@sjcrh/proteinpaint-client 2.217.0 → 2.218.0

package/dist/chunk-ET2KFCXK.js

@@ -0,0 +1,424 @@
+import {
+  CATEGORICAL,
+  COHORT,
+  CONDITION,
+  DATE,
+  DNA_METHYLATION,
+  FLOAT,
+  GENE_EXPRESSION,
+  GENE_VARIANT,
+  INTEGER,
+  ISOFORM_EXPRESSION,
+  JUNCTION,
+  METABOLITE_INTENSITY,
+  MULTIVALUE,
+  PROTEOME_ABUNDANCE,
+  PSEUDOBULK,
+  SAMPLELST,
+  SINGLECELL_CELLTYPE,
+  SINGLECELL_GENE_EXPRESSION,
+  SINGLECELL_NUMERIC_VALUE,
+  SNP,
+  SNP_LIST,
+  SNP_LOCUS,
+  SSGSEA,
+  SURVIVAL,
+  TERM_COLLECTION,
+  TermTypeGroups,
+  dtTerms,
+  dtdnamethylation,
+  dtgeneexpression,
+  dtmetaboliteintensity,
+  dtproteomeabundance,
+  dtssgsea
+} from "./chunk-LMG7Y5IN.js";
+
+// ../shared/utils/dist/src/terms.js
+var ROOT_SAMPLE_TYPE = 1;
+var DEFAULT_SAMPLE_TYPE = 2;
+var NumericModes = {
+  continuous: "continuous",
+  discrete: "discrete"
+};
+var dtTermTypes = new Set(dtTerms.map((t) => t.type));
+var TermTypes2Dt = {
+  [GENE_EXPRESSION]: dtgeneexpression,
+  [SSGSEA]: dtssgsea,
+  [DNA_METHYLATION]: dtdnamethylation,
+  [METABOLITE_INTENSITY]: dtmetaboliteintensity,
+  [PROTEOME_ABUNDANCE]: dtproteomeabundance
+};
+var typeGroup = {
+  [CATEGORICAL]: TermTypeGroups.DICTIONARY_VARIABLES,
+  [CONDITION]: TermTypeGroups.DICTIONARY_VARIABLES,
+  [FLOAT]: TermTypeGroups.DICTIONARY_VARIABLES,
+  [INTEGER]: TermTypeGroups.DICTIONARY_VARIABLES,
+  [SAMPLELST]: TermTypeGroups.DICTIONARY_VARIABLES,
+  [SURVIVAL]: TermTypeGroups.DICTIONARY_VARIABLES,
+  [DATE]: TermTypeGroups.DICTIONARY_VARIABLES,
+  [MULTIVALUE]: TermTypeGroups.DICTIONARY_VARIABLES,
+  [GENE_VARIANT]: TermTypeGroups.MUTATION_CNV_FUSION,
+  [SNP]: TermTypeGroups.SNP,
+  [SNP_LIST]: TermTypeGroups.SNP_LIST,
+  [SNP_LOCUS]: TermTypeGroups.SNP_LOCUS,
+  [GENE_EXPRESSION]: TermTypeGroups.GENE_EXPRESSION,
+  [ISOFORM_EXPRESSION]: TermTypeGroups.ISOFORM_EXPRESSION,
+  [JUNCTION]: TermTypeGroups.SPLICE_JUNCTION,
+  [SSGSEA]: TermTypeGroups.SSGSEA,
+  [DNA_METHYLATION]: TermTypeGroups.DNA_METHYLATION,
+  [METABOLITE_INTENSITY]: TermTypeGroups.METABOLITE_INTENSITY,
+  [PROTEOME_ABUNDANCE]: TermTypeGroups.PROTEOME_ABUNDANCE,
+  [PSEUDOBULK]: TermTypeGroups.PSEUDOBULK,
+  [TERM_COLLECTION]: TermTypeGroups.TERM_COLLECTION,
+  [SINGLECELL_CELLTYPE]: TermTypeGroups.SINGLECELL_CELLTYPE,
+  [SINGLECELL_GENE_EXPRESSION]: TermTypeGroups.SINGLECELL_GENE_EXPRESSION,
+  [SINGLECELL_NUMERIC_VALUE]: TermTypeGroups.SINGLECELL_NUMERIC_VALUE,
+  [COHORT]: TermTypeGroups.COHORT
+};
+var nonDictTypes = /* @__PURE__ */ new Set([
+  SNP,
+  SNP_LIST,
+  SNP_LOCUS,
+  GENE_EXPRESSION,
+  ISOFORM_EXPRESSION,
+  JUNCTION,
+  SSGSEA,
+  DNA_METHYLATION,
+  GENE_VARIANT,
+  METABOLITE_INTENSITY,
+  PROTEOME_ABUNDANCE,
+  PSEUDOBULK,
+  SINGLECELL_CELLTYPE,
+  SINGLECELL_GENE_EXPRESSION,
+  SINGLECELL_NUMERIC_VALUE,
+  COHORT
+]);
+for (const dtTermType of dtTermTypes) {
+  nonDictTypes.add(dtTermType);
+}
+var numericTypes = /* @__PURE__ */ new Set([
+  INTEGER,
+  FLOAT,
+  GENE_EXPRESSION,
+  ISOFORM_EXPRESSION,
+  JUNCTION,
+  SSGSEA,
+  DNA_METHYLATION,
+  METABOLITE_INTENSITY,
