@sjcrh/proteinpaint-client 2.185.0 → 2.186.0

package/dist/chunk-XM47XD6G.js

@@ -0,0 +1,215 @@
+import {
+  make_radios
+} from "./chunk-2YC6ZVE4.js";
+import {
+  initBinConfig
+} from "./chunk-I55NLUCQ.js";
+import {
+  format
+} from "./chunk-OAWQ6LOO.js";
+
+// termsetting/handlers/NumRegularBinEditor.ts
+var NumRegularBinEditor = class {
+  constructor(editHandler) {
+    this.dom = {};
+    this.editHandler = editHandler;
+    this.opts = editHandler.opts;
+    this.tw = editHandler.tw;
+    this.termsetting = editHandler.termsetting;
+  }
+  render(div) {
+    if (this.q?.type != "regular-bin") this.q = this.getDefaultQ();
+    this.editHandler.handler.density.setBinLines(this.getBoundaryOpts());
+    if (this.dom.binsTable) {
+      if (this.editHandler.dom.binsDiv?.node().contains(this.dom.binsTable.node())) return;
+      else {
+        this.dom.binsTable.remove();
+        delete this.dom.binsTable;
+      }
+    }
+    const binsTable = div.append("table");
+    this.dom.binsTable = binsTable;
+    this.renderBinSizeInput(binsTable.append("tr"));
+    this.renderFirstBinInput(binsTable.append("tr"));
+    this.renderLastBinInputs(binsTable.append("tr"));
+  }
+  getDefaultQ() {
+    if (this.tw.q.type == "regular-bin") return JSON.parse(JSON.stringify(this.tw.q));
+    const t = this.tw.term;
+    const defaultQ = this.termsetting.opts.use_bins_less && t.bins?.less || t.bins?.default;
+    if (defaultQ) return JSON.parse(JSON.stringify(defaultQ));
+    const binConfig = initBinConfig(this.editHandler.handler.density_data);
+    return typeof binConfig == "string" ? JSON.parse(binConfig) : binConfig;
+  }
+  renderBinSizeInput(tr) {
+    const handler = this.editHandler.handler;
+    tr.append("td").style("margin", "5px").style("opacity", 0.5).text("Bin Size");
+    const { min, max } = handler.density_data;
+    const q = this.q;
+    const origBinSize = q.bin_size;
+    this.dom.bin_size_input = tr.append("td").append("input").attr("type", "number").attr("value", "rounding" in q ? format(q.rounding || ".0f")(q.bin_size) : q.bin_size).attr("data-testid", "sjpp-num-reg-bin-editor-size").style("margin-left", "15px").style("width", "100px").style("color", () => q.bin_size > Math.abs(max - min) ? "red" : "").on("change", (event) => {
+      const newValue = Number(event.target.value);
+      if (newValue <= 0) {
+        window.alert("Please enter non-negative bin size.");
+        event.target.value = origBinSize;
+        return;
+      }
+      if ((max - min) / newValue > 100) {
+        window.alert("Bin size too small. Try setting a bigger value.");
+        event.target.value = origBinSize;
+        return;
+      }
+      q.bin_size = newValue;
+      this.dom.bin_size_input.style("color", q.bin_size > max - min ? "red" : newValue != origBinSize ? "green" : "");
+      handler.density.setBinLines(this.getBoundaryOpts());
+    });
+  }
+  renderFirstBinInput(tr) {
+    const handler = this.editHandler.handler;
+    const q = this.q;
+    if (!q.first_bin) throw "missing q.first_bin";
+    tr.append("td").style("margin", "5px").style("opacity", 0.5).text("First Bin Stop");
+    const { min, max } = handler.density_data;
+    const origValue = q.first_bin.stop;
+    this.dom.first_stop_input = tr.append("td").append("input").attr("type", "number").property("value", origValue).style("width", "100px").style("margin-left", "15px").on("change", (event) => {
+      const newValue = Number(event.target.value);
+      if (newValue < min || newValue > max) {
+        window.alert("First bin stop value out of bound.");
+        event.target.value = origValue;
+        return;
+      }
+      this.q.first_bin.stop = newValue;
+      handler.density.setBinLines(this.getBoundaryOpts());
+    });
+    tr.append("td").append("div").style("font-size", ".6em").style("opacity", 0.5).style("display", handler.density.no_density_data ? "none" : "block").text("Indicated by left-most red line. Drag to change.");
+  }
+  renderLastBinInputs(tr) {
+    const handler = this.editHandler.handler;
+    const q = this.q;
+    const isAuto = !q.last_bin || !Number.isFinite(q.last_bin.start);
+    tr.append("td").style("padding-top", "4px").style("opacity", 0.5).style("vertical-align", "top").text("Last Bin Start");
+    const td1 = tr.append("td").style("padding-left", "15px").style("vertical-align", "top");
+    const radio_div = td1.append("div");
+    const radios = make_radios({
+      holder: radio_div,
+      options: [
+        { label: "Automatic", value: "auto", checked: isAuto },
+        { label: "Fixed", value: "fixed", checked: !isAuto }
+      ],
+      callback: (v) => {
+        if (v == "auto") {
+          delete q.last_bin;
+          edit_div.style("display", "none");
+          handler.density.setBinLines(this.getBoundaryOpts());
+          return;
+        }
+        edit_div.style("display", "inline-block");
+        if (this.dom.last_start_input.property("value") == "") {
+          this.dom.last_start_input.property("value", this.tw.q.last_bin?.start || handler.density_data.max);
+        }
+        this.setLastBinStart();
+      }
+    });
+    this.dom.fixed_radio = radios.inputs.filter((_, i) => i === 1);
+    const edit_div = tr.append("td").append("div").style("display", isAuto ? "none" : "inline-block");
+    this.dom.last_start_input = edit_div.append("input").attr("type", "number").property("value", q.last_bin?.start || "").style("width", "100px").on("change", () => this.setLastBinStart());
+    edit_div.append("div").style("font-size", ".6em").style("opacity", 0.5).style("display", handler.density.no_density_data ? "none" : "block").text("Indicated by right-most red line. Drag to change.");
+  }
+  setLastBinStart() {
+    const q = this.q;
+    const { max } = this.editHandler.handler.density_data;
+    const strInput = this.dom.last_start_input.property("value");
+    if (strInput === "") return;
+    const inputValue = Number(strInput);
+    if (q.first_bin && inputValue <= q.first_bin.stop) {
+      window.alert("Last bin start cannot be smaller than first bin stop.");
+      this.dom.last_start_input.property("value", max);
+      return;
+    }
+    if (inputValue > max) {
+      window.alert("Last bin start value out of bound.");
+      this.dom.last_start_input.property("value", max);
+      return;
+    }
+    if (q.last_bin) q.last_bin.start = inputValue;
+    else
+      q.last_bin = {
+        start: inputValue,
+        stopunbounded: true,
+        stopinclusive: false
+      };
+    this.editHandler.handler.density.setBinLines(this.getBoundaryOpts());
+  }
+  getBoundaryOpts() {
+    const { min, max } = this.editHandler.handler.density_data;
+    const binLinesStop = this.q.last_bin?.start ?? max + Math.abs(this.q.first_bin.stop) - Math.min(min, 0);
+    const boundaryValues = [];
+    for (let i = this.q.first_bin.stop; i <= binLinesStop; i = i + this.q.bin_size) {
+      if (this.q.last_bin?.start === i) break;
+      if (i > binLinesStop) boundaryValues[boundaryValues.length - 1].isLastVisibleLine = true;
+      const isDraggable = i === this.q.first_bin.stop || i === this.q.bin_size - 1;
+      boundaryValues.push({ x: i, isDraggable, movesWithLineIndex: !isDraggable ? 0 : -1 });
+    }
+    if (this.q.last_bin) {
+      boundaryValues.push({
+        x: this.q.last_bin.start,
+        isDraggable: true,
+        isLastVisibleLine: true,
+        movesWithLineIndex: -1
+      });
+    }
+    return {
+      values: boundaryValues,
+      callback: (d, value) => {
+        if (d.index === 0) {
+          this.dom.first_stop_input.property("value", value);
+          this.q.first_bin.stop = value;
+        } else {
+          this.editHandler.handler.dom.last_start_input.property("value", value);
+          if (this.q.last_bin) this.q.last_bin.start = value;
+        }
+      }
+    };
+  }
+  getEditedQ(destroyDom = true) {
+    const bin_size = this.dom.bin_size_input.property("value");
+    const config = {
+      mode: "discrete",
+      type: "regular-bin",
+      startinclusive: this.editHandler.boundaryInclusion == "startinclusive",
+      stopinclusive: this.editHandler.boundaryInclusion == "stopinclusive",
+      bin_size: Number(bin_size),
+      first_bin: {
+        startunbounded: true,
+        stop: Number(this.dom.first_stop_input.property("value"))
+      },
+      rounding: bin_size.includes(".") && !bin_size.endsWith(".") ? `.${bin_size.split(".")[1].length}f` : ".0f"
+    };
+    if (this.dom.fixed_radio.property("checked")) {
+      config.last_bin = {
+        start: Number(this.dom.last_start_input.property("value")),
+        stopunbounded: true
+      };
+    }
+    if (destroyDom) {
+      for (const name of Object.keys(this.dom)) {
+        this.dom[name].remove();
+        delete this.dom[name];
+      }
+    }
+    return config;
+  }
+  undoEdits() {
+    this.q = this.getDefaultQ();
+    this.dom.binsTable.selectAll("*").remove();
+    this.renderBinSizeInput(this.dom.binsTable.append("tr"));
+    this.renderFirstBinInput(this.dom.binsTable.append("tr"));
+    this.renderLastBinInputs(this.dom.binsTable.append("tr"));
+    this.editHandler.handler.density.setBinLines(this.getBoundaryOpts());
+  }
+};
+
+export {
+  NumRegularBinEditor
+};
+//# sourceMappingURL=chunk-XM47XD6G.js.map

