@sjcrh/proteinpaint-client 2.180.0 → 2.180.1

package/dist/chunk-Z5XHVPCP.js

@@ -0,0 +1,386 @@
+import {
+  CNVkey2order
+} from "./chunk-OGZPMUPF.js";
+import {
+  TermTypes
+} from "./chunk-RTKRLATH.js";
+import {
+  colorScaleMap,
+  dtcnv,
+  dtfusionrna,
+  dtgeneexpression,
+  dtsnvindel,
+  dtsv
+} from "./chunk-SOYDFNWV.js";
+import {
+  convertUnits
+} from "./chunk-TV74I3Y5.js";
+
+// plots/matrix/matrix.cells.js
+function setNumericCellProps(cell, tw, anno, value, s, t, self2, 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 = self2.config.settings.matrix.twSpecificSettings?.[tw.$id]?.[key]?.color || anno.color || values[anno.key]?.color || self2.data.refs.byTermId?.[tw.$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 = self2.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 = self2.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, self2, 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} ${tw.term.unit}` : key : tw.term.values?.[key].label ? tw.term.values?.[key].label : "Exit code: " + key;
+  cell.fill = self2.config.settings.matrix.twSpecificSettings?.[tw.$id]?.[key]?.color || (key == 1 ? "#a1a3a6" : "#a3c88b");
+  cell.order = 0;
+  if (tw.q?.mode == "continuous") {
+    const twSpecificSettings = self2.config.settings.matrix.twSpecificSettings;
+    if (!twSpecificSettings[tw.$id]) twSpecificSettings[tw.$id] = {};
+    const twSettings = twSpecificSettings[tw.$id];
+    if (!twSettings.contBarH) twSettings.contBarH = s.barh;
+    if (!("gap" in twSettings)) twSettings.contBarGap = 4;
+    cell.exitCodeKey = tw.term.values?.[anno.key].label || "Exit code: " + anno.key;
+    cell.fill = self2.config.settings.matrix.twSpecificSettings?.[tw.$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, self2, 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 = self2.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 setGeneVariantCellProps(cell, tw, anno, value, s, t, self2, 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.$id,
+      value,
+      entry: { key: anno.key, label: cell.label, fill: cell.fill }
+    };
+  } else {
+    const values = anno.renderedValues || anno.filteredValues || anno.values || [anno.value];
+    const colorFromq = tw.q?.values && tw.q?.values[value.class]?.color;
+    cell.label = value.label || self2.mclass[value.class].label;
+    cell.fill = self2.getValueColor?.(value.value) || colorFromq || value.color || self2.mclass[value.class]?.color;
+    cell.class = value.class;
+    cell.value = value;
+    const colw = self2.dimensions.colw;
+    if (s.cellEncoding == "") {
+      cell.height = s.rowh / values.length;
+      cell.width = colw;
+      cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
+      cell.y = height * i;
+    } else if (value.dt == dtsnvindel || value.dt == dtfusionrna || value.dt == dtsv) {
+      if (s.cellEncoding == "single") {
+        cell.height = s.rowh;
+        cell.width = colw;
+        cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
+        cell.y = 0;
+      } else {
+        const divisor = 3;
+        cell.height = s.rowh / divisor;
+        cell.width = colw;
+        cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
+        cell.y = height * 0.33333;
+        if (s.oncoPrintSNVindelCellBorder) {
+          cell.border = true;
