@sjcrh/proteinpaint-client 2.193.0 → 2.195.0

package/dist/chunk-IDX6WU4U.js

@@ -0,0 +1,14 @@
+// src/block.lazyload.js
+var Block;
+async function blocklazyload(arg) {
+  if (!Block) {
+    const b = await import("./block-23BH5TZ3.js");
+    Block = b.Block;
+  }
+  return new Block(arg);
+}
+
+export {
+  blocklazyload
+};
+//# sourceMappingURL=chunk-IDX6WU4U.js.map

package/dist/chunk-IPGYIEPM.js

@@ -0,0 +1,263 @@
+import {
+  Matrix
+} from "./chunk-N7326KA3.js";
+import {
+  hierCluster_renderers_exports
+} from "./chunk-42FSM477.js";
+import {
+  hierCluster_interactivity_exports
+} from "./chunk-UKABZJQ7.js";
+import {
+  filterJoin,
+  getNormalRoot
+} from "./chunk-LYULXXGR.js";
+import {
+  clusterMethodLst,
+  distanceMethodLst,
+  dofetch3
+} from "./chunk-MNPTPENH.js";
+import {
+  deepEqual,
+  getCompInit
+} from "./chunk-M3J4MINX.js";
+import {
+  TermTypes2Dt,
+  dictionaryNumericTypes
+} from "./chunk-UAALI7MC.js";
+import {
+  colorScaleMap
+} from "./chunk-7KRS7L4U.js";
+import {
+  extent,
+  linear
+} from "./chunk-SOTB4FRE.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-IPGYIEPM.js.map

package/dist/chunk-IPGYIEPM.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/matrix/hierCluster.js"],
+  "sourcesContent": ["import { Matrix } from './matrix'\nimport { getCompInit, deepEqual } from '#rx'\nimport * as renderers from './hierCluster.renderers'\nimport * as interactivity from './hierCluster.interactivity'\nimport { dofetch3 } from '#common/dofetch'\nimport { extent } from 'd3-array'\nimport { scaleLinear } from 'd3-scale'\nimport { filterJoin, getNormalRoot } from '#filter'\nimport { clusterMethodLst, distanceMethodLst } from '#shared/clustering.js'\nimport { TermTypes2Dt, dictionaryNumericTypes } from '#shared/terms.js'\nimport { colorScaleMap } from '#shared/common.js'\n\nexport class HierCluster extends Matrix {\n\tstatic type = 'hierCluster'\n\n\tconstructor(opts) {\n\t\tsuper(opts)\n\t\tthis.type = HierCluster.type\n\t\tthis.chartType = HierCluster.type\n\t}\n\n\tasync init(appState) {\n\t\tawait super.init(appState)\n\n\t\tthis.maySetSandboxHeader(appState)\n\n\t\tthis.hcClipId = this.seriesClipId + '-hc'\n\t\tthis.dom.hcClipRect = this.dom.svg\n\t\t\t.select('defs')\n\t\t\t.append('clipPath')\n\t\t\t.attr('id', this.hcClipId)\n\t\t\t//.attr('clipPathUnits', 'objectBoundingBox')\n\t\t\t.attr('clipPathUnits', 'userSpaceOnUse')\n\t\t\t.append('rect')\n\t\t\t.attr('display', 'block')\n\n\t\tthis.dom.topDendrogram = this.dom.svg\n\t\t\t.insert('g', 'g')\n\t\t\t.attr('clip-path', `url(#${this.hcClipId})`)\n\t\t\t.append('g')\n\t\t\t.attr('class', 'sjpp-matrix-dendrogram')\n\t\t\t.attr('data-testid', 'hierCluster_top_dendrogram')\n\t\t\t.on('click', event => {\n\t\t\t\tconst clickedClusterId = this.getClusterFromTopDendrogram(event)\n\t\t\t\tif (clickedClusterId) {\n\t\t\t\t\tthis.clickedClusterIds = this.getAllChildrenClusterIds(clickedClusterId)\n\t\t\t\t\tthis.clickedClusterIds.push(clickedClusterId)\n\n\t\t\t\t\tconst clickedCluster = this.hierClusterData.clustering.col.mergedClusters.get(clickedClusterId)\n\t\t\t\t\tconst clickedClusterSampleNames = clickedCluster.children.map(c => c.name)\n\t\t\t\t\tthis.addSelectedSamplesOptions(clickedClusterSampleNames, event)\n\t\t\t\t} else {\n\t\t\t\t\t// if not clicking on a cluster, change highlighted cluster color from red back to black\n\t\t\t\t\tdelete this.clickedClusterIds\n\t\t\t\t}\n\n\t\t\t\t// rerender the row Dendrogram\n\t\t\t\tif (this.clickedLeftClusterIds) {\n\t\t\t\t\t// when