@sjcrh/proteinpaint-client 2.198.0 → 2.200.0

package/dist/chunk-26APRXD3.js

@@ -0,0 +1,254 @@
+import {
+  getMclassSorter,
+  getSampleGroupSorter,
+  getSampleSorter,
+  getTermSorter
+} from "./chunk-R6NM2HSH.js";
+import {
+  sample_match_termvaluesetting
+} from "./chunk-4WF3XDQP.js";
+import {
+  dtcnv,
+  dtfusionrna,
+  dtgeneexpression,
+  dtsnvindel
+} from "./chunk-6PNPHACF.js";
+import {
+  __export
+} from "./chunk-HFNDKYVF.js";
+
+// plots/matrix/matrix.groups.js
+var matrix_groups_exports = {};
+__export(matrix_groups_exports, {
+  classifyValues: () => classifyValues,
+  getSampleGroups: () => getSampleGroups,
+  getSampleOrder: () => getSampleOrder,
+  getTermOrder: () => getTermOrder,
+  stackSiblingCellsByClass: () => stackSiblingCellsByClass
+});
+function getTermOrder(data) {
+  const s = this.settings.matrix;
+  this.termSorter = getTermSorter(this, s);
+  const termOrder = [];
+  let totalIndex = 0, visibleGrpIndex = 0, numClusterTerms = 0;
+  this.mclassSorter = getMclassSorter(this);
+  for (const [grpIndex, grp] of this.termGroups.entries()) {
+    const lst = [];
+    for (const [index, tw] of grp.lst.entries()) {
+      const counts = { samples: 0, hits: 0 };
+      const countedSamples = /* @__PURE__ */ new Set();
+      for (const sd of data.lst) {
+        if (countedSamples.has(sd.sample)) continue;
+        countedSamples.add(sd.sample);
+        const anno = sd[tw.$id];
+        if (anno) {
+          const { filteredValues, countedValues, renderedValues } = this.classifyValues(anno, tw, grp, s, sd);
+          anno.filteredValues = filteredValues;
+          anno.countedValues = countedValues;
+          anno.renderedValues = renderedValues;
+          if (anno.countedValues?.length) {
+            const v = tw.term.values?.[anno.value];
+            if (v?.uncountable) continue;
+            counts.samples += 1;
+            counts.hits += anno.countedValues.length;
+            if (tw.q?.mode == "continuous") {
+              const v2 = anno.value;
+              if (!("minval" in counts) || counts.minval > v2) counts.minval = v2;
+              if (!("maxval" in counts) || counts.maxval < v2) counts.maxval = v2;
+            }
+          }
+        }
+      }
+      if (grp.type != "hierCluster" || counts.samples) lst.push({ tw, counts, index });
+      if (grp.type == "hierCluster") numClusterTerms++;
+    }
+    const termSorter = grp.sortTermsBy || grp.type == "hierCluster" ? getTermSorter(this, s, grp) : this.termSorter;
+    const processedLst = lst.filter((t) => {
+      if ("minNumSamples" in t.tw) return t.tw.minNumSamples <= t.counts.samples;
+      if (!grp.settings) return true;
+      return !("minNumSamples" in grp.settings) || t.counts.samples >= grp.settings.minNumSamples;
+    }).sort(termSorter);
+    if (!processedLst.length) continue;
+    for (const [index, t] of processedLst.entries()) {
+      const { tw, counts } = t;
+      const ref = data.refs.byTermId[t.tw.$id] || {};
+      termOrder.push({
+        grp,
+        grpIndex,
+        visibleGrpIndex,
+        tw,
+        index,
+        // rendered index
+        lstIndex: t.index,
+        // as-listed index, before applying term filters
+        processedLst,
+        prevGrpTotalIndex: totalIndex,
+        totalIndex: totalIndex + index,
+        ref,
+        allCounts: counts
+        // note: term label will be assigned after sample counts are known
+        // label: t.tw.label || t.tw.term.name,
+      });
+    }
+    totalIndex += processedLst.length;
+    visibleGrpIndex += 1;
+  }
+  this.numTerms = termOrder.length;
+  this.numClusterTerms = numClusterTerms;
+  return termOrder;
+}