+        }
+      }
+    } else if (value.dt == dtcnv || value.dt == dtgeneexpression) {
+      cell.height = s.rowh;
+      cell.width = colw;
+      cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
+      cell.y = 0;
+    } else {
+      throw `cannot set cell props for dt='${value.dt}'`;
+    }
+    if (value.class == "Blank" || value.class == "WT") {
+      cell.label = `${self2.dt2label[value.dt]} ${cell.label}`;
+    }
+    const byDt = self2.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: self2.config.settings.hierCluster?.termGroupName || "Gene Expression",
+        value: value.class,
+        order: -1,
+        entry: {
+          key: value.class,
+          label: "",
+          scale: self2.geneExpValues.scale,
+          domain: [0, 0.5, 1],
+          minLabel: self2.geneExpValues.min,
+          maxLabel: self2.geneExpValues.max,
+          order,
+          dt: value.dt,
+          origin: value.origin
+        }
+      };
+    } else {
+      const controlLabels = self2.settings.matrix.controlLabels;
+      const group = tw.legend?.group || (value.origin ? `${value.origin[0].toUpperCase() + value.origin.slice(1)} ${controlLabels.Mutations}` : controlLabels.Mutations);
+      return {
+        ref: t.ref,
+        group,
+        value: value.class,
+        order: -2,
+        entry: { key: value.class, label: cell.label, fill: cell.fill, order, dt: value.dt, origin: value.origin }
+      };
+    }
+  }
+}
+function setHierClusterCellProps(cell, tw, anno, value, s, t, self2, width, height, dx, dy, i) {
+  const values = anno.renderedValues || anno.filteredValues || anno.values || [anno.value];
+  cell.label = value.value;
+  cell.fill = self2.getValueColor?.(value.value);
+  cell.value = value;
+  const colw = self2.dimensions.colw;
+  cell.height = s.clusterRowh;
+  cell.width = colw;
+  cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
+  cell.y = height * i;
+  const hierCluster = self2.config.settings.hierCluster;
+  let groupName;
+  if (hierCluster?.termGroupName) {
+    groupName = hierCluster.termGroupName;
+  } else if (tw.term.type == "geneExpression") {
+    groupName = "Gene Expression";
+    const unit = self2.app.vocabApi.termdbConfig.queries?.geneExpression?.unit;
+    if (hierCluster?.zScoreTransformation) groupName += " (Z-score)";
+    else if (unit) groupName += ` (${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: self2.hierClusterValues.scale,
+      domain: colorScaleMap[self2.settings.hierCluster.colorScale].domain,
+      minLabel: self2.hierClusterValues.min,
+      maxLabel: self2.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,
+  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,
+  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) {
+  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 * 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-Z5XHVPCP.js.map

package/dist/chunk-Z5XHVPCP.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/matrix/matrix.cells.js"],
