@sjcrh/proteinpaint-client 2.198.0 → 2.200.0

package/dist/DE-DAW6ZKM7.js

@@ -0,0 +1,95 @@
+import {
+  appInit
+} from "./chunk-BQHPJY2M.js";
+import "./chunk-4KRGCOTL.js";
+import "./chunk-SKMFMGCD.js";
+import "./chunk-NUWJ4RN7.js";
+import "./chunk-ZEKIUYN3.js";
+import "./chunk-B7VDZ6VF.js";
+import "./chunk-D565DNJD.js";
+import "./chunk-CY4RQ5L6.js";
+import "./chunk-4KY4XKJV.js";
+import "./chunk-QDX2XUNF.js";
+import "./chunk-J4USU73L.js";
+import "./chunk-PRZWSBMA.js";
+import "./chunk-TKW5TW4Z.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-3SHZTAGF.js";
+import "./chunk-HYOEWQ5P.js";
+import "./chunk-6QCYT6G2.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-IIT367QZ.js";
+import "./chunk-RZGEKL77.js";
+import "./chunk-OTTMHVYH.js";
+import "./chunk-GNS6CQMA.js";
+import "./chunk-JVPWIVDT.js";
+import "./chunk-4WF3XDQP.js";
+import "./chunk-7JRDJNLR.js";
+import "./chunk-M3J4MINX.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-MPSLUEI4.js";
+import "./chunk-6PNPHACF.js";
+import "./chunk-WPHUM5S5.js";
+import "./chunk-JNITUVXP.js";
+import "./chunk-2KXLYFAO.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-VQZ2Z5YU.js";
+import "./chunk-UJELJXJG.js";
+import "./chunk-BZTWTH4Y.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-HFNDKYVF.js";
+
+// gdc/DE.ts
+async function init(arg, holder, genomes) {
+  const useGenome = arg.genome || "hg38";
+  const useDslabel = arg.dslabel || "GDC";
+  const genome = genomes[useGenome];
+  const massApi = await appInit({
+    //debug: arg.debugmode, // is debug accepted?
+    genome,
+    holder,
+    state: {
+      genome: useGenome,
+      dslabel: useDslabel,
+      termfilter: { filter0: arg.filter0 },
+      nav: { activeTab: 1, header_mode: "hidden" },
+      plots: [{ chartType: "DEinput" }]
+    },
+    opts: Object.assign(
+      {
+        // todo additional customizations
+        // dictionary:{header:'Select a variable to build Correlation Plot'}
+        // some way to make gene exp violin/boxplot to use log scale by default, but numeric dict term should not
+      },
+      arg.opts || {}
+    ),
+    app: arg.opts?.app || {}
+  });
+  const api = {
+    update: async (updateArg) => {
+      if (!massApi) return;
+      if ("filter0" in updateArg) {
+        massApi.dispatch({
+          type: "app_refresh",
+          subactions: [
+            {
+              type: "filter_replace",
+              filter0: updateArg.filter0
+            }
+          ]
+        });
+      }
+    },
+    triggerAbort: (reason = "") => massApi.triggerAbort(reason)
+  };
+  return api;
+}
+export {
+  init
+};
+//# sourceMappingURL=DE-DAW6ZKM7.js.map

package/dist/DEinput-XCR4VMR3.js

@@ -0,0 +1,409 @@
+import {
+  PlotBase,
+  Tabs,
+  excludeFilterByTag,
+  filterInit,
+  filterJoin,
+  filterPromptInit,
+  getNormalRoot,
+  make_radios,
+  negateFilter,
+  renderPreAnalysisData,
+  renderTable
+} from "./chunk-TKW5TW4Z.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-3SHZTAGF.js";
+import "./chunk-HYOEWQ5P.js";
+import "./chunk-6QCYT6G2.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-IIT367QZ.js";
+import "./chunk-RZGEKL77.js";
+import "./chunk-OTTMHVYH.js";
+import "./chunk-GNS6CQMA.js";
+import {
+  dofetch3
+} from "./chunk-JVPWIVDT.js";
+import "./chunk-4WF3XDQP.js";
+import {
+  termType2label
+} from "./chunk-7JRDJNLR.js";
+import {
+  copyMerge,
+  getCompInit
+} from "./chunk-M3J4MINX.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-MPSLUEI4.js";
+import {
+  TermTypeGroups,
+  getColors
+} from "./chunk-6PNPHACF.js";
+import "./chunk-WPHUM5S5.js";
+import "./chunk-JNITUVXP.js";
+import "./chunk-2KXLYFAO.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-VQZ2Z5YU.js";
+import "./chunk-UJELJXJG.js";
+import "./chunk-BZTWTH4Y.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import "./chunk-I6Y4O3RR.js";
+import {
+  rgb
