@sjcrh/proteinpaint-client 2.184.0 → 2.185.0

package/dist/chunk-2LSQTG2W.js

@@ -1,261 +0,0 @@
-import {
-  Matrix
-} from "./chunk-CJLWB4HZ.js";
-import {
-  hierCluster_renderers_exports
-} from "./chunk-JTX4Z2DL.js";
-import {
-  hierCluster_interactivity_exports
-} from "./chunk-QA52MW7K.js";
-import {
-  filterJoin,
-  getNormalRoot
-} from "./chunk-KBYRXJ6Y.js";
-import {
-  clusterMethodLst,
-  distanceMethodLst,
-  dofetch3
-} from "./chunk-RCYTUKAJ.js";
-import {
-  deepEqual,
-  getCompInit
-} from "./chunk-MVTCBVSX.js";
-import {
-  TermTypes2Dt
-} from "./chunk-SOED2SLH.js";
-import {
-  colorScaleMap
-} from "./chunk-XRVBHNCW.js";
-import {
-  extent,
-  linear
-} from "./chunk-OAWQ6LOO.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() : 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 = {
-        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-2LSQTG2W.js.map

package/dist/chunk-2LSQTG2W.js.map

@@ -1,7 +0,0 @@
-{
-  "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 } 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: 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\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-2QGWWYYS.js

@@ -1,102 +0,0 @@
-import {
-  renderTable
-} from "./chunk-KBYRXJ6Y.js";
-
-// termdb/handlers/termCollection.ts
-var SearchHandler = class {
-  async init(opts) {
-    this.callback = opts.callback;
-    this.app = opts.app;
-    opts.holder.style("display", "");
-    const tableDiv = opts.holder.append("div");
-    const termlst = opts.details.termlst ?? [];
-    renderTable({
-      columns: [{ label: "VARIABLES" }],
-      rows: termlst.map((t) => {
-        return [{ value: t.name }];
-      }),
-      div: tableDiv,
-      maxWidth: "30vw",
-      maxHeight: "40vh",
-      noButtonCallback: () => {
-      },
-      // FIXME to supply a real callback
-      striped: false,
-      showHeader: true,
-      //false,
-      selectAll: true,
-      columnButtons: void 0,
-      //Leave until table.js is typed
-      buttons: void 0
-    });
-    let categoryTable;
-    let ckSource = [];
-    if (opts.details.categoryKeys) {
-      ckSource = opts.details.categoryKeys;
-      const categoryDiv = opts.holder.append("div").style("margin-top", "15px");
-      const values = opts.details.termlst[0].values || {};
-      categoryTable = categoryDiv.append("div");
-      renderTable({
-        columns: [{ label: "CATEGORIES" }],
-        rows: ckSource.map((ck) => {
-          return [{ value: values[ck.key]?.label ?? ck.key, checked: ck.shown }];
-        }),
-        div: categoryTable,
-        maxWidth: "30vw",
-        maxHeight: "40vh",
-        noButtonCallback: () => {
-        },
-        // FIXME to supply a real callback
-        striped: false,
-        showHeader: true,
-        //false,
-        selectAll: true,
-        columnButtons: void 0,
-        //Leave until table.js is typed
-        buttons: void 0
-      });
-    }
-    opts.holder.append("div").style("float", "right").style("padding", "6px 20px").append("button").attr("class", "sjpp_apply_btn sja_filter_tag_btn").text("Select").on("click", () => {
-      const trs = tableDiv.select("table").select("tbody").node().querySelectorAll("tr");
-      const selectedTermlst = termlst.filter((term, i) => {
-        const checked = trs[i]?.querySelectorAll("td")[1]?.querySelector("input")?.checked;
-        return checked === true;
-      });
-      if (selectedTermlst.length === 0) {
-        alert("Please select at least one term");
-        return;
-      }
-      const propsByTermId = {};
-      if (opts.details.propsByTermId) {
-        for (const t of selectedTermlst) {
-          if (opts.details.propsByTermId[t.id]) propsByTermId[t.id] = opts.details.propsByTermId[t.id];
-        }
-      }
-      let categoryKeys;
-      if (categoryTable) {
-        const trs2 = categoryTable.select("table").select("tbody").node().querySelectorAll("tr");
-        categoryKeys = ckSource.map((ck, i) => {
-          const checked = trs2[i].querySelectorAll("td")[1].querySelector("input")?.checked;
-          return { key: ck.key, shown: !!checked };
-        });
-      }
-      opts.callback({
-        type: "termCollection",
-        termIds: selectedTermlst.map((i) => i.id),
-        termlst: selectedTermlst,
-        name: opts.details.name,
-        valueTransform: opts.details.valueTransformByPlots?.[opts.usecase.target],
-        // memberType = ds.cohort.termdb.termCollections[].type for client code
-        memberType: opts.details.memberType || opts.details.type,
-        categoryKeys,
-        isleaf: true,
-        propsByTermId
-      });
-    });
-  }
-};
-
-export {
-  SearchHandler
-};
-//# sourceMappingURL=chunk-2QGWWYYS.js.map