left dendrogram has highlight, clicking top dendro should cancel it\n\t\t\t\t\tdelete this.clickedLeftClusterIds\n\t\t\t\t\tthis.plotDendrogramHclust()\n\t\t\t\t} else this.plotDendrogramHclust('top')\n\t\t\t})\n\n\t\tthis.dom.leftDendrogram = this.dom.svg\n\t\t\t.insert('g', 'g')\n\t\t\t.attr('class', 'sjpp-matrix-dendrogram')\n\t\t\t.attr('data-testid', 'hierCluster_left_dendrogram')\n\t\t\t.on('click', event => {\n\t\t\t\tconst clickedLeftClusterId = this.getClusterFromLeftDendrogram(event)\n\t\t\t\tif (clickedLeftClusterId) {\n\t\t\t\t\tthis.clickedLeftClusterIds = this.getAllChildrenClusterIds(clickedLeftClusterId, true)\n\t\t\t\t\tthis.clickedLeftClusterIds.push(clickedLeftClusterId)\n\n\t\t\t\t\tconst clickedLeftCluster = this.hierClusterData.clustering.row.mergedClusters.get(clickedLeftClusterId)\n\n\t\t\t\t\tconst clickedLeftClusterRowsNames = clickedLeftCluster.children.map(c => c.name)\n\n\t\t\t\t\tthis.addSelectedRowsOptions(clickedLeftClusterRowsNames, event)\n\t\t\t\t} else {\n\t\t\t\t\t// if not clicking on a cluster, change highlighted cluster color from red back to black\n\t\t\t\t\tdelete this.clickedLeftClusterIds\n\t\t\t\t}\n\n\t\t\t\t// rerender the row Dendrogram\n\t\t\t\tif (this.clickedClusterIds) {\n\t\t\t\t\t// when top dendrogram has highlight, clicking left dendro should cancel it\n\t\t\t\t\tdelete this.clickedClusterIds\n\t\t\t\t\tthis.plotDendrogramHclust()\n\t\t\t\t} else this.plotDendrogramHclust('left')\n\t\t\t})\n\t\t//.attr('clip-path', `url(#${this.seriesClipId})`)\n\t}\n\n\tasync setHierClusterData(_data = {}) {\n\t\tthis.prevServerData = this.currServerData\n\t\tconst [d, twlst] = await this.requestData({})\n\t\tif (d.error) throw d.error\n\t\tthis.currServerData = structuredClone(d)\n\t\tif (!deepEqual(this.prevServerData, this.currServerData)) {\n\t\t\t// do not persist highlighted top/left dendrogram branch selection\n\t\t\t// when the cohort, clustering method, or other config changes the server data\n\t\t\tdelete this.clickedClusterIds\n\t\t\tdelete this.clickedLeftClusterIds\n\t\t}\n\t\tconst s = this.settings.hierCluster\n\n\t\tif (!d.clustering) {\n\t\t\t// stop-gap data validation, lacks essential data part\n\t\t\tif (d.gene) {\n\t\t\t\t// for now backend returns {gene:str, data:{}} if there's only 1 eligible gene\n\t\t\t\tthrow `Cannot do clustering: data is only available for 1 gene (${d.gene}). Try again by adding more genes.`\n\t\t\t}\n\t\t\t//throw 'Cannot do clustering: invalid server response (lacks .clustering{})'\n\t\t}\n\t\tthis.hierClusterData = d\n\n\t\tconst c = this.hierClusterData.clustering\n\t\tthis.setHierColorScale(c)\n\n\t\tconst samples = {}\n\n\t\t/* see comments inside plotDendrogramHclust() on structure of d.clustering.row{} and col{}\n\t\tassumes c.col is samples and c.row is non-sample things (genes for now); later may flip to c.row be samples instead!!\n\t\t*/\n\t\tfor (const [i, column] of c.col.order.entries()) {\n\t\t\tsamples[column.name] = { sample: column.name }\n\t\t\tfor (const [j, row] of c.row.order.entries()) {\n\t\t\t\tconst tw = twlst.find(tw => tw.$id === row.name || tw.id === row.name)\n\t\t\t\t// if (!tw) {\n\t\t\t\t// \tconsole.warn(`no matching tw for row.name='${row.name}'`)\n\t\t\t\t// \tcontinue\n\t\t\t\t// }\n\t\t\t\tconst value = c.matrix[j][i]\n\t\t\t\tsamples[column.name][tw.