+  PROTEOME_ABUNDANCE,
+  SINGLECELL_GENE_EXPRESSION,
+  SINGLECELL_NUMERIC_VALUE,
+  DATE,
+  PSEUDOBULK
+]);
+var dictionaryNumericTypes = /* @__PURE__ */ new Set([INTEGER, FLOAT, DATE]);
+var categoricalTypes = /* @__PURE__ */ new Set([CATEGORICAL, SNP]);
+var singleCellTerms = /* @__PURE__ */ new Set([
+  SINGLECELL_CELLTYPE,
+  SINGLECELL_GENE_EXPRESSION,
+  SINGLECELL_NUMERIC_VALUE
+  /*PSEUDOBULK*/
+]);
+function isSingleCellTerm(term) {
+  if (!term) return false;
+  if (typeof term !== "object") throw new Error("Term is not an object. Did you provide the type instead?");
+  return singleCellTerms.has(term.type);
+}
+function isNumericTerm(term) {
+  if (!term) return false;
+  return numericTypes.has(term.type);
+}
+function isNumericTw(tw) {
+  if (!tw?.term) return false;
+  return isNumericTerm(tw.term) || tw.term.type === TERM_COLLECTION && tw.term.memberType === "numeric" && tw.type === "TermCollectionTWFraction";
+}
+function isCategoricalTerm(term) {
+  if (!term) return false;
+  return categoricalTypes.has(term.type);
+}
+function isDictionaryType(type) {
+  return !isNonDictionaryType(type);
+}
+function isNonDictionaryType(type) {
+  if (!type) throw new Error("Type is not defined");
+  return nonDictTypes.has(type);
+}
+function isNumTermCollection(term) {
+  if (!term || !term.type) throw new Error("Term or term type is not defined");
+  return term.type === TERM_COLLECTION;
+}
+function equals(t1, t2) {
+  if (!t1) throw new Error("First term is not defined ");
+  if (!t2) throw new Error("Second term is not defined ");
+  if (t1.type !== t2.type) return false;
+  if (isDictionaryType(t1.type) && isDictionaryType(t2.type) && t1.type != SAMPLELST) return t1.id === t2.id;
+  switch (t1.type) {
+    case GENE_EXPRESSION:
+      return t1.gene == t2.gene;
+    case ISOFORM_EXPRESSION:
+      return t1.isoform == t2.isoform;
+    case JUNCTION:
+      return t1.chr == t2.chr && t1.start == t2.start && t1.stop == t2.stop && t1.strand == t2.strand;
+    case SSGSEA:
+      return t1.id == t2.id;
+    case DNA_METHYLATION:
+      return t1.chr == t2.chr && t1.start == t2.start && t1.stop == t2.stop;
+    case METABOLITE_INTENSITY:
+    case PROTEOME_ABUNDANCE:
+      return t1.name == t2.name;
+    case GENE_VARIANT:
+      return t1.gene == t2.gene || t1.chr == t2.chr && t1.start == t2.start && t1.stop == t2.stop;
+    // TO DO: Add more cases
+    // case SNP_LIST:
+    // case SNP_LOCUS:
+    // case SAMPLELST:
+    default:
+      return false;
+  }
+}
+function trimGvTermCopy(term, q) {
+  if (term?.type != GENE_VARIANT) return term;
+  delete term.childTerms;
+  if (q?.customset) clearGroupsetParentTerms(q.customset);
+  const lst = term.groupsetting?.lst;
+  if (!lst?.length) return term;
+  if (q?.type == "predefined-groupset") {
+    const idx = q.predefined_groupset_idx;
+    term.groupsetting.lst = lst.map((groupset, i) => i === idx ? groupset : null);
+    clearDtTermMnames(term.groupsetting.lst[idx]);
+    clearGroupsetParentTerms(term.groupsetting.lst[idx]);
+  } else {