package/dist/chunk-2VNTM6TR.js

@@ -1,129 +0,0 @@
-import {
-  keyupEnter
-} from "./chunk-KBYRXJ6Y.js";
-
-// src/block.mds.svcnv.share.js
-function rnabamtk_initparam(c) {
-  if (!c.dna_mintotalreads) c.dna_mintotalreads = 8;
-  if (!c.rna_mintotalreads) c.rna_mintotalreads = 8;
-  if (!c.hetsnp_minbaf) c.hetsnp_minbaf = 0.3;
-  if (!c.hetsnp_maxbaf) c.hetsnp_maxbaf = 0.7;
-  if (c.rnapileup_q == void 0) c.rnapileup_q = 0;
-  if (!c.rnapileup_Q) c.rnapileup_Q = 13;
-  if (!c.binompvaluecutoff) c.binompvaluecutoff = 0.05;
-  if (!c.clientcolor_snpinuse) c.clientcolor_snpinuse = "blue";
-  if (!c.clientcolor_markernotinuse) c.clientcolor_markernotinuse = "#bbb";
-}
-function configPanel_rnabam(tk, block, loadTk) {
-  const c = tk.checkrnabam;
-  if (!c) return;
-  tk.tkconfigtip.d.append("hr");
-  const d = tk.tkconfigtip.d.append("div").style("margin", "15px 0px");
-  d.append("div").style("opacity", 0.5).style("font-size", ".9em").text("Finding heterozygous SNPs in DNA");
-  {
-    const row = d.append("div").style("margin-top", "5px");
-    row.append("span").html("DNA minimum total read count ");
-    row.append("input").attr("type", "number").style("width", "50px").property("value", c.dna_mintotalreads).on("keyup", (event) => {
-      if (!keyupEnter(event)) return;
-      let v = Number.parseInt(event.target.value);
-      if (!v || v <= 0) return;
-      if (c.dna_mintotalreads == v) {
-        return;
-      }
-      c.dna_mintotalreads = v;
-      loadTk(tk, block);
-    });
-    row.append("div").style("opacity", ".5").style("font-size", ".8em").text("If a SNP's total coverage is below cutoff, it will be skipped.");
-  }
-  {
-    const row = d.append("div").style("margin-top", "5px");
-    row.append("span").html("Heterozygous SNP BAF range&nbsp;&nbsp;");
-    row.append("input").attr("type", "number").style("width", "50px").property("value", c.hetsnp_minbaf).on("keyup", (event) => {
-      if (!keyupEnter(event)) return;
-      let v = Number.parseFloat(event.target.value);
-      if (!v || v <= 0) return;
-      if (c.hetsnp_minbaf == v) {
-        return;
-      }
-      c.hetsnp_minbaf = v;
-      loadTk(tk, block);
-    });
-    row.append("span").style("opacity", ".5").style("font-size", ".8em").html("&nbsp;&leq; BAF &leq;&nbsp;");
-    row.append("input").attr("type", "number").style("width", "50px").property("value", c.hetsnp_maxbaf).on("keyup", (event) => {
-      if (!keyupEnter(event)) return;
-      let v = Number.parseFloat(event.target.value);
-      if (!v || v <= 0) return;
-      if (c.hetsnp_maxbaf == v) {
-        return;
-      }
-      c.hetsnp_maxbaf = v;
-      loadTk(tk, block);
-    });
-    row.append("div").style("opacity", ".5").style("font-size", ".8em").text("If a SNP's BAF (B-allele fraction) is within this range, it is heterozygous.");
-  }
-  d.append("div").style("margin-top", "20px").style("opacity", 0.5).style("font-size", ".9em").text("Counting alleles in RNA-seq BAM file");
-  {
-    const row = d.append("div").style("margin-top", "5px");
-    row.append("span").html("Skip alignments with mapQ smaller than&nbsp;");
-    row.append("input").attr("type", "number").style("width", "50px").property("value", c.rnapileup_q).on("keyup", (event) => {
-      if (!keyupEnter(event)) return;
-      let v = Number.parseInt(event.target.value);
-      if (!v || v < 0) return;
-      if (c.rnapileup_q == v) {
-        return;
-      }
-      c.rnapileup_q = v;
-      loadTk(tk, block);
-    });
-  }
-  {
-    const row = d.append("div").style("margin-top", "5px");
-    row.append("span").html("Skip bases with baseQ/BAQ smaller than&nbsp;");
-    row.append("input").attr("type", "number").style("width", "50px").property("value", c.rnapileup_Q).on("keyup", (event) => {
-      if (!keyupEnter(event)) return;
-      let v = Number.parseInt(event.target.value);
-      if (!v || v <= 0) return;
-      if (c.rnapileup_Q == v) {
-        return;
-      }
-      c.rnapileup_Q = v;
-      loadTk(tk, block);
-    });
-  }
-  d.append("div").style("margin-top", "20px").style("opacity", 0.5).style("font-size", ".9em").text("Binomial test on whether a heterozygous SNP shows allelic bias in RNA");
-  {
-    const row = d.append("div").style("margin-top", "5px");
-    row.append("span").html("P-value cutoff&nbsp;");
-    row.append("input").attr("type", "number").style("width", "50px").property("value", c.binompvaluecutoff).on("keyup", (event) => {
-      if (!keyupEnter(event)) return;
-      let v = Number.parseFloat(event.target.value);
-      if (!v || v <= 0 || v >= 1) return;
-      if (c.binompvaluecutoff == v) {
-        return;
-      }
-      c.binompvaluecutoff = v;
-      loadTk(tk, block);
-    });
-  }
-  {
-    const row = d.append("div").style("margin-top", "5px");
-    row.append("span").html("RNA minimum total read count&nbsp;");
-    row.append("input").attr("type", "number").style("width", "50px").property("value", c.rna_mintotalreads).on("keyup", (event) => {
-      if (!keyupEnter(event)) return;
-      let v = Number.parseInt(event.target.value);
-      if (!v || v <= 0) return;
-      if (c.rna_mintotalreads == v) {
-        return;
-      }
-      c.rna_mintotalreads = v;
-      loadTk(tk, block);
-    });
-    row.append("div").style("opacity", ".5").style("font-size", ".8em").text("If a SNP's total read count from RNA is below cutoff, it won't do binomial test.");
-  }
-}
-
-export {
-  rnabamtk_initparam,
-  configPanel_rnabam
-};
-//# sourceMappingURL=chunk-2VNTM6TR.js.map