$id] = {\n\t\t\t\t\tkey: tw.term.name,\n\t\t\t\t\tvalues: [\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tsample: column.name,\n\t\t\t\t\t\t\tdt: TermTypes2Dt[this.state.config.dataType],\n\t\t\t\t\t\t\tlabel: s.termGroupName,\n\t\t\t\t\t\t\t// gene: tw.term.name,\n\t\t\t\t\t\t\t// chr: tw.term.chr,\n\t\t\t\t\t\t\t// pos: `${tw.term.start}-${tw.term.stop}`,\n\t\t\t\t\t\t\tvalue\n\t\t\t\t\t\t\t// the color will be computed in matrix.cells, so that\n\t\t\t\t\t\t\t// it can get updated even when there are no nonsetting state diff\n\t\t\t\t\t\t}\n\t\t\t\t\t]\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\tthis.hcTermNameOrder =\n\t\t\tthis.settings.hierCluster.sortClusterRows == 'asListed'\n\t\t\t\t? twlst.map(t => t.term.name)\n\t\t\t\t: this.settings.hierCluster.sortClusterRows == 'byName'\n\t\t\t\t? twlst.map(t => t.term.name).sort()\n\t\t\t\t: dictionaryNumericTypes.has(this.config.dataType)\n\t\t\t\t? c.row.order.map(row => twlst.find(t => t.$id == row.name || t.term.id == row.name)?.term.name)\n\t\t\t\t: c.row.order.map(row => twlst.find(t => t.$id == row.name)?.term.name)\n\n\t\tif (this.hcTermNameOrder.includes(undefined)) throw `unable to map row.name to term.name`\n\n\t\tthis.hcTermSorter = (a, b) => {\n\t\t\tconst i = this.hcTermNameOrder.indexOf(a.tw.term.name)\n\t\t\tconst j = this.hcTermNameOrder.indexOf(b.tw.term.name)\n\t\t\tif (i == -1 && j == -1) return 0\n\t\t\tif (i == -1) return 1\n\t\t\tif (j == -1) return -1\n\t\t\treturn i - j\n\t\t}\n\n\t\tthis.hcSampleNameOrder = c.col.order.map(col => col.name)\n\t\tthis.hcSampleSorter = (a, b) => {\n\t\t\tconst i = this.hcSampleNameOrder.indexOf(a.sample)\n\t\t\tconst j = this.hcSampleNameOrder.indexOf(b.sample)\n\t\t\tif (i == -1 && j == -1) return 0\n\t\t\tif (i == -1) return 1\n\t\t\tif (j == -1) return -1\n\t\t\treturn i - j\n\t\t}\n\n\t\t// from d.byTermId to byTermId: change byTermId keys from gene names to $ids\n\t\tconst byTermId = {}\n\t\tfor (const tw of twlst) {\n\t\t\tif (d.byTermId?.[tw.term.name]) byTermId[tw.$id] = d.byTermId[tw.term.name]\n\t\t}\n\t\tthis.hierClusterSamples = {\n\t\t\trefs: { byTermId, bySampleId: d.bySampleId },\n\t\t\tlst: c.col.order.map(c => samples[c.name]),\n\t\t\tsamples,\n\t\t\tremovedHierClusterTerms: d.removedHierClusterTerms\n\t\t}\n\t}\n\n\tasync requestData() {\n\t\t// may revert to using {signal} argument if detectStale() is used to wrap this function\n\t\tconst body = this.currRequestOpts?.hierCluster || this.getHCRequestBody(this.state)\n\t\tconst twlst = this.hcTermGroup.lst\n\t\tconst data = await dofetch3('termdb/cluster', { body, signal: this.api.getAbortSignal?.() })\n\t\t// return the twlst that was submitted in the data request, this data-to-twlst reference will not be affected by race condition\n\t\treturn [data, twlst]\n\t}\n\n\tgetHCRequestBody(state) {\n\t\tthis.hcTermGroup =\n\t\t\tthis.config.termgroups.find(grp => grp.type == 'hierCluster') ||\n\t\t\tthis.termOrder?.find(t => t.grp.type == 'hierCluster')?.grp\n\n\t\tconst s = state.config.settings.hierCluster\n\t\t// temporary fix to get rid of hard/soft filter and only keep dictionary legend filter,\n\t\t// soft filter shouldn't be used to filter out any samples for hierCluster\n\t\t// TODO: add hard filter back to filter out samples\n\t\tconst dictionaryLegendFilter = {\n\t\t\ttype: 'tvslst',\n\t\t\tin: true,\n\t\t\tjoin: 'and',\n\t\t\tlst: state.config.legendValueFilter.lst.filter(f => !f.tvs.legendFilterType)\n\t\t}\n\t\tconst terms = this.getClusterRowTermsAsParameter()\n\t\tif (!terms.length) throw 'no data'\n\t\t// !!! NOTE !!!