+} from "./chunk-Q5RDQNIT.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-HFNDKYVF.js";
+
+// plots/DEinput.ts
+var colorScale = getColors(5);
+var DEinputPlot = class _DEinputPlot extends PlotBase {
+  constructor(opts, api) {
+    super(opts, api);
+    this.components = {};
+    this.type = _DEinputPlot.type;
+    this.opts = opts;
+    this.dom = this.getDom();
+    this.groups = [];
+  }
+  static {
+    this.type = "DEinput";
+  }
+  getDom() {
+    const header = this.opts?.header?.html("Differential Gene Expression") || void 0;
+    const holder = this.opts.holder.append("div").style("margin", "10px");
+    const expressionSource = holder.append("div").style("margin-bottom", "15px");
+    const table = holder.append("div");
+    const btns = holder.append("div").style("margin-top", "5px");
+    const addGroup = btns.append("div").style("display", "inline-block");
+    const submit = btns.append("div").style("display", "none").style("margin-left", "15px").attr("class", "sja_new_filter_btn sja_menuoption");
+    const loading = holder.append("div").style("display", "none").style("margin", "20px 10px").text("Loading...");
+    const preAnalysis = holder.append("div").style("display", "none").style("margin-top", "20px").style("margin-left", "5px");
+    const dom = { header, expressionSource, table, addGroup, submit, loading, preAnalysis };
+    return dom;
+  }
+  getState(appState) {
+    const config = appState.plots.find((p) => p.id === this.id);
+    if (!config) {
+      throw `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`;
+    }
+    return {
+      termfilter: appState.termfilter,
+      config,
+      // quick fix to skip history tracking as needed
+      _scope_: appState._scope_
+    };
+  }
+  async init() {
+    await this.renderExpressionSourceUI();
+  }
+  // TODO: handle errors
+  async main() {
+    this.dom.preAnalysis.selectAll("*").remove();
+    if (!this.expressionSource || this.expressionSource === "pseudobulk" && !this.pseudobulk) {
+      this.dom.table.style("display", "none");
+      this.dom.addGroup.style("display", "none");
+      this.dom.submit.style("display", "none");
+      return;
+    }
+    this.dom.addGroup.style("display", "inline-block");
+    this.makeGroupsUI();
+    this.hasCohort0 = this.groups.some((g) => g.filter.lst.some((item) => item.tvs?.term.type == "cohort"));
+    this.mayRenderSubmit();
+  }
+  async renderExpressionSourceUI() {
+    const config = this.app.vocabApi.termdbConfig;
+    const hasBulk = !!config.queries?.rnaseqGeneCount;
+    const terms = config.termType2terms?.[TermTypeGroups.PSEUDOBULK] || [];
+    const hasPseudobulk = terms.length > 0;
+    if (!hasBulk && !hasPseudobulk)
+      throw new Error("No gene expression count data configured for differential analysis");
+    if (hasBulk && !hasPseudobulk) {
+      this.expressionSource = "bulk";
+      return;
+    }
+    if (!hasBulk) {
+      this.expressionSource = "pseudobulk";
+      this.renderPseudobulkSelection(this.dom.expressionSource, terms);
+      return;
+    }
+    const tabs = [
+      {
+        label: "Bulk RNA-seq",
+        active: true,
+        callback: async () => {
+          this.expressionSource = "bulk";
+          await this.main();
+        }
+      },
+      {
+        label: "Single-cell pseudobulk",
+        callback: async (_event, tab) => {
+          this.expressionSource = "pseudobulk";
+          tab.contentHolder.selectAll("*").remove();
+          this.renderPseudobulkSelection(tab.contentHolder, terms);
+          await this.main();
+        }
+      }
+    ];
+    await new Tabs({ holder: this.dom.expressionSource, tabs }).main();
+  }
+  renderPseudobulkSelection(holder, terms) {
+    const assayMap = /* @__PURE__ */ new Map();
+    for (const term of terms) {
+      if (!assayMap.has(term.assay)) assayMap.set(term.assay, /* @__PURE__ */ new Map());
+      const memberMap = assayMap.get(term.assay);