+    delete term.groupsetting.lst;
+  }
+  return term;
+}
+function forEachGvTw(obj, callback) {
+  if (!obj || typeof obj != "object") return;
+  if (obj.q && obj.term?.type == GENE_VARIANT) callback(obj);
+  for (const value of Object.values(obj)) forEachGvTw(value, callback);
+}
+function trimGvTermsForSave(obj) {
+  forEachGvTw(obj, (tw) => {
+    delete tw.term.childTerms;
+    delete tw.term.groupsetting;
+    if (tw.q.customset) clearGroupsetParentTerms(tw.q.customset);
+  });
+  return obj;
+}
+function getGvGeneKey(term) {
+  const genes = term?.genes?.length ? term.genes : term ? [term] : [];
+  const keys = genes.map((gene) => {
+    if (getGvGeneKind(gene) == "coord") {
+      const region = getGvQueryRegion(gene);
+      return region ? `${region.chr}:${region.start + 1}-${region.stop}` : void 0;
+    }
+    return gene.gene || gene.name;
+  }).filter((key) => typeof key == "string" && key);
+  if (!keys.length || keys.length != genes.length) return "";
+  return keys.sort().join(",");
+}
+var gvQCacheKeyPrefix = "gv:";
+function getGvQCacheKey(term) {
+  const key = getGvGeneKey(term);
+  return key ? gvQCacheKeyPrefix + key : "";
+}
+function getGvGeneKind(gene) {
+  if (gene?.kind) return gene.kind;
+  if (gene?.gene || gene?.name && !gene.chr) return "gene";
+  if (gene?.chr) return "coord";
+  return void 0;
+}
+function trimGvQForCache(q) {
+  const copy = structuredClone(q);
+  delete copy.isAtomic;
+  delete copy.hiddenValues;
+  delete copy.dtLst;
+  if (copy.customset) {
+    clearDtTermMnames(copy.customset);
+    clearGroupsetParentTerms(copy.customset);
+  }
+  return copy;
+}
+function getGvQueryRegion(gene) {
+  if (!gene?.chr || !Number.isInteger(gene.start) || !Number.isInteger(gene.stop)) return;
+  return { chr: gene.chr, start: gene.start, stop: gene.stop };
+}
+function restoreGvQueryEntry(v, queries) {
+  if (!queries || v?.$q === void 0) return false;
+  Object.assign(v, queries[v.$q]);
+  delete v.$q;
+  return true;
+}
+function matchesGvQueryEntry(entry, v) {
+  if (entry.gene) return entry.gene == v.gene;
+  const r = entry.region;
+  if (r) return !!v.region && r.chr == v.region.chr && r.start == v.region.start && r.stop == v.region.stop;
+  return true;
+}
+function setGroupsetParentTerms(groupset, term) {
+  if (term?.type != GENE_VARIANT) throw "parent of a groupset tvs must be a geneVariant term";
+  const parentTerm = structuredClone(term);
+  delete parentTerm.childTerms;
+  delete parentTerm.groupsetting;
+  walkTvs(groupset, (tvs) => {
+    if (!dtTermTypes.has(tvs.term?.type)) throw `groupset tvs term is not a dt term`;
+    tvs.term.parentTerm = parentTerm;
+  });
+  return groupset;
+}
+function clearGroupsetParentTerms(groupset) {
+  walkTvs(groupset, (tvs) => {
+    if (tvs.term) delete tvs.term.parentTerm;
+  });
+  return groupset;
+}
+function walkTvs(obj, fn) {
+  if (!obj || typeof obj != "object") return;
+  if (obj.type == "tvs" && obj.tvs) {
+    fn(obj.tvs);
+    return;
+  }
+  for (const k in obj) walkTvs(obj[k], fn);
+}
+function getDtsFromGroups(groups) {