+  "sourcesContent": ["import { convertUnits } from '#shared/helpers.js'\nimport { dtsnvindel, dtcnv, dtfusionrna, dtgeneexpression, dtsv, dtmetaboliteintensity } from '#shared/common.js'\nimport { TermTypes } from '#shared/terms.js'\nimport { colorScaleMap } from '#shared/common.js'\nimport { CNVkey2order } from './matrix.legend'\n/*\n\tcell: a matrix cell data\n\ttw: termwrapper\n\tanno: the current annotation\n\tvalues: the available annotation values for a term\n\tt: an entry in this.termOrder\n\ts: plotConfig.settings.matrix\n*/\nfunction setNumericCellProps(cell, tw, anno, value, s, t, self, width, height, dx, dy, i) {\n\tconst key = anno.key\n\tconst values = tw.term.values || {}\n\tcell.label = 'label' in anno ? anno.label : values[key]?.label ? values[key].label : key\n\tcell.fill =\n\t\tself.config.settings.matrix.twSpecificSettings?.[tw.$id]?.[key]?.color ||\n\t\tanno.color ||\n\t\tvalues[anno.key]?.color ||\n\t\tself.data.refs.byTermId?.[tw.$id]?.bins?.find(b => anno.key == b.name)?.color\n\tcell.order = t.ref.bins ? t.ref.bins.findIndex(bin => bin.name == key) : 0\n\tif (tw.q?.mode == 'continuous') {\n\t\tconst twSpecificSettings = self.config.settings.matrix.twSpecificSettings\n\t\tif (!twSpecificSettings[tw.$id]) twSpecificSettings[tw.$id] = {}\n\t\tconst twSettings = twSpecificSettings[tw.$id]\n\t\tif (!twSettings.contBarH) twSettings.contBarH = s.barh\n\t\tif (!('gap' in twSettings)) twSettings.contBarGap = 4\n\n\t\tconst specialValue = tw.term.values?.[cell.key]\n\n\t\t// handle uncomputable values\n\t\t// TODO: the server response data should not have uncomputable values when mode='continuous'\n\t\t// this may be implemented in getData(), but will require lots of testing since it is used\n\t\t// by multiple charts\n\t\tif (specialValue?.uncomputable) {\n\t\t\tcell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace\n\t\t\tcell.y = height * i\n\t\t\tcell.height = twSettings.contBarH\n\t\t\tcell.fill = 'transparent'\n\t\t\t//cell.label = specialValue.label\n\t\t\tconst group = tw.legend?.group || tw.$id\n\t\t\treturn //{ ref: t.ref, group, value: specialValue.label || specialValue.key, entry: { key, label: cell.label, fill: cell.fill } }\n\t\t}\n\n\t\t// TODO: may use color scale instead of bars\n\t\tcell.fill = self.config.settings.matrix.twSpecificSettings?.[tw.$id]?.contBarColor || '#555'\n\t\tif (s.transpose) {\n\t\t\tcell.height = t.scale(cell.key)\n\t\t\tcell.x = twSettings.contBarGap // - cell.width\n\t\t} else {\n\t\t\tconst vc = cell.term.valueConversion\n\t\t\tlet renderV = vc ? cell.key * vc.scaleFactor : cell.key\n\t\t\tif (tw.q.convert2ZScore) {\n\t\t\t\trenderV = (renderV - t.mean) / t.std\n\n\t\t\t\t// show positive z-score as soft red and negative z-score as soft blue\n\t\t\t\tcell.fill = renderV > 0 ? '#FF6666' : '#6666FF'\n\t\t\t\tcell.zscoreLabel = ` (Z-score: ${renderV.toFixed(2)})`\n\t\t\t}\n\t\t\tcell.label =\n\t\t\t\t'label' in anno\n\t\t\t\t\t? anno.label\n\t\t\t\t\t: values[key]?.label\n\t\t\t\t\t? values[key].label\n\t\t\t\t\t: tw.term.unit\n\t\t\t\t\t? `${cell.key.toFixed(2)} ${tw.term.unit}`\n\t\t\t\t\t: cell.key.toFixed(2)\n\t\t\tcell.height = renderV >= 0 ? t.scales.pos(renderV) : t.scales.neg(renderV)\n\t\t\tcell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace\n\t\t\tcell.y =\n\t\t\t\trenderV >= 0\n\t\t\t\t\t? t.counts.posMaxHt + twSettings.contBarGap - cell.height\n\t\t\t\t\t: t.counts.posMaxHt + twSettings.contBarGap\n\t\t\tcell.convertedValueLabel = !vc ? '' : convertUnits(cell.key, vc.fromUnit, vc.toUnit, vc.scaleFactor)\n\t\t}\n\t} else {\n\t\tcell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace\n\t\tcell.y = height * i\n\t\tconst group = tw.legend?.group || tw.