+      if (!memberMap.has(term.memberId)) memberMap.set(term.memberId, []);
+      memberMap.get(term.memberId).push(term);
+    }
+    const renderAssay = (assayHolder, assay, memberMap) => {
+      assayHolder.selectAll("*").remove();
+      const renderMember = (memberHolder, memberId, memberTerms) => {
+        memberHolder.selectAll("*").remove();
+        memberHolder.append("div").style("opacity", 0.7).text(`Select from ${memberId}:`);
+        make_radios({
+          holder: memberHolder,
+          inputName: `sjpp-de-pseudobulk-${this.id}-${assay}-${memberId}`,
+          options: memberTerms.map((term) => ({
+            label: term.name,
+            value: term.id,
+            checked: this.pseudobulk?.assay === assay && this.pseudobulk?.memberId === memberId && this.pseudobulk?.category === (term.category || term.id),
+            testid: `sjpp-de-pseudobulk-category-${term.id}`
+          })),
+          styles: { display: "block", padding: "3px 5px" },
+          callback: async (value) => {
+            const term = memberTerms.find((term2) => term2.id == value);
+            this.pseudobulk = { assay, memberId, category: term.category || term.id };
+            await this.main();
+          }
+        });
+      };
+      if (memberMap.size === 1) {
+        const [memberId, memberTerms] = memberMap.entries().next().value;
+        renderMember(assayHolder, memberId, memberTerms);
+      } else {
+        const memberTabs = Array.from(memberMap, ([memberId, memberTerms]) => ({
+          label: memberId,
+          callback: (_event, tab) => renderMember(tab.contentHolder, memberId, memberTerms)
+        }));
+        new Tabs({ holder: assayHolder, tabs: memberTabs }).main();
+      }
+    };
+    if (assayMap.size === 1) {
+      const [assay, memberMap] = Array.from(assayMap)[0];
+      holder.append("div").text("Single-cell pseudobulk " + termType2label(assay));
+      renderAssay(holder.append("div"), assay, memberMap);
+    } else {
+      const assayTabs = Array.from(assayMap, ([assay, memberMap]) => ({
+        label: termType2label(assay),
+        callback: (_event, tab) => renderAssay(tab.contentHolder, assay, memberMap)
+      }));
+      new Tabs({ holder, tabs: assayTabs, linePosition: "right", tabsPosition: "vertical" }).main();
+    }
+  }
+  async makeGroupsUI() {
+    if (!this.filterPrompt) {
+      this.filterPrompt = await filterPromptInit({
+        holder: this.dom.addGroup,
+        vocabApi: this.app.vocabApi,
+        emptyLabel: "Add group",
+        /** 'hide_search' by default expands all terms. Passing the
+         * header_mode in opts gives the caller the flexibility to choose. */
+        header_mode: this.opts?.header_mode || "hide_search",
+        callback: async (f) => {
+          const filter2 = getNormalRoot(f);
+          this.addNewGroup(filter2, this.groups);
+          await this.main();
+        },
+        debug: this.opts.debug
+      });
+    }
+    const filter = structuredClone(this.state?.termfilter?.filter);
+    this.filterPrompt.main(excludeFilterByTag(filter, "cohortFilter"));
+    if (!this.groups.length) {
+      this.dom.table.style("display", "none");
+      return;
+    }
+    this.dom.table.style("display", "block").selectAll("*").remove();
+    const tableArg = {
+      div: this.dom.table,
+      columns: [
+        {},
+        // blank column to add delete buttons
+        {
+          label: "NAME",
+          editCallback: async (i, cell) => {
+            const newName = cell.value;
+            const index = this.groups.findIndex((group) => group.name == newName);
+            if (index != -1) {
+              alert(`Group named ${newName} already exists`);
+              await this.main();
+            } else {
+              this.groups[i].name = newName;
+              await this.main();
+            }
+          }
+        },
+        {
+          label: "COLOR",