+function getSampleGroups(data) {
+  const s = this.settings.matrix;
+  const defaultSampleGrp = {
+    id: this.config.divideBy?.$id,
+    name: this.config.divideBy ? "Not annotated" : "",
+    lst: []
+  };
+  const sampleGroups = /* @__PURE__ */ new Map();
+  const term = this.config.divideBy?.term || {};
+  const $id = this.config.divideBy?.$id || "-";
+  const exclude = this.config.divideBy?.exclude || [];
+  const values = term.values || {};
+  const ref = data.refs.byTermId[$id] || {};
+  for (const row of data.lst) {
+    if ($id in row) {
+      const key = row[$id].key;
+      const name = key in values && values[key].label ? values[key].label : key;
+      if (!sampleGroups.has(key)) {
+        const grp = {
+          name: `${name}`,
+          // convert to a string
+          id: key,
+          lst: [],
+          tw: this.config.divideBy,
+          legendGroups: {},
+          isExcluded: exclude.includes(key)
+        };
+        if (ref.bins && s.sortSampleGrpsBy == "name") grp.order = ref.bins.findIndex((bin) => bin.name == key);
+        else delete grp.order;
+        sampleGroups.set(key, grp);
+      }
+      sampleGroups.get(key).lst.push(row);
+    } else {
+      defaultSampleGrp.lst.push(row);
+    }
+  }
+  const sampleGrpsArr = [...sampleGroups.values()];
+  const n = sampleGroups.size;
+  if (n > 100 && sampleGrpsArr.filter((sg) => sg.lst.length < 3).length > 0.8 * n) {
+    const l = s.controlLabels;
+    throw `Did not group ${l.samples} by "${term.name}": too many ${l.sample} groups (${n}), with the majority of groups having <= 2 ${l.samples} per group.`;
+  }
+  if (defaultSampleGrp.lst.length && !sampleGroups.size) {
+    sampleGroups.set(void 0, defaultSampleGrp);
+    sampleGrpsArr.push(...sampleGroups.values());
+  }
+  this.asListedSampleOrder = [];
+  for (const grp of sampleGrpsArr) {
+    this.asListedSampleOrder.push(...grp.lst.map((s2) => s2.sample));
+  }
+  const selectedDictTerms = this.termOrder.filter((t) => t.tw.sortSamples && t.tw.term.type != "geneVariant");
+  const noGrpSampleSorter = getSampleSorter(this, s, data.lst, {
+    skipSorter: (p, tw) => !p.types?.includes("geneVariant") && selectedDictTerms.find((t) => t.tw.$id === tw.$id)
+  });
+  const noGrpSampleOrder = data.lst.sort(noGrpSampleSorter);
+  const allowedSamples = noGrpSampleOrder.slice(0, s.maxSample);
+  const dataFilter = (d) => allowedSamples.includes(d);
+  const hitsPerSample = (t, c) => t + (typeof c == "object" && c.countedValues?.length ? 1 : 0);
+  const countHits = (total, d) => total + (Object.values(d).reduce(hitsPerSample, 0) ? 1 : 0);
+  const grpLstSampleSorter = getSampleSorter(this, s, data.lst);
+  for (const grp of sampleGrpsArr) {
+    grp.lst = grp.lst.filter(dataFilter);
+    grp.totalCountedValues = grp.lst.reduce(countHits, 0);
+    grp.lst.sort(grpLstSampleSorter);
+  }
+  const sampleGrpSorter = getSampleGroupSorter(this);
+  return sampleGrpsArr.sort(sampleGrpSorter);
+}
+function getSampleOrder(data) {
+  const s = this.settings.matrix;
+  this.visibleSampleGrps = /* @__PURE__ */ new Set();
+  const sampleOrder = [];
+  let total = 0, numHiddenGrps = 0;
+  for (const [grpIndex, grp] of this.sampleGroups.entries()) {
+    if (!grp.lst.length) continue;
+    if (grp.isExcluded) numHiddenGrps++;
+    let processedLst = grp.lst;
+    for (const [index, row] of processedLst.entries()) {
+      sampleOrder.push({
+        grp,
+        grpIndex: grpIndex - numHiddenGrps,
+        // : this.sampleGroups.length,
+        row,
+        index,
+        prevGrpTotalIndex: total,
+        totalIndex: total + index,
+        totalHtAdjustments: 0,
+        // may be required when transposed???