+  const dts = /* @__PURE__ */ new Set();
+  for (const group of groups) {
+    for (const dt of getDtsFromFilter(group.filter)) dts.add(dt);
+  }
+  return [...dts];
+}
+function getDtsFromFilter(filter) {
+  const dts = /* @__PURE__ */ new Set();
+  for (const item of filter.lst) {
+    if (item.type == "tvslst") {
+      for (const dt of getDtsFromFilter(item)) dts.add(dt);
+    } else {
+      dts.add(item.tvs.term.dt);
+    }
+  }
+  return dts;
+}
+function clearDtTermMnames(obj) {
+  walkTvs(obj, (tvs) => {
+    if (tvs.term) delete tvs.term.mnames;
+  });
+  return obj;
+}
+function getQuerySampleTypesByTerms(sampleTypesByTerms, querySampleTypes) {
+  if (!sampleTypesByTerms) return;
+  const querySampleTypesByTerms = {};
+  for (const [term, values] of Object.entries(sampleTypesByTerms)) {
+    const queryValues = {};
+    for (const [value, sampleTypes] of Object.entries(values)) {
+      const filteredSampleTypes = sampleTypes.filter((sampleType) => querySampleTypes.includes(sampleType));
+      if (filteredSampleTypes.length) queryValues[value] = filteredSampleTypes;
+    }
+    if (Object.keys(queryValues).length) querySampleTypesByTerms[term] = queryValues;
+  }
+  if (!Object.keys(querySampleTypesByTerms).length) return;
+  return querySampleTypesByTerms;
+}
+var typeMap = {
+  categorical: "Categorical",
+  condition: "Condition",
+  float: "Numerical",
+  integer: "Numerical",
+  date: "Date",
+  geneExpression: "Gene Expression",
+  isoformExpression: "Isoform Expression",
+  [JUNCTION]: "Splice junction",
+  ssGSEA: "Geneset Expression",
+  dnaMethylation: "DNA Methylation",
+  geneVariant: "Gene Variant",
+  metaboliteIntensity: "Metabolite Intensity",
+  proteomeAbundance: "Proteome Abundance",
+  proteomeDAP: "Proteome DAP",
+  multivalue: "Multi Value",
+  singleCellGeneExpression: "Single Cell, Gene Expression",
+  singleCellCellType: "Single Cell, Cell Type",
+  singleCellNumericValue: "Single Cell, Numeric Value",
+  snplocus: "SNP Locus",
+  snp: "SNP",
+  snplst: "SNP List",
+  termCollection: "Term Collection"
+};
+function termItemType(t) {
+  switch (t.type) {
+    case JUNCTION:
+      return "Splice junction";
+    case GENE_EXPRESSION:
+    case SINGLECELL_GENE_EXPRESSION:
+      return "Gene";
+    case ISOFORM_EXPRESSION:
+      return "Isoform";
+    case SSGSEA:
+      return "Gene set";
+    case METABOLITE_INTENSITY:
+      return "Metabolite";
+    // keep adding here
+    default:
+      return "Variable";
+  }
+}
+function termType2label(type) {
+  const s = typeMap[type];
+  if (s) return s;
+  throw new Error("termType2label(): unknown value");
+}
+function getDateFromNumber(value) {
+  const year = Math.floor(value);
+  const january1st = new Date(year, 0, 1);
+  const totalDays = getDaysInYear(year);
+  const time = Math.round((value - year) * totalDays) * oneDayTime;
+  const date = new Date(january1st.getTime() + time);
+  return date;
+}
+var oneDayTime = 24 * 60 * 60 * 1e3;
+function getDateStrFromNumber(value) {
+  const date = getDateFromNumber(value);
