.config.settings.matrix.twSpecificSettings?.[tw.$id]?.[key]?.color || (key == 1 ? "#a1a3a6" : "#a3c88b");
-  cell.order = 0;
-  if (tw.q?.mode == "continuous") {
-    const twSpecificSettings = self.config.settings.matrix.twSpecificSettings;
-    if (!twSpecificSettings[tw.$id]) twSpecificSettings[tw.$id] = {};
-    const twSettings = twSpecificSettings[tw.$id];
-    if (!twSettings.contBarH) twSettings.contBarH = s.barh;
-    if (!("gap" in twSettings)) twSettings.contBarGap = 4;
-    cell.exitCodeKey = tw.term.values?.[anno.key].label || "Exit code: " + anno.key;
-    cell.fill = self.config.settings.matrix.twSpecificSettings?.[tw.$id]?.[anno.key]?.color || (anno.key == 1 ? "#a1a3a6" : "#a3c88b");
-    if (s.transpose) {
-      cell.height = t.scale(cell.key);
-      cell.x = twSettings.contBarGap;
-    } else {
-      const vc = cell.term.valueConversion;
-      let renderV = vc ? cell.key * vc.scaleFactor : cell.key;
-      if (tw.q.convert2ZScore) {
-        renderV = (renderV - t.mean) / t.std;
-        cell.zscoreLabel = ` (Z-score: ${renderV.toFixed(2)})`;
-      }
-      cell.label = tw.term.unit ? `${cell.key.toFixed(2)} ${tw.term.unit}` : cell.key.toFixed(2);
-      cell.height = renderV >= 0 ? t.scales.pos(renderV) : t.scales.neg(renderV);
-      cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
-      cell.y = renderV >= 0 ? t.counts.posMaxHt + twSettings.contBarGap - cell.height : t.counts.posMaxHt + twSettings.contBarGap;
-      cell.convertedValueLabel = !vc ? "" : convertUnits(cell.key, vc.fromUnit, vc.toUnit, vc.scaleFactor);
-    }
-  } else {
-    const vc = cell.term.valueConversion;
-    cell.timeToEventKey = vc ? convertUnits(anno.value, vc.fromUnit, vc.toUnit, vc.scaleFactor) : anno.value.toFixed(2);
-    cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
-    cell.y = height * i;
-    const group = tw.legend?.group || tw.$id;
-    return { ref: t.ref, group, value: key, entry: { key, label: cell.label, fill: cell.fill } };
-  }
-}
-function setCategoricalCellProps(cell, tw, anno, value, s, t, self, width, height, dx, dy, i) {
-  const values = tw.term.values || {};
-  const key = anno.key;
-  cell.label = "label" in anno ? anno.label : values[key]?.label ? values[key].label : key;
-  cell.fill = self.config.settings.matrix.twSpecificSettings?.[tw.$id]?.[key]?.color || anno.color || values[anno.key]?.color;
-  cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
-  cell.y = height * i;
-  const group = tw.legend?.group || tw.$id;
-  return { ref: t.ref, group, value: anno.key, entry: { key, label: cell.label, fill: cell.fill } };
-}
-function setMultivalueCellProps(cell, tw, anno, value, s, t, self, width, height, dx, dy, i) {
-  const key = value?.key ?? anno.key;
-  const values = tw.term.values || {};
-  cell.key = key;
-  cell.label = values[key]?.label || key;
-  cell.fill = self.config.settings.matrix.twSpecificSettings?.[tw.$id]?.[key]?.color || values[key]?.color;
-  cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
-  cell.y = height * i;
-  const group = tw.legend?.group || tw.$id;
-  return { ref: t.ref, group, value: key, entry: { key, label: cell.label, fill: cell.fill } };
-}
-function setGeneVariantCellProps(cell, tw, anno, value, s, t, self, width, height, dx, dy, i) {
-  if (tw.q?.type == "predefined-groupset" || tw.q?.type == "custom-groupset") {
-    cell.label = value;
-    const groupset = tw.q.type == "custom-groupset" ? tw.q.customset : tw.term.groupsetting.lst[tw.q.predefined_groupset_idx];
-    if (!groupset) throw "groupset not found";
-    const group = groupset.groups.find((group2) => group2.name == value);
-    if (!group) throw "group not found";
-    cell.fill = group.color;
-    cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
-    cell.y = height * i;
-    return {
-      ref: t.ref,
-      group: tw.legend?.group || tw.$id,
-      value,
-      entry: { key: anno.key, label: cell.label, fill: cell.fill }
-    };
-  } else {
-    const values = anno.renderedValues || anno.filteredValues || anno.values || [anno.value];
-    const colorFromq = tw.q?.values && tw.q?.values[value.class]?.color;
-    cell.label = value.label || self.mclass[value.class].label;
-    cell.fill = self.getValueColor?.(value.value) || colorFromq || value.color || self.mclass[value.class]?.color;
-    cell.class = value.class;
-    cell.value = value;
-    const colw = self.dimensions.colw;
-    if (s.cellEncoding == "") {