+        grpTotals: { htAdjustment: 0 },
+        // may be required when transposed???
+        processedLst
+      });
+    }
+    if (!grp.isExcluded) total += processedLst.length;
+    this.visibleSampleGrps.add(grp);
+  }
+  this.unfilteredSampleOrder = sampleOrder;
+  return sampleOrder.filter((so) => !so.grp.isExcluded);
+}
+function classifyValues(anno, tw, grp, s, sample) {
+  const values = "value" in anno ? [anno.value] : anno.values;
+  if (!values) return { filteredValues: null, countedValues: null, renderedValues: null };
+  const isSpecific = [tw.valueFilter || grp.valueFilter].filter((v) => v && true);
+  if (isSpecific.length && isSpecific[0].type !== "tvs" && isSpecific[0].type !== "tvslst")
+    throw `unknown matrix value filter type='${isSpecific.type}'`;
+  let filteredValues = !isSpecific.length ? values : values.filter((v) => sample_match_termvaluesetting(v, isSpecific[0], tw.term, sample));
+  const renderedValues = [];
+  if (tw.term.type == "geneVariant" && tw.q?.type == "values") {
+    filteredValues.sort(this.mclassSorter);
+    if (s.cellEncoding == "") renderedValues.push(...filteredValues);
+    else {
+      const sortedFilteredValues = [];
+      for (const dt of [dtcnv, dtsnvindel, dtfusionrna, dtgeneexpression]) {
+        const v = dt == dtgeneexpression ? filteredValues.find((v2) => v2.dt === dt) : filteredValues.find((v2) => v2.dt === dt && v2.class !== "WT" && v2.class !== "Blank");
+        if (v) renderedValues.push(v);
+        const oneDtV = filteredValues.filter((v2) => v2.dt === dt);
+        sortedFilteredValues.push(...oneDtV);
+      }
+      filteredValues = sortedFilteredValues;
+    }
+  } else {
+    renderedValues.push(...filteredValues);
+  }
+  return {
+    filteredValues,
+    countedValues: filteredValues.filter((v) => {
+      if (tw.term.type == "geneVariant") {
+        if (tw.q?.type == "predefined-groupset" || tw.q?.type == "custom-groupset") {
+          const groupset = tw.q.type == "predefined-groupset" ? tw.term.groupsetting.lst[tw.q.predefined_groupset_idx] : tw.q.customset;
+          if (!groupset) throw "groupset not found";
+          const group = groupset.groups[0];
+          if (v != group.name) return false;
+        } else {
+          if (v.class == "WT" || v.class == "Blank" || s.geneVariantCountSamplesSkipMclass.includes(v.class))
+            return false;
+        }
+      }
+      return true;
+    }),
+    renderedValues
+  };
+}
+function stackSiblingCellsByClass(a, b) {
+  return a.class === b.class ? 0 : a.class === "Blank" ? 1 : b.class == "Blank" ? -1 : a.class < b.class ? -1 : 1;
+}
+
+export {
+  getTermOrder,
+  getSampleGroups,
+  getSampleOrder,
+  classifyValues,
+  stackSiblingCellsByClass,
+  matrix_groups_exports
+};
+//# sourceMappingURL=chunk-26APRXD3.js.map

package/dist/chunk-2GLA2SWU.js

@@ -0,0 +1,160 @@
+import {
+  Tabs,
+  addGeneSearchbox,
+  make_radios
+} from "./chunk-TKW5TW4Z.js";
+import {
+  Menu
+} from "./chunk-HYOEWQ5P.js";
+import {
+  termType2label
+} from "./chunk-7JRDJNLR.js";
+import {
+  TermTypeGroups
+} from "./chunk-6PNPHACF.js";
+
+// termdb/handlers/pseudobulk.ts