+          editCallback: async (i, cell) => {
+            this.groups[i].color = cell.color;
+            this.main();
+          }
+        },
+        //{ label: '#SAMPLE' }, // will re-enable when filtered sample count can be supported for gdc
+        { label: "FILTER" }
+      ],
+      rows: [],
+      striped: false,
+      // no alternating row bg color so delete button appears more visible
+      showLines: false
+    };
+    for (const g of this.groups) {
+      tableArg.rows.push([
+        {},
+        // blank cell to add delete button
+        { value: g.name },
+        // to allow click to show <input>
+        { color: g.color },
+        // { value: 'n=' + (await self.vocabApi.getFilteredSampleCount(g.filter)) }, // will re-enable when filtered sample count can be supported for gdc
+        {}
+        // blank cell to show filter ui
+      ]);
+    }
+    renderTable(tableArg);
+    for (const [i, row] of tableArg.rows.entries()) {
+      row[0].__td.append("div").attr("class", "sja_menuoption").style("padding", "1px 6px").html("&times;").on("click", () => {
+        this.groups.splice(i, 1);
+        this.main();
+      });
+      const group = this.groups[i];
+      filterInit({
+        holder: row[3].__td,
+        vocabApi: this.app.vocabApi,
+        header_mode: "hide_search",
+        callback: (f) => {
+          if (!f || f.lst.length == 0) {
+            const i2 = this.groups.findIndex((g) => g.name == group.name);
+            this.groups.splice(i2, 1);
+          } else {
+            group.filter = f;
+          }
+          this.main();
+        }
+      }).main(group.filter);
+    }
+    this.dom.addGroup.select(".sja_new_filter_btn").style("pointer-events", "auto").style("opacity", 1);
+  }
+  addNewGroup(filter, groups, name) {
+    if (!groups) throw "groups is missing";
+    if (!name) {
+      const base = "New group";
+      name = base;
+      for (let i = 0; ; i++) {
+        name = base + (i === 0 ? "" : " " + i);
+        if (!groups.find((g) => g.name === name)) break;
+      }
+    }
+    const newGroup = {
+      name,
+      filter,
+      color: rgb(colorScale(groups.length)).formatHex()
+    };
+    groups.push(newGroup);
+  }
+  mayRenderSubmit() {
+    if (!this.groups.length || this.groups.length == 1 && this.hasCohort0) {
+      this.dom.submit.style("display", "none");
+      return;
+    }
+    this.dom.submit.style("display", "inline-block");
+    if (this.groups.length == 1) {
+      this.dom.submit.text(`Submit (${this.groups[0].name} vs others)`);
+      this.dom.submit.on("click", async () => {
+        const groups = [this.groups[0]];
+        const otherGroup = {
+          name: "Not in " + groups[0].name,
+          color: "#ccc",
+          filter: negateFilter(groups[0].filter)
+        };
+        groups.push(otherGroup);
+        await this.clickSubmit(groups);
+      });
+    } else if (this.groups.length == 2) {
+      this.dom.addGroup.select(".sja_new_filter_btn").style("pointer-events", "none").style("opacity", 0.5);
+      this.dom.submit.text(`Submit (${this.groups[0].name} vs ${this.groups[1].name})`);
+      this.dom.submit.on("click", async () => {
+        await this.clickSubmit(this.groups);
+      });
+    } else {
+      throw new Error("cannot exceed 2 groups");
+    }
+  }
+  async clickSubmit(groups) {
+    this.dom.loading.style("display", "block");
+    const samplelstTW = {
+      q: { groups: [] },
+      term: {
+        name: groups.map((g) => g.name).join(" vs "),
+        type: "samplelst",
+        values: {}
+      }
+    };
+    if (this.expressionSource === "pseudobulk") samplelstTW.pseudobulk = this.pseudobulk;
+    const filter0 = this.hasCohort0 ? null : this.state.termfilter.filter0;
+    for (const g of groups) {
+      const samples = await this.app.vocabApi.getFilteredSampleList(
+        filterJoin([g.filter, this.state.termfilter.filter]),