\n\t\t// all parameters here must remove payload properties that are\n\t\t// not relevant to the data request, so that the dofetch and/or\n\t\t// browser caching would work\n\n\t\t// Checking if cluster and distance method for hierarchial clustering is valid\n\t\tif (!clusterMethodLst.find(i => i.value == s.clusterMethod)) throw 'Invalid cluster method'\n\t\tif (!distanceMethodLst.find(i => i.value == s.distanceMethod)) throw 'Invalid distance method'\n\t\tconst body = {\n\t\t\tgenome: state.vocab.genome,\n\t\t\tdslabel: state.vocab.dslabel,\n\t\t\tdataType: state.config.dataType,\n\t\t\tclusterMethod: s.clusterMethod,\n\t\t\tdistanceMethod: s.distanceMethod,\n\t\t\tzScoreTransformation: s.zScoreTransformation,\n\t\t\tterms,\n\t\t\tfilter: getNormalRoot(filterJoin([state.filter, dictionaryLegendFilter])),\n\t\t\tfilter0: state.filter0\n\t\t}\n\t\tif (state.config.dataType == 'proteomeAbundance') {\n\t\t\tbody.proteomeDetails = {\n\t\t\t\torganism: state.config.proteomeDetails?.organism,\n\t\t\t\tassay: state.config.proteomeDetails?.assay,\n\t\t\t\tcohort: state.config.proteomeDetails?.cohort\n\t\t\t}\n\t\t}\n\t\treturn body\n\t}\n\n\tcombineData() {\n\t\tif (!this.hierClusterSamples) return\n\t\tconst d = this.data // matrix data\n\t\tconst removedHierClusterTerms = this.hierClusterSamples.removedHierClusterTerms\n\t\tconst samples = {}\n\t\tconst lst = []\n\t\t// the gene expression samples will be used as a filter for the matrix samples\n\t\tfor (const sampleId in this.hierClusterSamples.samples) {\n\t\t\tconst s = this.hierClusterSamples.samples[sampleId]\n\t\t\tsamples[sampleId] = s\n\t\t\tlst.push(s)\n\t\t\tif (sampleId in d.samples) Object.assign(s, d.samples[sampleId])\n\t\t\tconst _ref_ = this.hierClusterSamples.refs.bySampleId[sampleId] || {}\n\t\t\tif (!s._ref_) s._ref_ = _ref_\n\t\t\t// hierCluster refs.bySampleId will overwrite matrix reference properties with the same name\n\t\t\telse Object.assign(s._ref_, _ref_)\n\t\t}\n\n\t\t// combine this.hierClusterSamples.refs.byTermId into this.data.refs.byTermId\n\t\tconst t = this.hierClusterSamples.refs.byTermId\n\t\tfor (const $id of Object.keys(t)) {\n\t\t\td.refs.byTermId[$id] = Object.assign({}, d.refs.byTermId[$id] || {}, t[$id])\n\t\t}\n\t\tthis.data = { samples, lst, refs: d.refs, removedHierClusterTerms }\n\t}\n\n\tsetHierColorScale(c) {\n\t\tconst hc = this.settings.hierCluster\n\t\tconst scale = scaleLinear(colorScaleMap[hc.colorScale].domain, colorScaleMap[hc.colorScale].range).clamp(true)\n\t\tconst globalMinMaxes = []\n\t\tfor (const row of c.matrix) {\n\t\t\tglobalMinMaxes.push(...extent(row))\n\t\t}\n\t\tconst absMax = Math.min(hc.zScoreCap, Math.max(...extent(globalMinMaxes).map(Math.abs)))\n\t\t// if zScore transformation is not performed, should use min/max value from data\n\t\tconst [min, max] = hc.zScoreTransformation\n\t\t\t? [-absMax, absMax]\n\t\t\t: [Math.min(...globalMinMaxes), Math.max(...globalMinMaxes)]\n\t\t// what's purpose of assigning this.hierClusterValues{}, to signal something to matrix code?\n\t\tthis.hierClusterValues = { scale, min, max }\n\t}\n\n\tgetValueColor(value) {\n\t\tconst hc = this.settings.hierCluster\n\t\tif (hc.zScoreTransformation) {\n\t\t\tconst zScoreCap = this.settings.hierCluster.zScoreCap\n\t\t\treturn this.hierClusterValues.scale((value - -zScoreCap) / (zScoreCap * 2))\n\t\t} else {\n\t\t\treturn this.hierClusterValues.scale(value / this.hierClusterValues.max)\n\t\t}\n\t}\n\n\t/* returns list of gene terms as request parameter, e.g. {gene,chr,start,stop}\n\trequest parameter only need term but not tw, as it will simply fetch continuous sample values on terms without transform\n\n\tuse of this function is unfortunate because:\n\t\tthe incomplete migration of {name} to {gene} for gene-based term\n\t\tgeneset edit ui is hardcoded to return {name}\n\t\texisting plot states contain {name}\n\n\t!!! migration instruction !!!