+  return date.toLocaleDateString("en-US", {
+    year: "numeric",
+    month: "long"
+  });
+}
+function getDaysInYear(year) {
+  const isLeap = new Date(year, 1, 29).getMonth() === 1;
+  const days = isLeap ? 366 : 365;
+  return days;
+}
+
+export {
+  ROOT_SAMPLE_TYPE,
+  DEFAULT_SAMPLE_TYPE,
+  NumericModes,
+  dtTermTypes,
+  TermTypes2Dt,
+  typeGroup,
+  numericTypes,
+  dictionaryNumericTypes,
+  isSingleCellTerm,
+  isNumericTerm,
+  isNumericTw,
+  isCategoricalTerm,
+  isDictionaryType,
+  isNonDictionaryType,
+  isNumTermCollection,
+  equals,
+  trimGvTermCopy,
+  forEachGvTw,
+  trimGvTermsForSave,
+  gvQCacheKeyPrefix,
+  getGvQCacheKey,
+  trimGvQForCache,
+  restoreGvQueryEntry,
+  matchesGvQueryEntry,
+  setGroupsetParentTerms,
+  getDtsFromGroups,
+  clearDtTermMnames,
+  getQuerySampleTypesByTerms,
+  termItemType,
+  termType2label,
+  getDateFromNumber,
+  getDateStrFromNumber
+};
+//# sourceMappingURL=chunk-ET2KFCXK.js.map

package/dist/chunk-EYIZTX33.js

@@ -0,0 +1,263 @@
+import {
+  hierCluster_interactivity_exports
+} from "./chunk-IKZAWD7P.js";
+import {
+  Matrix
+} from "./chunk-M37J6Z5U.js";
+import {
+  hierCluster_renderers_exports
+} from "./chunk-5Q6TANNH.js";
+import {
+  filterJoin,
+  getNormalRoot
+} from "./chunk-YS7Y257H.js";
+import {
+  clusterMethodLst,
+  distanceMethodLst,
+  dofetch3
+} from "./chunk-XJYVMXMZ.js";
+import {
+  TermTypes2Dt,
+  dictionaryNumericTypes
+} from "./chunk-ET2KFCXK.js";
+import {
+  colorScaleMap
+} from "./chunk-LMG7Y5IN.js";
+import {
+  deepEqual,
+  getCompInit
+} from "./chunk-HBNB5TRH.js";
+import {
+  extent,
+  linear
+} from "./chunk-4OLM3KSB.js";
+
+// plots/matrix/hierCluster.js
+var HierCluster = class _HierCluster extends Matrix {
+  static type = "hierCluster";
+  constructor(opts) {
+    super(opts);
+    this.type = _HierCluster.type;
+    this.chartType = _HierCluster.type;
+  }
+  async init(appState) {
+    await super.init(appState);
+    this.maySetSandboxHeader(appState);
+    this.hcClipId = this.seriesClipId + "-hc";
+    this.dom.hcClipRect = this.dom.svg.select("defs").append("clipPath").attr("id", this.hcClipId).attr("clipPathUnits", "userSpaceOnUse").append("rect").attr("display", "block");
+    this.dom.topDendrogram = this.dom.svg.insert("g", "g").attr("clip-path", `url(#${this.hcClipId})`).append("g").attr("class", "sjpp-matrix-dendrogram").attr("data-testid", "hierCluster_top_dendrogram").on("click", (event) => {
+      const clickedClusterId = this.getClusterFromTopDendrogram(event);
+      if (clickedClusterId) {
+        this.clickedClusterIds = this.getAllChildrenClusterIds(clickedClusterId);
+        this.clickedClusterIds.push(clickedClusterId);
+        const clickedCluster = this.hierClusterData.clustering.col.mergedClusters.get(clickedClusterId);
+        const clickedClusterSampleNames = clickedCluster.children.map((c) => c.name);
+        this.addSelectedSamplesOptions(clickedClusterSampleNames, event);
+      } else {
+        delete this.clickedClusterIds;
+      }
+      if (this.clickedLeftClusterIds) {