+var SearchHandler = class {
+  constructor() {
+  }
+  async init(opts) {
+    const pseudobulkTerms = this.validateOpts(opts);
+    this.callback = opts.callback;
+    this.app = opts.app;
+    this.genome = opts.genomeObj;
+    const holder = opts.holder.append("div").style("padding", "10px 0px");
+    this.map = this.buildRenderingDataMap(pseudobulkTerms);
+    this.renderPseudobulkSearch(holder);
+  }
+  validateOpts(opts) {
+    if (!opts) throw new Error("opts is required");
+    if (!opts.app) throw new Error("opts.app is required");
+    if (!opts.holder) throw new Error("opts.holder is required");
+    if (opts.genomeObj == null || typeof opts.genomeObj !== "object") throw new Error("genomeObj is required");
+    if (!opts.callback) throw new Error("opts.callback is required");
+    const pseudobulkTerms = opts.app.vocabApi.termdbConfig?.termType2terms?.[TermTypeGroups.PSEUDOBULK];
+    if (!pseudobulkTerms) {
+      throw new Error(
+        `termType2terms[${TermTypeGroups.PSEUDOBULK}]:[] is required in termdbConfig for pseudobulk handler`
+      );
+    }
+    return pseudobulkTerms;
+  }
+  /** Builds a map from assay to memberId to terms */
+  buildRenderingDataMap(pseudobulkTerms) {
+    const map = /* @__PURE__ */ new Map();
+    for (const term of pseudobulkTerms) {
+      const { assay, memberId } = term;
+      if (!map.has(assay)) map.set(assay, /* @__PURE__ */ new Map());
+      const assayMap = map.get(assay);
+      if (!assayMap.has(memberId)) assayMap.set(memberId, []);
+      assayMap.get(memberId).push(term);
+    }
+    return map;
+  }
+  /** If more than one assay, render tabs for each assay. Member IDs within
+   * an assay are rendered as tabs when there is more than one. */
+  renderPseudobulkSearch(holder) {
+    if (!this.map || this.map.size < 1) throw new Error("map is not initialized");
+    if (this.map.size === 1) {
+      const label = termType2label(this.map.keys().next().value);
+      holder.append("div").text("Single-cell pseudobulk " + label);
+      this.renderMemberIdsByAssay(holder.append("div"), this.map);
+      return;
+    }
+    const tabs = this.buildTabsOpts(this.map);
+    new Tabs({ holder, tabs, linePosition: "right", tabsPosition: "vertical" }).main();
+  }
+  buildTabsOpts(map) {
+    const tabs = [];
+    for (const [key, valuesMap] of map.entries()) {
+      const label = termType2label(key);
+      tabs.push({
+        label,
+        active: false,
+        callback: (_, tab) => {
+          this.renderMemberIdsByAssay(tab.contentHolder, /* @__PURE__ */ new Map([[key, valuesMap]]));
+        }
+      });
+    }
+    return tabs;
+  }
+  renderMemberIdsByAssay(holder, map) {
+    const memberIdMap = map.values().next().value;
+    holder.selectAll("*").remove();
+    this.renderTermdByMemberId(holder, memberIdMap);
+  }
+  renderTermdByMemberId(holder, memberIdMap) {
+    const layout = holder.append("div").style("display", "flex").style("align-items", "flex-start").style("gap", "30px");
+    const pseudoTermsWrapper = layout.append("div").attr("data-testid", "sjpp-pseudobulk-terms-wrapper");
+    const geneSearchWrapper = layout.append("div").attr("data-testid", "sjpp-pseudobulk-gene-search-wrapper");