package/dist/chunk-XVA3UOWD.js

@@ -0,0 +1,263 @@
+import {
+  hierCluster_renderers_exports
+} from "./chunk-BT4OOYPT.js";
+import {
+  hierCluster_interactivity_exports
+} from "./chunk-GSU4PZN3.js";
+import {
+  Matrix
+} from "./chunk-GAOUV4ID.js";
+import {
+  filterJoin,
+  getNormalRoot
+} from "./chunk-2YC6ZVE4.js";
+import {
+  clusterMethodLst,
+  distanceMethodLst,
+  dofetch3
+} from "./chunk-I55NLUCQ.js";
+import {
+  deepEqual,
+  getCompInit
+} from "./chunk-MVTCBVSX.js";
+import {
+  NUMERIC_DICTIONARY_TERM,
+  TermTypes2Dt
+} from "./chunk-EGWVYY7K.js";
+import {
+  colorScaleMap
+} from "./chunk-AMYSEKPF.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() : this.config.dataType === NUMERIC_DICTIONARY_TERM ? 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-XVA3UOWD.js.map

package/dist/chunk-XVA3UOWD.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 { TermTypes, TermTypes2Dt, NUMERIC_DICTIONARY_TERM } 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: this.config.dataType === NUMERIC_DICTIONARY_TERM\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"]
+}