+        delete this.clickedLeftClusterIds;
+        this.plotDendrogramHclust();
+      } else this.plotDendrogramHclust("top");
+    });
+    this.dom.leftDendrogram = this.dom.svg.insert("g", "g").attr("class", "sjpp-matrix-dendrogram").attr("data-testid", "hierCluster_left_dendrogram").on("click", (event) => {
+      const clickedLeftClusterId = this.getClusterFromLeftDendrogram(event);
+      if (clickedLeftClusterId) {
+        this.clickedLeftClusterIds = this.getAllChildrenClusterIds(clickedLeftClusterId, true);
+        this.clickedLeftClusterIds.push(clickedLeftClusterId);
+        const clickedLeftCluster = this.hierClusterData.clustering.row.mergedClusters.get(clickedLeftClusterId);
+        const clickedLeftClusterRowsNames = clickedLeftCluster.children.map((c) => c.name);
+        this.addSelectedRowsOptions(clickedLeftClusterRowsNames, event);
+      } else {
+        delete this.clickedLeftClusterIds;
+      }
+      if (this.clickedClusterIds) {
+        delete this.clickedClusterIds;
+        this.plotDendrogramHclust();
+      } else this.plotDendrogramHclust("left");
+    });
+  }
+  async setHierClusterData(_data = {}) {
+    this.prevServerData = this.currServerData;
+    const [d, twlst] = await this.requestData({});
+    if (d.error) throw d.error;
+    this.currServerData = structuredClone(d);
+    if (!deepEqual(this.prevServerData, this.currServerData)) {
+      delete this.clickedClusterIds;
+      delete this.clickedLeftClusterIds;
+    }
+    const s = this.settings.hierCluster;
+    if (!d.clustering) {
+      if (d.gene) {
+        throw `Cannot do clustering: data is only available for 1 gene (${d.gene}). Try again by adding more genes.`;
+      }
+    }
+    this.hierClusterData = d;
+    const c = this.hierClusterData.clustering;
+    this.setHierColorScale(c);
+    const samples = {};
+    for (const [i, column] of c.col.order.entries()) {
+      samples[column.name] = { sample: column.name };
+      for (const [j, row] of c.row.order.entries()) {
+        const tw = twlst.find((tw2) => tw2.$id === row.name || tw2.id === row.name);
+        const value = c.matrix[j][i];
+        samples[column.name][tw.$id] = {
+          key: tw.term.name,
+          values: [
+            {
+              sample: column.name,
+              dt: TermTypes2Dt[this.state.config.dataType],
+              label: s.termGroupName,
+              // gene: tw.term.name,
+              // chr: tw.term.chr,
+              // pos: `${tw.term.start}-${tw.term.stop}`,
+              value
+              // the color will be computed in matrix.cells, so that
+              // it can get updated even when there are no nonsetting state diff
+            }
+          ]
+        };
+      }
+    }
+    this.hcTermNameOrder = this.settings.hierCluster.sortClusterRows == "asListed" ? twlst.map((t) => t.term.name) : this.settings.hierCluster.sortClusterRows == "byName" ? twlst.map((t) => t.term.name).sort() : dictionaryNumericTypes.has(this.config.dataType) ? c.row.order.map((row) => twlst.find((t) => t.$id == row.name || t.term.id == row.name)?.term.name) : c.row.order.map((row) => twlst.find((t) => t.$id == row.name)?.term.name);