package/dist/chunk-4X6J6CZA.js

@@ -1,107 +0,0 @@
-import {
-  dofetch3
-} from "./chunk-RCYTUKAJ.js";
-import {
-  DNA_METHYLATION,
-  GENE_EXPRESSION,
-  SINGLECELL_CELLTYPE
-} from "./chunk-SOED2SLH.js";
-
-// plots/volcano/model/VolcanoModel.ts
-var VolcanoModel = class {
-  constructor(app, termType) {
-    this.app = app;
-    this.termType = termType;
-  }
-  /** May use mapper instead as more termTypes are added */
-  async getData(config, settings) {
-    this.config = config;
-    this.settings = settings;
-    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
-    };
-    this.addConfounderTw(body);
-    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
-    };
-    this.addConfounderTw(body);
-    return body;
-  }
-  //This is a workaround until the server can accept an arr of confounder tws
-  addConfounderTw(body) {
-    const confounders = this.config?.confounderTws;
-    if (confounders?.length) {
-      body.tw = this.config.confounderTws[0];
-      if (confounders.length > 1) body.tw2 = this.config.confounderTws[1];
-    }
-  }
-  //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-4X6J6CZA.js.map

package/dist/chunk-4X6J6CZA.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../plots/volcano/model/VolcanoModel.ts"],
-  "sourcesContent": ["import type { MassAppApi } from '#mass/types/mass'\nimport { dofetch3 } from '#common/dofetch'\nimport type { DERequest, DiffMethRequest, TermdbSingleCellDEgenesRequest } from '#types'\nimport { DNA_METHYLATION, GENE_EXPRESSION, SINGLECELL_CELLTYPE } from '#shared/terms.js'\n\nexport class VolcanoModel {\n\tapp: MassAppApi\n\tconfig!: any\n\tsettings!: any\n\ttermType: string\n\n\tconstructor(app: MassAppApi, termType: string) {\n\t\tthis.app = app\n\t\tthis.termType = termType\n\t}\n\n\t/** May use mapper instead as more termTypes are added */\n\tasync getData(config: any, settings: any) {\n\t\tthis.config = config\n\t\tthis.settings = settings\n\n\t\tif (this.termType === GENE_EXPRESSION) {\n\t\t\tconst body = await this.getGERequestBody()\n\t\t\treturn await dofetch3('termdb/DE', { body })\n\t\t}\n\t\tif (this.termType === DNA_METHYLATION) {\n\t\t\tconst body = await this.getDMRequestBody()\n\t\t\treturn await dofetch3('termdb/diffMeth', { body })\n\t\t}\n\t\tif (this.termType === SINGLECELL_CELLTYPE) {\n\t\t\tconst body = await this.getSCCTRequestBody()\n\t\t\treturn await dofetch3('termdb/singlecellDEgenes', { body })\n\t\t} else {\n\t\t\tthrow new Error(`Volcano plot does not support route for termType='${this.termType}'`)\n\t\t}\n\t}\n\n\t//Gene expression\n\tasync getGERequestBody() {\n\t\tawait this.getOtherSamples(this.config.samplelst)\n\t\tconst state = this.app.getState()\n\t\tconst