@sjcrh/proteinpaint-client 2.182.0 → 2.183.0

package/dist/chunk-Q7PYFSNU.js

@@ -0,0 +1,107 @@
+import {
+  dofetch3
+} from "./chunk-7RN3L2BX.js";
+import {
+  DNA_METHYLATION,
+  GENE_EXPRESSION,
+  SINGLECELL_CELLTYPE
+} from "./chunk-6ITDJ5UR.js";
+
+// plots/volcano/model/VolcanoModel.ts
+var VolcanoModel = class {
+  constructor(app, config, settings) {
+    this.app = app;
+    this.config = config;
+    this.settings = settings;
+    this.termType = config.termType;
+  }
+  /** May use mapper instead as more termTypes are added */
+  async getData() {
+    if (this.termType === GENE_EXPRESSION) {
+      const body = await this.getGERequestBody();
+      return await dofetch3("termdb/DE", { body });
+    }
+    if (this.termType === DNA_METHYLATION) {
+      const body = await this.getDMRequestBody();
+      return await dofetch3("termdb/diffMeth", { body });
+    }
+    if (this.termType === SINGLECELL_CELLTYPE) {
+      const body = await this.getSCCTRequestBody();
+      return await dofetch3("termdb/singlecellDEgenes", { body });
+    } else {
+      throw new Error(`Volcano plot does not support route for termType='${this.termType}'`);
+    }
+  }
+  //Gene expression
+  async getGERequestBody() {
+    await this.getOtherSamples(this.config.samplelst);
+    const state = this.app.getState();
+    const body = {
+      genome: this.app.vocabApi.vocab.genome,
+      dslabel: this.app.vocabApi.vocab.dslabel,
+      method: this.settings.method,
+      min_count: this.settings.minCount,
+      min_total_count: this.settings.minTotalCount,
+      samplelst: this.config.samplelst,
+      filter: state.termfilter.filter,
+      filter0: state.termfilter.filter0,
+      cpm_cutoff: this.settings.cpmCutoff
+    };
+    const confounders = this.config?.confounderTws;
+    if (confounders?.length) {
+      body.tw = this.config.confounderTws[0];
+      if (confounders.length > 1) body.tw2 = this.config.confounderTws[1];
+    }
+    return body;
+  }
+  //DNA methylation
+  async getDMRequestBody() {
+    await this.getOtherSamples(this.config.samplelst);
+    const state = this.app.getState();
+    const body = {
+      genome: this.app.vocabApi.vocab.genome,
+      dslabel: this.app.vocabApi.vocab.dslabel,
+      samplelst: this.config.samplelst,
+      filter: state.termfilter.filter,
+      filter0: state.termfilter.filter0,
+      min_samples_per_group: this.settings.minSamplesPerGroup
+    };
+    const confounders = this.config?.confounderTws;
+    if (confounders?.length) {
+      body.tw = this.config.confounderTws[0];
+      if (confounders.length > 1) body.tw2 = this.config.confounderTws[1];
+    }
+    return body;
+  }
+  //Single cell cell type
+  getSCCTRequestBody() {
+    const body = {
+      genome: this.app.vocabApi.vocab.genome,
+      dslabel: this.app.vocabApi.vocab.dslabel,
+      sample: this.config.sample,
+      termId: this.config.termId,
+      categoryName: this.config.categoryName
+    };
+    return body;
+  }
+  /** retrieve the sampleId/sampleName for samples in
+   * the "others" group instead of using {in: false} */
+  async getOtherSamples(samplelst) {
+    const othersSamplesGroup = samplelst.groups.find((g) => !g.in);
+    if (!othersSamplesGroup) return;
+    const state = this.app.getState();
+    const samplesGroup = samplelst.groups.find((g) => g.in);
+    othersSamplesGroup.values = [];
+    for (const s of await this.app.vocabApi.getFilteredSampleList(state.termfilter.filter)) {
+      if (samplesGroup.values.indexOf((i) => i.sampleId == s.id) == -1) {
+        othersSamplesGroup.values.push({ sampleId: s.id, sample: s.name });
+      }
+    }
+    othersSamplesGroup.in = true;
+  }
+};
+
+export {
+  VolcanoModel
+};
+//# sourceMappingURL=chunk-Q7PYFSNU.js.map

package/dist/chunk-QMI222IJ.js

@@ -0,0 +1,386 @@
+import {
+  CNVkey2order
+} from "./chunk-DNCSPTOQ.js";
+import {
+  TermTypes
+} from "./chunk-6ITDJ5UR.js";
+import {
+  colorScaleMap,
+  dtcnv,
+  dtfusionrna,
+  dtgeneexpression,
+  dtsnvindel,
+  dtsv
+} from "./chunk-XYFDBYOY.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-QMI222IJ.js.map