+    if (this.hcTermNameOrder.includes(void 0)) throw `unable to map row.name to term.name`;
+    this.hcTermSorter = (a, b) => {
+      const i = this.hcTermNameOrder.indexOf(a.tw.term.name);
+      const j = this.hcTermNameOrder.indexOf(b.tw.term.name);
+      if (i == -1 && j == -1) return 0;
+      if (i == -1) return 1;
+      if (j == -1) return -1;
+      return i - j;
+    };
+    this.hcSampleNameOrder = c.col.order.map((col) => col.name);
+    this.hcSampleSorter = (a, b) => {
+      const i = this.hcSampleNameOrder.indexOf(a.sample);
+      const j = this.hcSampleNameOrder.indexOf(b.sample);
+      if (i == -1 && j == -1) return 0;
+      if (i == -1) return 1;
+      if (j == -1) return -1;
+      return i - j;
+    };
+    const byTermId = {};
+    for (const tw of twlst) {
+      if (d.byTermId?.[tw.term.name]) byTermId[tw.$id] = d.byTermId[tw.term.name];
+    }
+    this.hierClusterSamples = {
+      refs: { byTermId, bySampleId: d.bySampleId },
+      lst: c.col.order.map((c2) => samples[c2.name]),
+      samples,
+      removedHierClusterTerms: d.removedHierClusterTerms
+    };
+  }
+  async requestData() {
+    const body = this.currRequestOpts?.hierCluster || this.getHCRequestBody(this.state);
+    const twlst = this.hcTermGroup.lst;
+    const data = await dofetch3("termdb/cluster", { body, signal: this.api.getAbortSignal?.() });
+    return [data, twlst];
+  }
+  getHCRequestBody(state) {
+    this.hcTermGroup = this.config.termgroups.find((grp) => grp.type == "hierCluster") || this.termOrder?.find((t) => t.grp.type == "hierCluster")?.grp;
+    const s = state.config.settings.hierCluster;
+    const dictionaryLegendFilter = {
+      type: "tvslst",
+      in: true,
+      join: "and",
+      lst: state.config.legendValueFilter.lst.filter((f) => !f.tvs.legendFilterType)
+    };
+    const terms = this.getClusterRowTermsAsParameter();
+    if (!terms.length) throw "no data";
+    if (!clusterMethodLst.find((i) => i.value == s.clusterMethod)) throw "Invalid cluster method";
+    if (!distanceMethodLst.find((i) => i.value == s.distanceMethod)) throw "Invalid distance method";
+    const body = {
+      genome: state.vocab.genome,
+      dslabel: state.vocab.dslabel,
+      dataType: state.config.dataType,
+      clusterMethod: s.clusterMethod,
+      distanceMethod: s.distanceMethod,
+      zScoreTransformation: s.zScoreTransformation,
+      terms,
+      filter: getNormalRoot(filterJoin([state.filter, dictionaryLegendFilter])),
+      filter0: state.filter0
+    };
+    if (state.config.dataType == "proteomeAbundance") {
+      body.proteomeDetails = {
+        organism: state.config.proteomeDetails?.organism,
+        assay: state.config.proteomeDetails?.assay,
+        cohort: state.config.proteomeDetails?.cohort
+      };
+    }
+    return body;
+  }
+  combineData() {
+    if (!this.hierClusterSamples) return;
+    const d = this.data;