$id\n\t\treturn { ref: t.ref, group, value: key, entry: { key, label: cell.label, fill: cell.fill } }\n\t}\n}\n\nfunction setSurvivalCellProps(cell, tw, anno, value, s, t, self, width, height, dx, dy, i) {\n\tconst key = tw.q?.mode == 'continuous' ? anno.value : anno.key\n\tcell.key = key\n\tcell.label =\n\t\ttw.q?.mode == 'continuous'\n\t\t\t? tw.term.unit\n\t\t\t\t? `${key} ${tw.term.unit}`\n\t\t\t\t: key\n\t\t\t: tw.term.values?.[key].label\n\t\t\t? tw.term.values?.[key].label\n\t\t\t: 'Exit code: ' + key\n\tcell.fill =\n\t\tself.config.settings.matrix.twSpecificSettings?.[tw.$id]?.[key]?.color || (key == 1 ? '#a1a3a6' : '#a3c88b')\n\tcell.order = 0\n\tif (tw.q?.mode == 'continuous') {\n\t\tconst twSpecificSettings = self.config.settings.matrix.twSpecificSettings\n\t\tif (!twSpecificSettings[tw.$id]) twSpecificSettings[tw.$id] = {}\n\t\tconst twSettings = twSpecificSettings[tw.$id]\n\t\tif (!twSettings.contBarH) twSettings.contBarH = s.barh\n\t\tif (!('gap' in twSettings)) twSettings.contBarGap = 4\n\n\t\tcell.exitCodeKey = tw.term.values?.[anno.key].label || 'Exit code: ' + anno.key\n\t\tcell.fill =\n\t\t\tself.config.settings.matrix.twSpecificSettings?.[tw.$id]?.[anno.key]?.color ||\n\t\t\t(anno.key == 1 ? '#a1a3a6' : '#a3c88b')\n\t\tif (s.transpose) {\n\t\t\tcell.height = t.scale(cell.key)\n\t\t\tcell.x = twSettings.contBarGap\n\t\t} else {\n\t\t\tconst vc = cell.term.valueConversion\n\t\t\tlet renderV = vc ? cell.key * vc.scaleFactor : cell.key\n\t\t\tif (tw.q.convert2ZScore) {\n\t\t\t\trenderV = (renderV - t.mean) / t.std\n\t\t\t\tcell.zscoreLabel = ` (Z-score: ${renderV.toFixed(2)})`\n\t\t\t}\n\t\t\tcell.label = tw.term.unit ? `${cell.key.toFixed(2)} ${tw.term.unit}` : cell.key.toFixed(2)\n\t\t\tcell.height = renderV >= 0 ? t.scales.pos(renderV) : t.scales.neg(renderV)\n\t\t\tcell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace\n\t\t\tcell.y =\n\t\t\t\trenderV >= 0\n\t\t\t\t\t? t.counts.posMaxHt + twSettings.contBarGap - cell.height\n\t\t\t\t\t: t.counts.posMaxHt + twSettings.contBarGap\n\t\t\tcell.convertedValueLabel = !vc ? '' : convertUnits(cell.key, vc.fromUnit, vc.toUnit, vc.scaleFactor)\n\t\t}\n\t} else {\n\t\tconst vc = cell.term.valueConversion\n\t\tcell.timeToEventKey = vc ? convertUnits(anno.value, vc.fromUnit, vc.toUnit, vc.scaleFactor) : anno.value.toFixed(2)\n\t\tcell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace\n\t\tcell.y = height * i\n\t\tconst group = tw.legend?.group || tw.$id\n\t\treturn { ref: t.ref, group, value: key, entry: { key, label: cell.label, fill: cell.fill } }\n\t}\n}\n\nfunction setCategoricalCellProps(cell, tw, anno, value, s, t, self, width, height, dx, dy, i) {\n\tconst values = tw.term.values || {}\n\tconst key = anno.key\n\tcell.label = 'label' in anno ? anno.label : values[key]?.label ? values[key].label : key\n\tcell.fill =\n\t\tself.config.settings.matrix.twSpecificSettings?.[tw.$id]?.[key]?.color || anno.color || values[anno.key]?.color\n\tcell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace\n\tcell.y = height * i\n\tconst group = tw.legend?.group || tw.