\n\t- term.name is for display only, if a term is gene-based, it has term.gene=str\n\t- 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\n\n\t*/\n\tgetClusterRowTermsAsParameter() {\n\t\tconst lst = this.hcTermGroup.lst.map(this.opts.app.vocabApi.getTwMinCopy)\n\t\t// this helps caching by having a more consistent URL string\n\t\tlst.sort((a, b) => (a.term.name < b.term.name ? -1 : 1))\n\t\treturn lst\n\t}\n}\n\nfor (const methods of [renderers, interactivity]) {\n\tfor (const methodName in methods) HierCluster.prototype[methodName] = methods[methodName]\n}\n\nexport const hierClusterInit = getCompInit(HierCluster)\nexport const componentInit = hierClusterInit\n"],
+  "mappings": 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+  "names": ["tw", "c"]
+}

package/dist/chunk-IQTEW3SK.js

@@ -0,0 +1,119 @@
+import {
+  GENE_EXPRESSION,
+  METABOLITE_INTENSITY,
+  PROTEOME_ABUNDANCE,
+  SINGLECELL_GENE_EXPRESSION
+} from "./chunk-UAALI7MC.js";
+
+// common/termutils.js
+function sample_match_termvaluesetting(row, filter, geneVariant$ids) {
+  const lst = !filter ? [] : filter.type == "tvslst" ? filter.lst : [filter];
+  let numberofmatchedterms = 0;
+  for (const item of lst) {
+    if (item.type == "tvslst") {
+      if (sample_match_termvaluesetting(row, item)) {
+        numberofmatchedterms++;
+      }
+    } else {
+      const t = item.tvs;
+      let samplevalue;
+      if (t.term.type == "geneVariant") {
+        samplevalue = geneVariant$ids.map((g) => row[g]).filter((s) => s);
+      } else if (t.term.type == "integer" || t.term.type == "float" || t.term.type == GENE_EXPRESSION || t.term.type == METABOLITE_INTENSITY || t.term.type == PROTEOME_ABUNDANCE) {
+        samplevalue = row[t.term.id] || row[t.term.$id]?.key;
+      } else if (t.term.type == "survival") {
+        samplevalue = row[t.term.$id]?.key;
+      } else {
+        samplevalue = row[t.term.id] || row[t.term.$id]?.value;
+      }
+      let thistermmatch;
+      if (t.term.type == "categorical") {
+        if (samplevalue === void 0) {
+          if (t.isnot) thistermmatch = !thistermmatch;
+          if (thistermmatch) numberofmatchedterms++;
+          continue;
+        }
+        const valueset = t.valueset ? t.valueset : new Set(t.values.map((i) => i.key));
+        thistermmatch = valueset.has(samplevalue);
+      } else if (t.term.type == "integer" || t.term.type == "float" || t.term.type == GENE_EXPRESSION || t.term.type == METABOLITE_INTENSITY || t.term.type == PROTEOME_ABUNDANCE) {
+        if (samplevalue === void 0) {
+          if (t.isnot) thistermmatch = !thistermmatch;
+          if (thistermmatch) numberofmatchedterms++;
+          continue;
+        }
+        for (const range of t.ranges) {
+          if ("value" in range) {
+            thistermmatch = samplevalue === range.value;
+            if (thistermmatch) break;
+          } else if (samplevalue == range.name) {
+            thistermmatch = true;
+            break;
+          } else {
+            if (t.term.values) {
+              const v = t.term.values[samplevalue.toString()];
+              if (v && v.uncomputable) {
+                continue;
+              }
+            }