+        filter0
+      );
+      const sampleIds = samples.map((s) => {
+        return { sampleId: s.id };
+      });
+      samplelstTW.q.groups.push({
+        name: g.name,
+        in: true,
+        values: sampleIds
+      });
+      samplelstTW.term.values[g.name] = {
+        color: g.color,
+        key: g.name,
+        label: g.name
+      };
+    }
+    const body = {
+      genome: this.app.vocabApi.vocab.genome,
+      dslabel: this.app.vocabApi.vocab.dslabel,
+      samplelst: { groups: samplelstTW.q.groups },
+      filter: this.state.termfilter.filter,
+      filter0,
+      preAnalysis: true
+    };
+    if (this.expressionSource === "pseudobulk") body.pseudobulk = this.pseudobulk;
+    const preAnalysisData = await dofetch3("termdb/DE", { body });
+    this.dom.loading.style("display", "none");
+    this.dom.preAnalysis.style("display", "block").selectAll("*").remove();
+    this.dom.preAnalysis.append("div").style("font-weight", "bold").text("Samples with gene expression data:");
+    renderPreAnalysisData({
+      preAnalysisData,
+      samplelstTW,
+      groups: samplelstTW.q.groups,
+      holder: this.dom.preAnalysis,
+      self: this
+    });
+  }
+};
+var DEinputInit = getCompInit(DEinputPlot);
+var componentInit = DEinputInit;
+async function getPlotConfig(opts) {
+  const config = {
+    chartType: "DEinput",
+    settings: {}
+  };
+  return copyMerge(config, opts);
+}
+export {
+  DEinputInit,
+  componentInit,
+  getPlotConfig
+};
+//# sourceMappingURL=DEinput-XCR4VMR3.js.map

package/dist/DEinput-XCR4VMR3.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/DEinput.ts"],
+  "sourcesContent": ["import { PlotBase } from './PlotBase.ts'\nimport { getCompInit, copyMerge, type ComponentApi, type RxComponent } from '#rx'\nimport {\n\tfilterInit,\n\tfilterPromptInit,\n\tgetNormalRoot,\n\texcludeFilterByTag,\n\tfilterJoin,\n\tnegateFilter\n} from '#filter/filter'\nimport { getColors } from '#shared/common.js'\nimport { rgb } from 'd3-color'\nimport { make_radios, renderTable, Tabs } from '#dom'\nimport { dofetch3 } from '#common/dofetch'\nimport { renderPreAnalysisData } from '#mass/groups'\nimport { TermTypeGroups, termType2label } from '#shared/terms.js'\n\nconst colorScale = getColors(5)\n\nclass DEinputPlot extends PlotBase implements RxComponent {\n\tstatic type = 'DEinput'\n\n\t// expected RxComponent props, some are already declared/set in PlotBase\n\ttype: string\n\tparentId?: string\n\tdom!: {\n\t\t[index: string]: any\n\t}\n\tcomponents: {\n\t\t[name: string]: ComponentApi | { [name: string]: ComponentApi }\n\t} = {}\n\t// expected class-specific props\n\tconfig: any\n\tgroups: any[]\n\tfilterPrompt: any\n\texpressionSource?: 'bulk' | 'pseudobulk'\n\tpseudobulk?: { assay: string; memberId: string; category: string }\n\thasCohort0?: boolean\n\n\tconstructor(opts, api) {\n\t\tsuper(opts, api)\n\t\tthis.type = DEinputPlot.type\n\t\tthis.opts = opts\n\t\tthis.dom = this.getDom()\n\t\tthis.groups = []\n\t}\n\n\tgetDom() {\n\t\tconst header = this.opts?.header?.html('Differential Gene Expression') || undefined\n\t\tconst holder = this.opts.holder.append('div').style('margin', '10px')\n\t\tconst expressionSource = holder.append('div').style('margin-bottom', '15px')\n\t\tconst table = holder.append('div')\n\t\tconst btns = holder.append('div').style('margin-top', '5px')\n\t\tconst addGroup = btns.append('div').style('display', 'inline-block')\n\t\tconst submit = btns\n\t\t\t.append('div')\n\t\t\t.style('display', 'none')\n\t\t\t.style('margin-left', '15px')\n\t\t\t.attr('class', 'sja_new_filter_btn sja_menuoption')\n\t\tconst loading = holder.append('div').style('display', 'none').style('margin', '20px 10px').text('Loading...')