$id\n\treturn { ref: t.ref, group, value: anno.key, entry: { key, label: cell.label, fill: cell.fill } }\n}\n\nexport function setGeneVariantCellProps(cell, tw, anno, value, s, t, self, width, height, dx, dy, i) {\n\tif (tw.q?.type == 'predefined-groupset' || tw.q?.type == 'custom-groupset') {\n\t\t// groupsetting in use\n\t\t// value is name of group assignment\n\t\tcell.label = value\n\t\tconst groupset =\n\t\t\ttw.q.type == 'custom-groupset' ? tw.q.customset : tw.term.groupsetting.lst[tw.q.predefined_groupset_idx]\n\t\tif (!groupset) throw 'groupset not found'\n\t\tconst group = groupset.groups.find(group => group.name == value)\n\t\tif (!group) throw 'group not found'\n\t\tcell.fill = group.color\n\t\tcell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace\n\t\tcell.y = height * i\n\t\treturn {\n\t\t\tref: t.ref,\n\t\t\tgroup: tw.legend?.group || tw.$id,\n\t\t\tvalue,\n\t\t\tentry: { key: anno.key, label: cell.label, fill: cell.fill }\n\t\t}\n\t} else {\n\t\t// groupsetting not in use\n\t\t// value is mutation object\n\t\tconst values = anno.renderedValues || anno.filteredValues || anno.values || [anno.value]\n\t\tconst colorFromq = tw.q?.values && tw.q?.values[value.class]?.color\n\t\tcell.label = value.label || self.mclass[value.class].label\n\t\t// may be overriden by a color scale by dt, if applicable below\n\t\tcell.fill = self.getValueColor?.(value.value) || colorFromq || value.color || self.mclass[value.class]?.color\n\t\tcell.class = value.class\n\t\tcell.value = value\n\n\t\tconst colw = self.dimensions.colw\n\t\tif (s.cellEncoding == '') {\n\t\t\tcell.height = s.rowh / values.length\n\t\t\tcell.width = colw\n\t\t\tcell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace\n\t\t\tcell.y = height * i\n\t\t} else if (value.dt == dtsnvindel || value.dt == dtfusionrna || value.dt == dtsv) {\n\t\t\tif (s.cellEncoding == 'single') {\n\t\t\t\t// when CNV is not displayed, show as tall bar\n\t\t\t\tcell.height = s.rowh\n\t\t\t\tcell.width = colw\n\t\t\t\tcell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace\n\t\t\t\tcell.y = 0\n\t\t\t} else {\n\t\t\t\tconst divisor = 3\n\t\t\t\tcell.height = s.rowh / divisor\n\t\t\t\tcell.width = colw\n\t\t\t\tcell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace\n\t\t\t\tcell.y = height * 0.33333\n\t\t\t\tif (s.oncoPrintSNVindelCellBorder) {\n\t\t\t\t\t// show white cell border for SNVindel in oncoPrint mode\n\t\t\t\t\tcell.border = true\n\t\t\t\t}\n\t\t\t}\n\t\t} else if (value.dt == dtcnv || value.dt == dtgeneexpression) {\n\t\t\tcell.height = s.rowh\n\t\t\tcell.width = colw\n\t\t\tcell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace\n\t\t\tcell.y = 0\n\t\t} else {\n\t\t\tthrow `cannot set cell props for dt='${value.dt}'`\n\t\t}\n\n\t\t// distinguish between not tested or wildtype by\n\t\t// dt: snvindel vs CNV vs SV, etc\n\t\tif (value.class == 'Blank' || value.class == 'WT') {\n\t\t\tcell.label = `${self.dt2label[value.dt]} ${cell.label}`\n\t\t}\n\n\t\t// return the corresponding legend item data\n\t\tconst byDt = self.state.termdbConfig.assayAvailability?.byDt\n\t\tconst order = CNVkey2order(value.class)\n\t\tif (value.dt == dtcnv) {\n\t\t\tif (t.scales && value.class.startsWith('CNV_')) {\n\t\t\t\t// const max = t.scales.max // value.value < 0 ? self.cnvValues.maxLoss : self.cnvValues.maxGain\n\t\t\t\tconst { /*maxLoss,*/ maxGain, minLoss, /*minGain,*/ absMax } = t.scales\n\t\t\t\t/** CNV values are presented on an equidistant range.