+            let left, right;
+            if (range.startunbounded) {
+              left = true;
+            } else if ("start" in range) {
+              if (range.startinclusive) {
+                left = samplevalue >= range.start;
+              } else {
+                left = samplevalue > range.start;
+              }
+            }
+            if (range.stopunbounded) {
+              right = true;
+            } else if ("stop" in range) {
+              if (range.stopinclusive) {
+                right = samplevalue <= range.stop;
+              } else {
+                right = samplevalue < range.stop;
+              }
+            }
+            thistermmatch = left && right;
+          }
+          if (thistermmatch) break;
+        }
+      } else if (t.term.type == "condition") {
+        const key = getPrecomputedKey(t);
+        const anno = samplevalue && samplevalue[key];
+        if (anno) {
+          thistermmatch = Array.isArray(anno) ? t.values.find((d) => anno.includes(d.key)) : t.values.find((d) => d.key == anno);
+        }
+      } else if (t.term.type == "survival") {
+        if (samplevalue === void 0) {
+          if (t.isnot) thistermmatch = !thistermmatch;
+          if (thistermmatch) numberofmatchedterms++;
+          continue;
+        }
+        const valueset = t.valueset ? t.valueset : new Set(t.values.map((i) => i.key));
+        thistermmatch = valueset.has(samplevalue);
+      } else if (t.term.type == "geneVariant" && t.legendFilterType == "geneVariant_hard") {
+        const f = t.values[0];
+        thistermmatch = samplevalue.find((s) => {
+          for (const v of s.values) {
+            if (v.dt == f.dt && (!v.origin || v.origin == f.origin) && f.mclasslst.includes(v.class)) return true;
+          }
+        }) && true;
+      } else if (t.term.type == SINGLECELL_GENE_EXPRESSION) {
+      } else {
+        throw "unknown term type";
+      }
+      if (t.isnot) {
+        thistermmatch = !thistermmatch;
+      }
+      if (thistermmatch) numberofmatchedterms++;
+    }
+    if (filter.join == "or" && numberofmatchedterms) return true;
+  }
+  if (numberofmatchedterms == lst.length) return true;
+}
+
+export {
+  sample_match_termvaluesetting
+};
+//# sourceMappingURL=chunk-IQTEW3SK.js.map

package/dist/chunk-J7W2DGAL.js

@@ -0,0 +1,226 @@
+import {
+  SINGLECELL_CELLTYPE,
+  SINGLECELL_GENE_EXPRESSION
+} from "./chunk-UAALI7MC.js";
+
+// test/testdata/data.ts
+function getSamplelstTw() {
+  const values = [
+    {
+      sampleId: 42,
+      sample: "2660"
+    },
+    {
+      sampleId: 44,
+      sample: "2688"
+    },
+    {
+      sampleId: 45,
+      sample: "2702"
+    },
+    {
+      sampleId: 46,
+      sample: "2716"
+    },
+    {
+      sampleId: 59,
+      sample: "2898"
+    },
+    {
+      sampleId: 60,
+      sample: "2912"
+    },
+    {
+      sampleId: 67,
+      sample: "3010"
+    },
+    {
+      sampleId: 68,
+      sample: "3024"
+    },
+    {
+      sampleId: 69,
+      sample: "3038"
+    },
+    {
+      sampleId: 70,
+      sample: "3052"
+    },
+    {
+      sampleId: 73,
+      sample: "3094"
+    },
+    {
+      sampleId: 79,
+      sample: "3178"
+    },
+    {
+      sampleId: 80,
+      sample: "3192"
+    }
+  ];
+  return {
+    term: {
+      name: "termdbtest samplelst",
+      type: "samplelst",
+      values: {
+        "Group 1": {
+          key: "Group 1",
+          label: "Group 1",
+          list: values
+        },
+        "Not in Group 1": {