+    this.renderPseudobulkTerms(pseudoTermsWrapper, memberIdMap, geneSearchWrapper);
+  }
+  renderPseudobulkTerms(holder, memberIdMap, geneSearchHolder) {
+    if (memberIdMap.size === 1) {
+      const [memberId, terms] = memberIdMap.entries().next().value;
+      this.renderCategoryRadios(holder, memberId, terms, geneSearchHolder);
+      return;
+    }
+    const memberEntries = Array.from(memberIdMap.entries());
+    const tabs = memberEntries.map(([memberId, terms]) => ({
+      label: memberId,
+      active: false,
+      testid: `sjpp-pseudobulk-member-${memberId}`,
+      callback: (_, tab) => {
+        this.selectedTerm = void 0;
+        geneSearchHolder.selectAll("*").remove();
+        tab.contentHolder.selectAll("*").remove();
+        this.renderCategoryRadios(tab.contentHolder, memberId, terms, geneSearchHolder);
+      }
+    }));
+    new Tabs({ holder, tabs }).main();
+  }
+  renderCategoryRadios(holder, memberId, terms, geneSearchHolder) {
+    if (!terms || terms.length < 1) throw new Error("No terms found for memberId");
+    holder.append("div").style("opacity", 0.7).text(`Select from ${memberId}:`);
+    const options = terms.map((term) => ({
+      label: term.name,
+      value: term.id,
+      checked: false,
+      testid: `sjpp-pseudobulk-category-${term.id}`
+    }));
+    make_radios({
+      holder,
+      inputName: `sjpp-pseudobulk-category-radios-${memberId}`,
+      options,
+      styles: { display: "block", padding: "3px 5px" },
+      callback: (value) => {
+        const term = terms.find((term2) => term2.id == value);
+        if (!term) throw new Error(`No pseudobulk term found for category ${value}`);
+        this.selectedTerm = term;
+        this.renderGeneSelection(geneSearchHolder);
+      }
+    });
+  }
+  renderGeneSelection(holder) {
+    holder.selectAll("*").remove();
+    const geneSearch = addGeneSearchbox({
+      tip: new Menu({ padding: "0px" }),
+      genome: this.genome,
+      row: holder,
+      searchOnly: "gene",
+      callback: () => {
+        if (!geneSearch.geneSymbol) throw new Error("No gene selected");
+        if (!this.selectedTerm) throw new Error("No pseudobulk cell type selected");
+        this.callback(createPseudobulkTerm(this.selectedTerm, geneSearch.geneSymbol));
+      }
+    });
+  }
+};
+function createPseudobulkTerm(selectedTerm, gene) {
+  const category = selectedTerm.category || selectedTerm.id;
+  const name = `${selectedTerm.assay} ${category} ${gene}`;
+  return { ...selectedTerm, id: name, category, gene, name };
+}
+
+export {
+  SearchHandler,
+  createPseudobulkTerm
+};
+//# sourceMappingURL=chunk-2GLA2SWU.js.map

package/dist/chunk-2GLA2SWU.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../termdb/handlers/pseudobulk.ts"],