\n\t\t\t\t * The color interpolators use a 0-1 arg.\n\t\t\t\t * Dividing the raw value by the max abs loss/gain calculates\n\t\t\t\t * a value in the 0-1 range. This will match the color in the\n\t\t\t\t * legend and cell according to the equidistant range,\n\t\t\t\t * displayed in the legend. See the scale creation is in\n\t\t\t\t * matrix.layout.js for more details.*/\n\t\t\t\tvalue.scaledValue = value.value < 0 ? value.value / -absMax : value.value / absMax\n\t\t\t\tcell.fill = value.value < 0 ? t.scales.loss(value.scaledValue) : t.scales.gain(value.scaledValue)\n\n\t\t\t\treturn {\n\t\t\t\t\tref: t.ref,\n\t\t\t\t\tgroup: 'CNV',\n\t\t\t\t\tvalue: value.class,\n\t\t\t\t\torder: -1,\n\t\t\t\t\tentry: {\n\t\t\t\t\t\tkey: value.class,\n\t\t\t\t\t\tlabel: cell.label,\n\t\t\t\t\t\tscale: value.class == 'CNV_loss' ? t.scales.loss : t.scales.gain,\n\t\t\t\t\t\tdomain: t.domain ? t.domain : value.class == 'CNV_loss' ? [0, -minLoss] : [0, maxGain],\n\t\t\t\t\t\tcolors: t.range,\n\t\t\t\t\t\tscales: value.dt == 4 && t.scales,\n\t\t\t\t\t\tminLabel: 0,\n\t\t\t\t\t\tmaxLabel: value.class == 'CNV_loss' ? minLoss : maxGain,\n\t\t\t\t\t\torder,\n\t\t\t\t\t\tdt: value.dt,\n\t\t\t\t\t\torigin: value.origin\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\tconst group = 'CNV'\n\t\t\t\treturn {\n\t\t\t\t\tref: t.ref,\n\t\t\t\t\tgroup,\n\t\t\t\t\tvalue: value.class,\n\t\t\t\t\torder: -1,\n\t\t\t\t\tentry: { key: value.class, label: cell.label, fill: cell.fill, order, dt: value.dt, origin: value.origin }\n\t\t\t\t}\n\t\t\t}\n\t\t} else if (value.dt == dtfusionrna && byDt?.[dtfusionrna]) {\n\t\t\tconst group = 'Fusion RNA'\n\t\t\treturn {\n\t\t\t\tref: t.ref,\n\t\t\t\tgroup,\n\t\t\t\tvalue: value.class,\n\t\t\t\torder: -1,\n\t\t\t\tentry: { key: value.class, label: cell.label, fill: cell.fill, order, dt: value.dt, origin: value.origin }\n\t\t\t}\n\t\t} else if (value.dt == dtsv && byDt?.[dtsv]) {\n\t\t\tconst group = 'Structural Variation'\n\t\t\treturn {\n\t\t\t\tref: t.ref,\n\t\t\t\tgroup,\n\t\t\t\tvalue: value.class,\n\t\t\t\torder: -1,\n\t\t\t\tentry: { key: value.class, label: cell.label, fill: cell.fill, order, dt: value.dt, origin: value.origin }\n\t\t\t}\n\t\t} else if (value.dt == dtgeneexpression) {\n\t\t\treturn {\n\t\t\t\tref: t.ref,\n\t\t\t\tgroup: self.config.settings.hierCluster?.termGroupName || 'Gene Expression',\n\t\t\t\tvalue: value.class,\n\t\t\t\torder: -1,\n\t\t\t\tentry: {\n\t\t\t\t\tkey: value.class,\n\t\t\t\t\tlabel: '',\n\t\t\t\t\tscale: self.geneExpValues.scale,\n\t\t\t\t\tdomain: [0, 0.5, 1],\n\t\t\t\t\tminLabel: self.geneExpValues.min,\n\t\t\t\t\tmaxLabel: self.geneExpValues.max,\n\t\t\t\t\torder,\n\t\t\t\t\tdt: value.dt,\n\t\t\t\t\torigin: value.origin\n\t\t\t\t}\n\t\t\t}\n\t\t} else {\n\t\t\tconst controlLabels = self.settings.matrix.controlLabels\n\t\t\tconst group =\n\t\t\t\ttw.legend?.group ||\n\t\t\t\t(value.origin\n\t\t\t\t\t? `${value.origin[0].toUpperCase() + value.origin.slice(1)} ${controlLabels.Mutations}`\n\t\t\t\t\t: controlLabels.Mutations)\n\t\t\treturn {\n\t\t\t\tref: t.ref,\n\t\t\t\tgroup,\n\t\t\t\tvalue: value.class,\n\t\t\t\torder: -2,\n\t\t\t\tentry: { key: value.class, label: cell.label, fill: cell.fill, order, dt: value.dt, origin: value.origin }\n\t\t\t}\n\t\t}\n\t}\n}\n\nexport function setHierClusterCellProps(cell, tw, anno, value, s, t, self, width, height, dx, dy, i) {\n\tconst values = anno.renderedValues || anno.filteredValues || anno.values || [anno.value]\n\tcell.label = value.value\n\t// may overriden by a color scale by dt, if applicable below\n\tcell.fill = self.getValueColor?.