+          key: "Not in Group 1",
+          label: "Not in Group 1",
+          list: values
+        }
+      }
+    },
+    q: {
+      mode: "discrete",
+      groups: [
+        {
+          name: "Group 1",
+          in: true,
+          values
+        },
+        {
+          name: "Not in Group 1",
+          in: false,
+          values
+        }
+      ],
+      isAtomic: true
+    }
+  };
+}
+function getCategoryGroupsetting() {
+  return {
+    id: "diaggrp",
+    q: {
+      type: "custom-groupset",
+      customset: {
+        name: "A versus B",
+        groups: [
+          {
+            name: "Test A",
+            type: "values",
+            values: [{ key: "Acute lymphoblastic leukemia" }, { key: "Wilms tumor" }]
+          },
+          {
+            name: "Test B",
+            type: "values",
+            values: [
+              { key: "Central nervous system (CNS)" },
+              { key: "Acute myeloid leukemia" },
+              { key: "Non-Hodgkin lymphoma" }
+            ]
+          }
+        ]
+      }
+    }
+  };
+}
+function getGenesetMutTw() {
+  return {
+    term: {
+      genes: [
+        { kind: "gene", gene: "TP53", type: "geneVariant" },
+        { kind: "gene", gene: "KRAS", type: "geneVariant" },
+        { kind: "gene", gene: "AKT1", type: "geneVariant" },
+        { kind: "gene", gene: "BCR", type: "geneVariant" }
+      ],
+      type: "geneVariant"
+    },
+    q: { type: "predefined-groupset" }
+  };
+}
+function getGeneVariantTw(position = false) {
+  return {
+    term: {
+      genes: [
+        position ? { kind: "coord", chr: "chr12", start: 25205246, stop: 25250936, name: "KRASregion", type: "geneVariant" } : { kind: "gene", gene: "TP53", type: "geneVariant" }
+      ],
+      type: "geneVariant"
+    },
+    q: { type: "predefined-groupset", predefined_groupset_idx: 0, hiddenValues: {} }
+  };
+}
+function getSsgseaTw(isBin = false) {
+  return {
+    term: { id: "HALLMARK_ADIPOGENESIS", type: "ssGSEA", name: "HALLMARK_ADIPOGENESIS" },
+    q: isBin ? {
+      type: "regular-bin",
+      startinclusive: true,
+      bin_size: 0.2,
+      first_bin: { stop: -0.4 },
+      last_bin: { start: 0.8 },
+      mode: "discrete"
+    } : { mode: "continuous" }
+  };
+}
+function getScgeneexpTw(gene = "KRAS") {
+  return {
+    term: {
+      type: SINGLECELL_GENE_EXPRESSION,
+      id: gene,
+      gene,
+      name: gene,
+      sample: {
+        sID: "1_patient"
+      }
+    },
+    q: {
+      mode: "continuous"
+    }
+  };
+}
+function getScctTw() {
+  return {
+    term: {
+      type: SINGLECELL_CELLTYPE,
+      id: "CellType",
+      name: "Cell Type",
+      sample: {
+        sID: "1_patient"
+      },
+      plot: "UMAP",
+      colorBy: "CellType",
+      values: {
+        T_NK: {
+          key: "T_NK",
+          value: "T_NK"
+        },
+        Blast: {
+          key: "Blast",
+          value: "Blast"
+        },
+        Monocyte: {
+          key: "Monocyte",
+          value: "Monocyte"
+        }
+      },
+      groupsetting: {
+        disabled: false
+      }
+    }
+  };
+}
+function getCategoricalTermcollectionTw() {
+  return {
+    type: "TermCollectionTWQual",
+    term: { type: "termCollection", name: "Assay Availability" }
+  };
+}
+
+export {
+  getSamplelstTw,
+  getCategoryGroupsetting,
+  getGenesetMutTw,
+  getGeneVariantTw,
+  getSsgseaTw,
+  getScgeneexpTw,
+  getScctTw,
+  getCategoricalTermcollectionTw
+};
+//# sourceMappingURL=chunk-J7W2DGAL.js.map