@sjcrh/proteinpaint-client 2.183.0 → 2.183.1

package/dist/chunk-Q7PYFSNU.js

@@ -1,107 +0,0 @@
-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

@@ -1,386 +0,0 @@
-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