\n\t\tconst preAnalysis = holder\n\t\t\t.append('div')\n\t\t\t.style('display', 'none')\n\t\t\t.style('margin-top', '20px')\n\t\t\t.style('margin-left', '5px')\n\t\tconst dom = { header, expressionSource, table, addGroup, submit, loading, preAnalysis }\n\t\treturn dom\n\t}\n\n\tgetState(appState) {\n\t\tconst config = appState.plots.find(p => p.id === this.id)\n\t\tif (!config) {\n\t\t\tthrow `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`\n\t\t}\n\t\treturn {\n\t\t\ttermfilter: appState.termfilter,\n\t\t\tconfig,\n\t\t\t// quick fix to skip history tracking as needed\n\t\t\t_scope_: appState._scope_\n\t\t}\n\t}\n\n\tasync init() {\n\t\tawait this.renderExpressionSourceUI()\n\t}\n\n\t// TODO: handle errors\n\tasync main() {\n\t\tthis.dom.preAnalysis.selectAll('*').remove()\n\t\tif (!this.expressionSource || (this.expressionSource === 'pseudobulk' && !this.pseudobulk)) {\n\t\t\tthis.dom.table.style('display', 'none')\n\t\t\tthis.dom.addGroup.style('display', 'none')\n\t\t\tthis.dom.submit.style('display', 'none')\n\t\t\treturn\n\t\t}\n\t\tthis.dom.addGroup.style('display', 'inline-block')\n\t\tthis.makeGroupsUI()\n\t\tthis.hasCohort0 = this.groups.some(g => g.filter.lst.some(item => item.tvs?.term.type == 'cohort'))\n\t\tthis.mayRenderSubmit()\n\t}\n\n\tasync renderExpressionSourceUI() {\n\t\tconst config = this.app.vocabApi.termdbConfig\n\t\tconst hasBulk = !!config.queries?.rnaseqGeneCount\n\t\tconst terms = config.termType2terms?.[TermTypeGroups.PSEUDOBULK] || []\n\t\tconst hasPseudobulk = terms.length > 0\n\t\tif (!hasBulk && !hasPseudobulk)\n\t\t\tthrow new Error('No gene expression count data configured for differential analysis')\n\n\t\tif (hasBulk && !hasPseudobulk) {\n\t\t\tthis.expressionSource = 'bulk'\n\t\t\treturn\n\t\t}\n\n\t\tif (!hasBulk) {\n\t\t\tthis.expressionSource = 'pseudobulk'\n\t\t\tthis.renderPseudobulkSelection(this.dom.expressionSource, terms)\n\t\t\treturn\n\t\t}\n\n\t\tconst tabs = [\n\t\t\t{\n\t\t\t\tlabel: 'Bulk RNA-seq',\n\t\t\t\tactive: true,\n\t\t\t\tcallback: async () => {\n\t\t\t\t\tthis.expressionSource = 'bulk'\n\t\t\t\t\tawait this.main()\n\t\t\t\t}\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Single-cell pseudobulk',\n\t\t\t\tcallback: async (_event, tab) => {\n\t\t\t\t\tthis.expressionSource = 'pseudobulk'\n\t\t\t\t\ttab.contentHolder.selectAll('*').remove()\n\t\t\t\t\tthis.renderPseudobulkSelection(tab.contentHolder, terms)\n\t\t\t\t\tawait this.main()\n\t\t\t\t}\n\t\t\t}\n\t\t]\n\t\tawait new Tabs({ holder: this.dom.expressionSource, tabs }).main()\n\t}\n\n\trenderPseudobulkSelection(holder, terms) {\n\t\tconst assayMap = new Map<string, Map<string, any[]>>()\n\t\tfor (const term of terms) {\n\t\t\tif (!assayMap.has(term.assay)) assayMap.set(term.assay, new Map())\n\t\t\tconst memberMap = assayMap.get(term.assay)!\n\t\t\tif (!memberMap.has(term.memberId)) memberMap.set(term.memberId, [])\n\t\t\tmemberMap.get(term.memberId)!.push(term)\n\t\t}\n\n\t\tconst renderAssay = (assayHolder, assay, memberMap) => {\n\t\t\tassayHolder.selectAll('*').remove()\n\t\t\tconst renderMember = (memberHolder, memberId, memberTerms) => {\n\t\t\t\tmemberHolder.selectAll('*').remove()\n\t\t\t\tmemberHolder.append('div').style('opacity', 0.7).text(`Select from ${memberId}:`)\n\t\t\t\tmake_radios({\n\t\t\t\t\tholder: memberHolder,\n\t\t\t\t\tinputName: `sjpp-de-pseudobulk-${this.id}-${assay}-${memberId}`,\n\t\t\t\t\toptions: memberTerms.map(term => ({\n\t\t\t\t\t\tlabel: term.name,\n\t\t\t\t\t\tvalue: term.id,\n\t\t\t\t\t\tchecked:\n\t\t\t\t\t\t\tthis.pseudobulk?.assay === assay &&\n\t\t\t\t\t\t\tthis.pseudobulk?.memberId === memberId &&\n\t\t\t\t\t\t\tthis.pseudobulk?.category === (term.category || term.id),\n\t\t\t\t\t\ttestid: `sjpp-de-pseudobulk-category-${term.id}`\n\t\t\t\t\t})),\n\t\t\t\t\tstyles: { display: 'block', padding: '3px 5px' },\n\t\t\t\t\tcallback: async value => {\n\t\t\t\t\t\tconst term = memberTerms.find(term => term.id == value)\n\t\t\t\t\t\tthis.pseudobulk = { assay, memberId, category: term.category || term.id }\n\t\t\t\t\t\tawait this.main()\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t\t}\n\n\t\t\tif (memberMap.size === 1) {\n\t\t\t\tconst [memberId, memberTerms] = memberMap.entries().next().value\n\t\t\t\trenderMember(assayHolder, memberId, memberTerms)\n\t\t\t} else {\n\t\t\t\tconst memberTabs = Array.from(memberMap, ([memberId, memberTerms]) => ({\n\t\t\t\t\tlabel: memberId,\n\t\t\t\t\tcallback: (_event, tab) => renderMember(tab.contentHolder, memberId, memberTerms)\n\t\t\t\t}))\n\t\t\t\tnew Tabs({ holder: assayHolder, tabs: memberTabs }).main()\n\t\t\t}\n\t\t}\n\n\t\tif (assayMap.size === 1) {\n\t\t\tconst [assay, memberMap] = Array.from(assayMap)[0]\n\t\t\tholder.append('div').text('Single-cell pseudobulk ' + termType2label(assay))\n\t\t\trenderAssay(holder.append('div'), assay, memberMap)\n\t\t} else {\n\t\t\tconst assayTabs = Array.from(assayMap, ([assay, memberMap]) => ({\n\t\t\t\tlabel: termType2label(assay),\n\t\t\t\tcallback: (_event, tab) => renderAssay(tab.contentHolder, assay, memberMap)\n\t\t\t}))\n\t\t\tnew Tabs({ holder, tabs: assayTabs, linePosition: 'right', tabsPosition: 'vertical' }).main()\n\t\t}\n\t}\n\n\tasync makeGroupsUI() {\n\t\t// filter prompt\n\t\tif (!this.filterPrompt) {\n\t\t\tthis.filterPrompt = await filterPromptInit({\n\t\t\t\tholder: this.dom.addGroup,\n\t\t\t\tvocabApi: this.app.vocabApi,\n\t\t\t\temptyLabel: 'Add group',\n\t\t\t\t/** 'hide_search' by default expands all terms. Passing the\n\t\t\t\t * header_mode in opts gives the caller the flexibility to choose. */\n\t\t\t\theader_mode: this.opts?.header_mode || 'hide_search',\n\t\t\t\tcallback: async f => {\n\t\t\t\t\tconst filter = getNormalRoot(f)\n\t\t\t\t\tthis.addNewGroup(filter, this.groups)\n\t\t\t\t\tawait this.main()\n\t\t\t\t},\n\t\t\t\tdebug: this.opts.debug\n\t\t\t})\n\t\t}\n\n\t\t// filterPrompt.main() always empties the filterUiRoot data\n\t\tconst filter = structuredClone(this.state?.termfilter?.filter)\n\t\tthis.filterPrompt.main(excludeFilterByTag(filter, 'cohortFilter')) // provide mass filter to limit the term tree\n\n\t\tif (!this.groups.length) {\n\t\t\t// no groups, hide table\n\t\t\tthis.dom.table.style('display', 'none')\n\t\t\treturn\n\t\t}\n\n\t\t// clear table and populate rows\n\t\tthis.dom.table.style('display', 'block').selectAll('*').remove()\n\t\tconst tableArg: any = {\n\t\t\tdiv: this.dom.table,\n\t\t\tcolumns: [\n\t\t\t\t{}, // blank column to add delete buttons\n\t\t\t\t{\n\t\t\t\t\tlabel: 'NAME',\n\t\t\t\t\teditCallback: async (i, cell) => {\n\t\t\t\t\t\tconst newName = cell.value\n\t\t\t\t\t\tconst index = this.groups.findIndex(group => group.name == newName)\n\t\t\t\t\t\tif (index != -1) {\n\t\t\t\t\t\t\talert(`Group named ${newName} already exists`)\n\t\t\t\t\t\t\tawait this.main()\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\tthis.groups[i].name = newName\n\t\t\t\t\t\t\tawait this.main()\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\tlabel: 'COLOR',\n\t\t\t\t\teditCallback: async (i, cell) => {\n\t\t\t\t\t\tthis.groups[i].color = cell.color\n\t\t\t\t\t\tthis.main()\n\t\t\t\t\t}\n\t\t\t\t},\n\t\t\t\t//{ label: '#SAMPLE' }, // will re-enable when filtered sample count can be supported for gdc\n\t\t\t\t{ label: 'FILTER' }\n\t\t\t],\n\t\t\trows: [],\n\t\t\tstriped: false, // no alternating row bg color so delete button appears more visible\n\t\t\tshowLines: false\n\t\t}\n\n\t\tfor (const g of this.groups) {\n\t\t\ttableArg.rows.push([\n\t\t\t\t{}, // blank cell to add delete button\n\t\t\t\t{ value: g.name }, // to allow click to show <input>\n\t\t\t\t{ color: g.color },\n\t\t\t\t// { value: 'n=' + (await self.vocabApi.getFilteredSampleCount(g.filter)) }, // will re-enable when filtered sample count can be supported for gdc\n\t\t\t\t{} // blank cell to show filter ui\n\t\t\t])\n\t\t}\n\n\t\trenderTable(tableArg)\n\n\t\t// after rendering table, iterate over rows again to fill cells with control elements\n\t\tfor (const [i, row] of tableArg.rows.entries()) {\n\t\t\t// add delete button in 1st cell\n\t\t\trow[0].