(value.value)\n\tcell.value = value\n\tconst colw = self.dimensions.colw\n\n\tcell.height = s.clusterRowh\n\tcell.width = colw\n\tcell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace\n\tcell.y = height * i\n\n\tconst hierCluster = self.config.settings.hierCluster\n\tlet groupName\n\tif (hierCluster?.termGroupName) {\n\t\tgroupName = hierCluster.termGroupName\n\t} else if (tw.term.type == 'geneExpression') {\n\t\tgroupName = 'Gene Expression'\n\t\tconst unit = self.app.vocabApi.termdbConfig.queries?.geneExpression?.unit\n\t\tif (hierCluster?.zScoreTransformation) groupName += ' (Z-score)'\n\t\telse if (unit) groupName += ` (${unit})`\n\t} else if (tw.term.type == 'metaboliteIntensity') {\n\t\tgroupName = 'Intensity'\n\t} else if (tw.term.type == 'proteomeAbundance') {\n\t\tgroupName = 'Protein Abundance'\n\t} else {\n\t\tgroupName = 'Heatmap color scale'\n\t}\n\n\treturn {\n\t\tref: t.ref,\n\t\tgroup: groupName,\n\t\torder: -1,\n\t\tentry: {\n\t\t\tlabel: '',\n\t\t\tscale: self.hierClusterValues.scale,\n\t\t\tdomain: colorScaleMap[self.settings.hierCluster.colorScale].domain,\n\t\t\tminLabel: self.hierClusterValues.min,\n\t\t\tmaxLabel: self.hierClusterValues.max,\n\t\t\torder: 0,\n\t\t\tdt: value.dt\n\t\t}\n\t}\n}\nexport function getEmptyCell(cellTemplate, s, d) {\n\tconst cell = Object.assign({}, cellTemplate)\n\tcell.fill = s.cellbg\n\tcell.height = s.rowh\n\tcell.width = d.colw\n\tcell.x = cell.totalIndex * d.dx + cell.grpIndex * s.colgspace\n\tcell.y = 0\n\treturn cell\n}\n\n// NOTE: may move these code by term.type to matrix.[categorical|*].js\n// if more term.type specific logic becomes harder to maintain here\n\n/*\n  Arguments\n\tcell: a matrix cell data\n\ttw: termwrapper\n\tanno: the current annotation\n\tvalue\n\tt: an entry in this.termOrder\n\ts: plotConfig.settings.matrix\n*/\nexport const setCellProps = {\n\t// some of these have been replaced by addOns{setCellProps} in matrix.xtw.ts,\n\t// but leaving here for now since non-classed tw's may still use these\n\tcategorical: setCategoricalCellProps,\n\tcondition: setCategoricalCellProps,\n\tinteger: setNumericCellProps,\n\tfloat: setNumericCellProps,\n\tsurvival: setSurvivalCellProps,\n\tgeneVariant: setGeneVariantCellProps,\n\thierCluster: setHierClusterCellProps,\n\t[TermTypes.GENE_EXPRESSION]: setNumericCellProps,\n\t[TermTypes.METABOLITE_INTENSITY]: setNumericCellProps,\n\t[TermTypes.PROTEOME_ABUNDANCE]: setNumericCellProps\n\t//termCollection: setTermCollectionCellProps\n}\n\nexport const maySetEmptyCell = {\n\tgeneVariant: setVariantEmptyCell,\n\tinteger: setNumericEmptyCell,\n\tfloat: setNumericEmptyCell,\n\tcategorical: setDefaultEmptyCell,\n\tcondition: setDefaultEmptyCell,\n\tsurvival: setNumericEmptyCell,\n\t[TermTypes.GENE_EXPRESSION]: setNumericEmptyCell,\n\t[TermTypes.METABOLITE_INTENSITY]: setNumericEmptyCell,\n\t[TermTypes.PROTEOME_ABUNDANCE]: setNumericEmptyCell\n}\n\nfunction