+  "sourcesContent": ["import type { AppApi } from '#rx'\nimport { TermTypeGroups, termType2label } from '#shared/terms.js'\nimport { Tabs, type TabsInputEntry, make_radios, type OptionEntry, Menu, addGeneSearchbox } from '#dom'\nimport type { ClientGenome } from 'types/clientGenome'\nimport type { PseudobulkTerm } from '#types'\n\n/** Human readable labels */\n\ntype PseudobulkSelection = Omit<PseudobulkTerm, 'category' | 'gene'> & {\n\tid: string\n\tcategory?: string\n}\n\nexport class SearchHandler {\n\tcallback!: (f?: any) => void\n\tapp!: AppApi\n\tgenome!: ClientGenome\n\tmap?: Map<string, Map<string, any[]>>\n\tselectedTerm?: PseudobulkSelection\n\n\tconstructor() {}\n\n\tasync init(opts) {\n\t\tconst pseudobulkTerms = this.validateOpts(opts)\n\t\tthis.callback = opts.callback\n\t\tthis.app = opts.app\n\t\tthis.genome = opts.genomeObj\n\t\tconst holder = opts.holder.append('div').style('padding', '10px 0px')\n\n\t\tthis.map = this.buildRenderingDataMap(pseudobulkTerms)\n\t\tthis.renderPseudobulkSearch(holder)\n\t}\n\n\tvalidateOpts(opts): any[] {\n\t\tif (!opts) throw new Error('opts is required')\n\t\tif (!opts.app) throw new Error('opts.app is required')\n\t\tif (!opts.holder) throw new Error('opts.holder is required')\n\t\tif (opts.genomeObj == null || typeof opts.genomeObj !== 'object') throw new Error('genomeObj is required')\n\t\tif (!opts.callback) throw new Error('opts.callback is required')\n\t\tconst pseudobulkTerms = opts.app.vocabApi.termdbConfig?.termType2terms?.[TermTypeGroups.PSEUDOBULK]\n\t\tif (!pseudobulkTerms) {\n\t\t\tthrow new Error(\n\t\t\t\t`termType2terms[${TermTypeGroups.PSEUDOBULK}]:[] is required in termdbConfig for pseudobulk handler`\n\t\t\t)\n\t\t}\n\t\treturn pseudobulkTerms\n\t}\n\n\t/** Builds a map from assay to memberId to terms */\n\tbuildRenderingDataMap(pseudobulkTerms): Map<string, Map<string, any[]>> {\n\t\tconst map = new Map()\n\t\tfor (const term of pseudobulkTerms) {\n\t\t\tconst { assay, memberId } = term\n\t\t\tif (!map.has(assay)) map.set(assay, new Map())\n\t\t\tconst assayMap = map.get(assay)\n\t\t\tif (!assayMap.has(memberId)) assayMap.set(memberId, [])\n\t\t\tassayMap.get(memberId).push(term)\n\t\t}\n\t\treturn map\n\t}\n\n\t/** If more than one assay, render tabs for each assay. Member IDs within\n\t * an assay are rendered as tabs when there is more than one. */\n\trenderPseudobulkSearch(holder) {\n\t\tif (!this.map || this.map.size < 1) throw new Error('map is not initialized')\n\t\tif (this.map.size === 1) {\n\t\t\t// only one assay\n\t\t\tconst label = termType2label(this.map.keys().next().value!)\n\t\t\tholder.append('div').text('Single-cell pseudobulk ' + label)\n\t\t\tthis.renderMemberIdsByAssay(holder.append('div'), this.map)\n\t\t\treturn\n\t\t}\n\t\tconst tabs = this.buildTabsOpts(this.map)\n\t\tnew Tabs({ holder, tabs, linePosition: 'right', tabsPosition: 'vertical' }).main()\n\t}\n\n\tbuildTabsOpts(map) {\n\t\tconst tabs: TabsInputEntry[] = []\n\t\tfor (const [key, valuesMap] of map.entries()) {\n\t\t\tconst label = termType2label(key)\n\t\t\ttabs.push({\n\t\t\t\tlabel,\n\t\t\t\tactive: false,\n\t\t\t\tcallback: (_, tab) => {\n\t\t\t\t\tthis.renderMemberIdsByAssay(tab.contentHolder, new Map([[key, valuesMap]]))\n\t\t\t\t}\n\t\t\t})\n\t\t}\n\t\treturn tabs\n\t}\n\n\trenderMemberIdsByAssay(holder, map) {\n\t\tconst memberIdMap = map.values().next().value\n\t\tholder.selectAll('*').remove()\n\t\tthis.renderTermdByMemberId(holder, memberIdMap)\n\t}\n\n\trenderTermdByMemberId(holder, memberIdMap) {\n\t\tconst