-      cell.height = s.rowh / values.length;
-      cell.width = colw;
-      cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
-      cell.y = height * i;
-    } else if (value.dt == dtsnvindel || value.dt == dtfusionrna || value.dt == dtsv) {
-      if (s.cellEncoding == "single") {
-        cell.height = s.rowh;
-        cell.width = colw;
-        cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
-        cell.y = 0;
-      } else {
-        const divisor = 3;
-        cell.height = s.rowh / divisor;
-        cell.width = colw;
-        cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
-        cell.y = height * 0.33333;
-        if (s.oncoPrintSNVindelCellBorder) {
-          cell.border = true;
-        }
-      }
-    } else if (value.dt == dtcnv || value.dt == dtgeneexpression) {
-      cell.height = s.rowh;
-      cell.width = colw;
-      cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
-      cell.y = 0;
-    } else {
-      throw `cannot set cell props for dt='${value.dt}'`;
-    }
-    if (value.class == "Blank" || value.class == "WT") {
-      cell.label = `${self.dt2label[value.dt]} ${cell.label}`;
-    }
-    const byDt = self.state.termdbConfig.assayAvailability?.byDt;
-    const order = CNVkey2order(value.class);
-    if (value.dt == dtcnv) {
-      if (t.scales && value.class.startsWith("CNV_")) {
-        const {
-          /*maxLoss,*/
-          maxGain,
-          minLoss,
-          /*minGain,*/
-          absMax
-        } = t.scales;
-        value.scaledValue = value.value < 0 ? value.value / -absMax : value.value / absMax;
-        cell.fill = value.value < 0 ? t.scales.loss(value.scaledValue) : t.scales.gain(value.scaledValue);
-        return {
-          ref: t.ref,
-          group: "CNV",
-          value: value.class,
-          order: -1,
-          entry: {
-            key: value.class,
-            label: cell.label,
-            scale: value.class == "CNV_loss" ? t.scales.loss : t.scales.gain,
-            domain: t.domain ? t.domain : value.class == "CNV_loss" ? [0, -minLoss] : [0, maxGain],
-            colors: t.range,
-            scales: value.dt == 4 && t.scales,
-            minLabel: 0,
-            maxLabel: value.class == "CNV_loss" ? minLoss : maxGain,
-            order,
-            dt: value.dt,
-            origin: value.origin
-          }
-        };
-      } else {
-        const group = "CNV";
-        return {
-          ref: t.ref,
-          group,
-          value: value.class,
-          order: -1,
-          entry: { key: value.class, label: cell.label, fill: cell.fill, order, dt: value.dt, origin: value.origin }
-        };
-      }
-    } else if (value.dt == dtfusionrna && byDt?.[dtfusionrna]) {
-      const group = "Fusion RNA";
-      return {
-        ref: t.ref,
-        group,
-        value: value.class,
-        order: -1,
-        entry: { key: value.class, label: cell.label, fill: cell.fill, order, dt: value.dt, origin: value.origin }
-      };
-    } else if (value.dt == dtsv && byDt?.[dtsv]) {
-      const group = "Structural Variation";
-      return {
-        ref: t.ref,
-        group,
-        value: value.class,
-        order: -1,
-        entry: { key: value.class, label: cell.label, fill: cell.fill, order, dt: value.dt, origin: value.origin }
-      };
-    } else if (value.dt == dtgeneexpression) {
-      return {
-        ref: t.ref,
-        group: self.config.settings.hierCluster?.termGroupName || "Gene Expression",
-        value: value.class,
-        order: -1,
-        entry: {
-          key: value.class,
-          label: "",
-          scale: self.geneExpValues.scale,
-          domain: [0, 0.5, 1],
-          minLabel: self.geneExpValues.min,
-          maxLabel: self.geneExpValues.max,
-          order,
-          dt: value.dt,
-          origin: value.origin
-        }
-      };
-    } else {
-      const controlLabels = self.settings.matrix.controlLabels;
-      const group = tw.legend?.group || (value.origin ? `${value.origin[0].toUpperCase() + value.origin.slice(1)} ${controlLabels.Mutations}` : controlLabels.Mutations);
-      return {
-        ref: t.ref,
-        group,
-        value: value.class,
-        order: -2,
-        entry: { key: value.class, label: cell.label, fill: cell.fill, order, dt: value.dt, origin: value.origin }
-      };
-    }
-  }
-}
-function setHierClusterCellProps(cell, tw, anno, value, s, t, self, width, height, dx, dy, i) {