+    const removedHierClusterTerms = this.hierClusterSamples.removedHierClusterTerms;
+    const samples = {};
+    const lst = [];
+    for (const sampleId in this.hierClusterSamples.samples) {
+      const s = this.hierClusterSamples.samples[sampleId];
+      samples[sampleId] = s;
+      lst.push(s);
+      if (sampleId in d.samples) Object.assign(s, d.samples[sampleId]);
+      const _ref_ = this.hierClusterSamples.refs.bySampleId[sampleId] || {};
+      if (!s._ref_) s._ref_ = _ref_;
+      else Object.assign(s._ref_, _ref_);
+    }
+    const t = this.hierClusterSamples.refs.byTermId;
+    for (const $id of Object.keys(t)) {
+      d.refs.byTermId[$id] = Object.assign({}, d.refs.byTermId[$id] || {}, t[$id]);
+    }
+    this.data = { samples, lst, refs: d.refs, removedHierClusterTerms };
+  }
+  setHierColorScale(c) {
+    const hc = this.settings.hierCluster;
+    const scale = linear(colorScaleMap[hc.colorScale].domain, colorScaleMap[hc.colorScale].range).clamp(true);
+    const globalMinMaxes = [];
+    for (const row of c.matrix) {
+      globalMinMaxes.push(...extent(row));
+    }
+    const absMax = Math.min(hc.zScoreCap, Math.max(...extent(globalMinMaxes).map(Math.abs)));
+    const [min, max] = hc.zScoreTransformation ? [-absMax, absMax] : [Math.min(...globalMinMaxes), Math.max(...globalMinMaxes)];
+    this.hierClusterValues = { scale, min, max };
+  }
+  getValueColor(value) {
+    const hc = this.settings.hierCluster;
+    if (hc.zScoreTransformation) {
+      const zScoreCap = this.settings.hierCluster.zScoreCap;
+      return this.hierClusterValues.scale((value - -zScoreCap) / (zScoreCap * 2));
+    } else {
+      return this.hierClusterValues.scale(value / this.hierClusterValues.max);
+    }
+  }
+  /* returns list of gene terms as request parameter, e.g. {gene,chr,start,stop}
+  	request parameter only need term but not tw, as it will simply fetch continuous sample values on terms without transform
+  
+  	use of this function is unfortunate because:
+  		the incomplete migration of {name} to {gene} for gene-based term
+  		geneset edit ui is hardcoded to return {name}
+  		existing plot states contain {name}
+  
+  	!!! migration instruction !!!
+  	- term.name is for display only, if a term is gene-based, it has term.gene=str
+  	- a geneVariant term can be based on a genomic range (and not a gene), in that case it won't have term.gene and cannot be used where gene is expected, e.g. gene-based clustering analysis
+  
+  	*/
+  getClusterRowTermsAsParameter() {
+    const lst = this.hcTermGroup.lst.map(this.opts.app.vocabApi.getTwMinCopy);
+    lst.sort((a, b) => a.term.name < b.term.name ? -1 : 1);
+    return lst;
+  }
+};
+for (const methods of [hierCluster_renderers_exports, hierCluster_interactivity_exports]) {
+  for (const methodName in methods) HierCluster.prototype[methodName] = methods[methodName];
+}
+var hierClusterInit = getCompInit(HierCluster);
+var componentInit = hierClusterInit;
+
+export {
+  HierCluster,
+  hierClusterInit,
+  componentInit
+};
+//# sourceMappingURL=chunk-EYIZTX33.js.map