layout = holder.append('div').style('display', 'flex').style('align-items', 'flex-start').style('gap', '30px')\n\t\tconst pseudoTermsWrapper = layout.append('div').attr('data-testid', 'sjpp-pseudobulk-terms-wrapper')\n\t\tconst geneSearchWrapper = layout.append('div').attr('data-testid', 'sjpp-pseudobulk-gene-search-wrapper')\n\t\tthis.renderPseudobulkTerms(pseudoTermsWrapper, memberIdMap, geneSearchWrapper)\n\t}\n\n\trenderPseudobulkTerms(holder, memberIdMap, geneSearchHolder) {\n\t\tif (memberIdMap.size === 1) {\n\t\t\tconst [memberId, terms] = memberIdMap.entries().next().value\n\t\t\tthis.renderCategoryRadios(holder, memberId, terms, geneSearchHolder)\n\t\t\treturn\n\t\t}\n\n\t\tconst memberEntries = Array.from(memberIdMap.entries()) as [string, any[]][]\n\t\tconst tabs: TabsInputEntry[] = memberEntries.map(([memberId, terms]) => ({\n\t\t\tlabel: memberId,\n\t\t\tactive: false,\n\t\t\ttestid: `sjpp-pseudobulk-member-${memberId}`,\n\t\t\tcallback: (_, tab) => {\n\t\t\t\tthis.selectedTerm = undefined\n\t\t\t\tgeneSearchHolder.selectAll('*').remove()\n\t\t\t\ttab.contentHolder.selectAll('*').remove()\n\t\t\t\tthis.renderCategoryRadios(tab.contentHolder, memberId, terms, geneSearchHolder)\n\t\t\t}\n\t\t}))\n\t\tnew Tabs({ holder, tabs }).main()\n\t}\n\n\trenderCategoryRadios(holder, memberId, terms, geneSearchHolder) {\n\t\tif (!terms || terms.length < 1) throw new Error('No terms found for memberId')\n\t\tholder.append('div').style('opacity', 0.7).text(`Select from ${memberId}:`)\n\n\t\tconst options: OptionEntry[] = terms.map(term => ({\n\t\t\tlabel: term.name,\n\t\t\tvalue: term.id,\n\t\t\tchecked: false,\n\t\t\ttestid: `sjpp-pseudobulk-category-${term.id}`\n\t\t}))\n\t\tmake_radios({\n\t\t\tholder,\n\t\t\tinputName: `sjpp-pseudobulk-category-radios-${memberId}`,\n\t\t\toptions,\n\t\t\tstyles: { display: 'block', padding: '3px 5px' },\n\t\t\tcallback: value => {\n\t\t\t\tconst term = terms.find(term => term.id == value)\n\t\t\t\tif (!term) throw new Error(`No pseudobulk term found for category ${value}`)\n\t\t\t\tthis.selectedTerm = term\n\t\t\t\tthis.renderGeneSelection(geneSearchHolder)\n\t\t\t}\n\t\t})\n\t}\n\n\trenderGeneSelection(holder) {\n\t\tholder.selectAll('*').remove()\n\t\tconst geneSearch = addGeneSearchbox({\n\t\t\ttip: new Menu({ padding: '0px' }),\n\t\t\tgenome: this.genome,\n\t\t\trow: holder,\n\t\t\tsearchOnly: 'gene',\n\t\t\tcallback: () => {\n\t\t\t\tif (!geneSearch.geneSymbol) throw new Error('No gene selected')\n\t\t\t\tif (!this.selectedTerm) throw new Error('No pseudobulk cell type selected')\n\t\t\t\tthis.callback(createPseudobulkTerm(this.selectedTerm, geneSearch.geneSymbol))\n\t\t\t}\n\t\t})\n\t}\n}\n\n/** Create a pseudobulk term for the selected cell type and gene. */\nexport function createPseudobulkTerm(selectedTerm: PseudobulkSelection, gene: string): PseudobulkTerm {\n\tconst category = selectedTerm.category || selectedTerm.id\n\tconst name = `${selectedTerm.assay} ${category} ${gene}`\n\treturn { ...selectedTerm, id: name, category, gene, name }\n}\n"],
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+  "names": ["term"]
+}