-  const values = anno.renderedValues || anno.filteredValues || anno.values || [anno.value];
-  cell.label = value.value;
-  cell.fill = self.getValueColor?.(value.value);
-  cell.value = value;
-  const colw = self.dimensions.colw;
-  cell.height = s.clusterRowh;
-  cell.width = colw;
-  cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
-  cell.y = height * i;
-  const hierCluster = self.config.settings.hierCluster;
-  let groupName;
-  if (hierCluster?.termGroupName) {
-    groupName = hierCluster.termGroupName;
-  } else if (tw.term.type == "geneExpression") {
-    groupName = "Gene Expression";
-    const unit = self.app.vocabApi.termdbConfig.queries?.geneExpression?.unit;
-    if (hierCluster?.zScoreTransformation) groupName += " (Z-score)";
-    else if (unit) groupName += ` (${unit})`;
-  } else if (tw.term.type == "metaboliteIntensity") {
-    groupName = "Intensity";
-  } else if (tw.term.type == "proteomeAbundance") {
-    groupName = "Protein Abundance";
-  } else {
-    groupName = "Heatmap color scale";
-  }
-  return {
-    ref: t.ref,
-    group: groupName,
-    order: -1,
-    entry: {
-      label: "",
-      scale: self.hierClusterValues.scale,
-      domain: colorScaleMap[self.settings.hierCluster.colorScale].domain,
-      minLabel: self.hierClusterValues.min,
-      maxLabel: self.hierClusterValues.max,
-      order: 0,
-      dt: value.dt
-    }
-  };
-}
-function getEmptyCell(cellTemplate, s, d) {
-  const cell = Object.assign({}, cellTemplate);
-  cell.fill = s.cellbg;
-  cell.height = s.rowh;
-  cell.width = d.colw;
-  cell.x = cell.totalIndex * d.dx + cell.grpIndex * s.colgspace;
-  cell.y = 0;
-  return cell;
-}
-var setCellProps = {
-  // some of these have been replaced by addOns{setCellProps} in matrix.xtw.ts,
-  // but leaving here for now since non-classed tw's may still use these
-  categorical: setCategoricalCellProps,
-  condition: setCategoricalCellProps,
-  multivalue: setMultivalueCellProps,
-  integer: setNumericCellProps,
-  float: setNumericCellProps,
-  survival: setSurvivalCellProps,
-  geneVariant: setGeneVariantCellProps,
-  hierCluster: setHierClusterCellProps,
-  [TermTypes.GENE_EXPRESSION]: setNumericCellProps,
-  [TermTypes.METABOLITE_INTENSITY]: setNumericCellProps,
-  [TermTypes.PROTEOME_ABUNDANCE]: setNumericCellProps
-  //termCollection: setTermCollectionCellProps
-};
-var maySetEmptyCell = {
-  geneVariant: setVariantEmptyCell,
-  integer: setNumericEmptyCell,
-  float: setNumericEmptyCell,
-  categorical: setDefaultEmptyCell,
-  condition: setDefaultEmptyCell,
-  multivalue: setDefaultEmptyCell,
-  survival: setNumericEmptyCell,
-  [TermTypes.GENE_EXPRESSION]: setNumericEmptyCell,
-  [TermTypes.METABOLITE_INTENSITY]: setNumericEmptyCell,
-  [TermTypes.PROTEOME_ABUNDANCE]: setNumericEmptyCell
-};
-function setVariantEmptyCell(siblingCells, cellTemplate, s, d) {
-  if (siblingCells.find((c) => c.value.dt == dtcnv)) return;
-  const cell = Object.assign({}, cellTemplate);
-  cell.fill = s.cellbg;
-  cell.height = s.rowh;
-  cell.width = d.colw;
-  cell.x = cell.totalIndex * d.dx + cell.grpIndex * s.colgspace;
-  cell.y = 0;
-  return cell;
-}
-function setNumericEmptyCell(siblingCells, cellTemplate, s, d, self) {
-  const q = cellTemplate.tw.q;
-  if (q.mode != "continuous") {
-    if (siblingCells.length) return;
-    setDefaultEmptyCell(siblingCells, cellTemplate, s, d);
-  } else {
-    if (q?.mode != "continuous") return;
-    const twSpecificSettings = self.config.settings.matrix.twSpecificSettings;
-    const twSettings = twSpecificSettings[cellTemplate.$id];
-    const h = twSettings ? twSettings.contBarH + 2 * twSettings.contBarGap : s.rowh;
-    if (cellTemplate.height >= h) return;
-    const cell = Object.assign({}, cellTemplate);
-    cell.fill = s.cellbg;
-    cell.height = h || s.rowh;
-    cell.width = d.colw;
-    cell.x = cell.totalIndex * d.dx + cell.grpIndex * s.colgspace;
-    cell.y = 0;
-    return cell;
-  }
-}
-function setDefaultEmptyCell(siblingCells, cellTemplate, s, d) {
-  if (siblingCells.length) return;
-  const cell = Object.assign({}, cellTemplate);
-  cell.fill = s.cellbg;
-  cell.height = s.rowh;
-  cell.width = d.colw;
-  cell.x = cell.totalIndex * d.dx + cell.grpIndex * s.colgspace;
-  cell.y = 0;
-  return cell;
-}
-
-export {
-  setGeneVariantCellProps,
-  setHierClusterCellProps,
-  getEmptyCell,
-  setCellProps,
-  maySetEmptyCell
-};
-//# sourceMappingURL=chunk-42VFF74T.js.map