body = {\n\t\t\tgenome: this.app.vocabApi.vocab.genome,\n\t\t\tdslabel: this.app.vocabApi.vocab.dslabel,\n\t\t\tmethod: this.settings.method,\n\t\t\tmin_count: this.settings.minCount,\n\t\t\tmin_total_count: this.settings.minTotalCount,\n\t\t\tsamplelst: this.config.samplelst,\n\t\t\tfilter: state.termfilter.filter,\n\t\t\tfilter0: state.termfilter.filter0,\n\t\t\tcpm_cutoff: this.settings.cpmCutoff\n\t\t} as Partial<DERequest> //remove Partial when storage_type is removed from DERequest\n\n\t\tthis.addConfounderTw(body)\n\n\t\treturn body\n\t}\n\n\t//DNA methylation\n\tasync getDMRequestBody() {\n\t\tawait this.getOtherSamples(this.config.samplelst)\n\t\tconst state = this.app.getState()\n\t\tconst body = {\n\t\t\tgenome: this.app.vocabApi.vocab.genome,\n\t\t\tdslabel: this.app.vocabApi.vocab.dslabel,\n\t\t\tsamplelst: this.config.samplelst,\n\t\t\tfilter: state.termfilter.filter,\n\t\t\tfilter0: state.termfilter.filter0,\n\t\t\tmin_samples_per_group: this.settings.minSamplesPerGroup\n\t\t} as Partial<DiffMethRequest>\n\n\t\tthis.addConfounderTw(body)\n\n\t\treturn body\n\t}\n\n\t//This is a workaround until the server can accept an arr of confounder tws\n\taddConfounderTw(body) {\n\t\tconst confounders = this.config?.confounderTws\n\t\tif (confounders?.length) {\n\t\t\tbody.tw = this.config.confounderTws[0]\n\t\t\tif (confounders.length > 1) body.tw2 = this.config.confounderTws[1]\n\t\t}\n\t}\n\n\t//Single cell cell type\n\tgetSCCTRequestBody(): TermdbSingleCellDEgenesRequest {\n\t\tconst body = {\n\t\t\tgenome: this.app.vocabApi.vocab.genome,\n\t\t\tdslabel: this.app.vocabApi.vocab.dslabel,\n\t\t\tsample: this.config.sample,\n\t\t\ttermId: this.config.termId,\n\t\t\tcategoryName: this.config.categoryName\n\t\t}\n\t\treturn body\n\t}\n\n\t/** retrieve the sampleId/sampleName for samples in\n\t * the \"others\" group instead of using {in: false} */\n\tasync getOtherSamples(samplelst) {\n\t\tconst othersSamplesGroup = samplelst.groups.find(g => !g.in)\n\t\tif (!othersSamplesGroup) return\n\n\t\tconst state = this.app.getState()\n\t\tconst samplesGroup = samplelst.groups.find(g => g.in)\n\t\tothersSamplesGroup.values = []\n\t\t// retrieve full list of samples based on current filter. put samples not in samplesGroup in \"others\" group\n\t\tfor (const s of await this.app.vocabApi.getFilteredSampleList(state.termfilter.filter)) {\n\t\t\t// s={id,name}, samplelst.groups[].values[]={sampleId,sample}\n\t\t\tif (samplesGroup.values.indexOf(i => i.sampleId == s.id) == -1) {\n\t\t\t\tothersSamplesGroup.values.push({ sampleId: s.id, sample: s.name })\n\t\t\t}\n\t\t}\n\t\tothersSamplesGroup.in = true\n\t}\n}\n"],
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