setVariantEmptyCell(siblingCells, cellTemplate, s, d) {\n\tif (siblingCells.find(c => c.value.dt == dtcnv)) return\n\tconst cell = Object.assign({}, cellTemplate)\n\tcell.fill = s.cellbg\n\tcell.height = s.rowh\n\tcell.width = d.colw\n\tcell.x = cell.totalIndex * d.dx + cell.grpIndex * s.colgspace\n\tcell.y = 0\n\treturn cell\n}\n\nfunction setNumericEmptyCell(siblingCells, cellTemplate, s, d) {\n\tconst q = cellTemplate.tw.q\n\tif (q.mode != 'continuous') {\n\t\tif (siblingCells.length) return\n\t\tsetDefaultEmptyCell(siblingCells, cellTemplate, s, d)\n\t} else {\n\t\tif (q?.mode != 'continuous') return\n\t\tconst twSpecificSettings = self.config.settings.matrix.twSpecificSettings\n\t\tconst twSettings = twSpecificSettings[cellTemplate.$id]\n\t\tconst h = twSettings ? twSettings.contBarH + 2 * contBarGap : s.rowh\n\t\tif (cellTemplate.height >= h) return\n\t\tconst cell = Object.assign({}, cellTemplate)\n\t\tcell.fill = s.cellbg\n\t\tcell.height = h || s.rowh\n\t\tcell.width = d.colw\n\t\tcell.x = cell.totalIndex * d.dx + cell.grpIndex * s.colgspace\n\t\tcell.y = 0\n\t\treturn cell\n\t}\n}\n\nfunction setDefaultEmptyCell(siblingCells, cellTemplate, s, d) {\n\t// assumes that valid value(s) will fill-up the cell\n\tif (siblingCells.length) return\n\tconst cell = Object.assign({}, cellTemplate)\n\tcell.fill = s.cellbg\n\tcell.height = s.rowh\n\tcell.width = d.colw\n\tcell.x = cell.totalIndex * d.dx + cell.grpIndex * s.colgspace\n\tcell.y = 0\n\treturn cell\n}\n"],
+  "mappings": 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+  "names": ["self", "group"]
+}

package/dist/chunk-ZGWYEVXK.js

@@ -0,0 +1,54 @@
+import {
+  addGeneSearchbox
+} from "./chunk-SAHCLNNL.js";
+import {
+  Menu
+} from "./chunk-CXMZYVZT.js";
+
+// termdb/handlers/snp.ts
+var SearchHandler = class {
+  init(opts) {
+    this.callback = opts.callback;
+    const geneSearch = addGeneSearchbox({
+      tip: new Menu({ padding: "0px" }),
+      genome: opts.genomeObj,
+      row: opts.holder,
+      searchOnly: "snp",
+      allowVariant: true,
+      callback: () => this.selectSnp(geneSearch)
+    });
+  }
+  async selectSnp(geneSearch) {
+    const { chr, ref, alt, fromWhat } = geneSearch;
+    if (!chr || !ref || !alt || !fromWhat) throw "missing chr, ref, alt, or fromWhat of snp";
+    let start, stop;
+    if (!geneSearch.start && !geneSearch.stop) {
+      if (geneSearch.pos) {
+        start = geneSearch.pos - 1;
+        stop = geneSearch.pos;
+      } else {
+        throw "missing coordinate of snp";
+      }
+    } else {
+      start = geneSearch.start;
+      stop = geneSearch.stop;
+    }
+    const term = {
+      id: fromWhat,
+      chr,
+      start,
+      stop,
+      name: fromWhat,
+      ref,
+      alt: typeof alt == "string" ? [alt] : alt,
+      // is string if input to geneSearch was in variant or hgvs format // TODO: update genesearch.ts to parse alternative alleles from any input format into arrays
+      type: "snp"
+    };
+    this.callback(term);
+  }
+};
+
+export {
+  SearchHandler
+};
+//# sourceMappingURL=chunk-ZGWYEVXK.js.map

package/dist/chunk-ZMY7LBL6.js

@@ -0,0 +1,55 @@
+import {
+  colorinframe
+} from "./chunk-SAHCLNNL.js";
+import {
+  IN_frame,
+  OUT_frame
+} from "./chunk-SOYDFNWV.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-ZMY7LBL6.js.map