__td\n\t\t\t\t.append('div')\n\t\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t\t.style('padding', '1px 6px')\n\t\t\t\t.html('&times;')\n\t\t\t\t.on('click', () => {\n\t\t\t\t\tthis.groups.splice(i, 1)\n\t\t\t\t\tthis.main()\n\t\t\t\t})\n\n\t\t\t// create filter ui in its cell\n\t\t\tconst group = this.groups[i]\n\t\t\tfilterInit({\n\t\t\t\tholder: row[3].__td,\n\t\t\t\tvocabApi: this.app.vocabApi,\n\t\t\t\theader_mode: 'hide_search',\n\t\t\t\tcallback: f => {\n\t\t\t\t\tif (!f || f.lst.length == 0) {\n\t\t\t\t\t\t// blank filter (user removed last tvs from this filter), delete this element from groups[]\n\t\t\t\t\t\tconst i = this.groups.findIndex(g => g.name == group.name)\n\t\t\t\t\t\tthis.groups.splice(i, 1)\n\t\t\t\t\t} else {\n\t\t\t\t\t\t// update filter\n\t\t\t\t\t\tgroup.filter = f\n\t\t\t\t\t}\n\t\t\t\t\tthis.main()\n\t\t\t\t}\n\t\t\t}).main(group.filter)\n\t\t}\n\n\t\tthis.dom.addGroup.select('.sja_new_filter_btn').style('pointer-events', 'auto').style('opacity', 1)\n\t}\n\n\taddNewGroup(filter, groups, name?: string) {\n\t\tif (!groups) throw 'groups is missing'\n\t\tif (!name) {\n\t\t\tconst base = 'New group'\n\t\t\tname = base\n\t\t\tfor (let i = 0; ; i++) {\n\t\t\t\tname = base + (i === 0 ? '' : ' ' + i)\n\t\t\t\tif (!groups.find(g => g.name === name)) break\n\t\t\t}\n\t\t}\n\t\tconst newGroup = {\n\t\t\tname,\n\t\t\tfilter,\n\t\t\tcolor: rgb(colorScale(groups.length)).formatHex()\n\t\t}\n\t\tgroups.push(newGroup)\n\t}\n\n\tmayRenderSubmit() {\n\t\tif (!this.groups.length || (this.groups.length == 1 && this.hasCohort0)) {\n\t\t\t// currently unable to negate filter0, so enforcing two-group\n\t\t\t// comparison when cohort0 is used\n\t\t\tthis.dom.submit.style('display', 'none')\n\t\t\treturn\n\t\t}\n\t\tthis.dom.submit.style('display', 'inline-block')\n\t\tif (this.groups.length == 1) {\n\t\t\t// single group of samples, compare with all other samples\n\t\t\tthis.dom.submit.text(`Submit (${this.groups[0].name} vs others)`)\n\t\t\tthis.dom.submit.on('click', async () => {\n\t\t\t\tconst groups = [this.groups[0]]\n\t\t\t\tconst otherGroup = {\n\t\t\t\t\tname: 'Not in ' + groups[0].name,\n\t\t\t\t\tcolor: '#ccc',\n\t\t\t\t\tfilter: negateFilter(groups[0].filter)\n\t\t\t\t}\n\t\t\t\tgroups.push(otherGroup)\n\t\t\t\tawait this.clickSubmit(groups)\n\t\t\t})\n\t\t} else if (this.groups.length == 2) {\n\t\t\t// two groups of samples, compare these groups\n\t\t\tthis.dom.addGroup.select('.sja_new_filter_btn').style('pointer-events', 'none').style('opacity', 0.5)\n\t\t\tthis.dom.submit.text(`Submit (${this.groups[0].name} vs ${this.groups[1].name})`)\n\t\t\tthis.dom.submit.on('click', async () => {\n\t\t\t\tawait this.clickSubmit(this.groups)\n\t\t\t})\n\t\t} else {\n\t\t\tthrow new Error('cannot exceed 2 groups')\n\t\t}\n\t}\n\n\tasync clickSubmit(groups) {\n\t\tthis.dom.loading.style('display', 'block')\n\t\tconst samplelstTW: any = {\n\t\t\tq: { groups: [] },\n\t\t\tterm: {\n\t\t\t\tname: groups.map(g => g.name).join(' vs '),\n\t\t\t\ttype: 'samplelst',\n\t\t\t\tvalues: {}\n\t\t\t}\n\t\t}\n\t\tif (this.expressionSource === 'pseudobulk') samplelstTW.pseudobulk = this.pseudobulk\n\t\t// ignore filter0 when cohort0 is used\n\t\tconst filter0 = this.hasCohort0 ? null : this.state.termfilter.filter0\n\t\tfor (const g of groups) {\n\t\t\tconst samples = await this.app.vocabApi.getFilteredSampleList(\n\t\t\t\tfilterJoin([g.filter, this.state.termfilter.filter]),\n\t\t\t\tfilter0\n\t\t\t)\n\t\t\tconst sampleIds = samples.map(s => {\n\t\t\t\treturn { sampleId: s.id }\n\t\t\t})\n\t\t\tsamplelstTW.q.groups.push({\n\t\t\t\tname: g.name,\n\t\t\t\tin: true,\n\t\t\t\tvalues: sampleIds\n\t\t\t})\n\t\t\tsamplelstTW.term.values[g.name] = {\n\t\t\t\tcolor: g.color,\n\t\t\t\tkey: g.name,\n\t\t\t\tlabel: g.name\n\t\t\t}\n\t\t}\n\n\t\t// get actual numbers of samples with rnaseq count\n\t\tconst body: any = {\n\t\t\tgenome: this.app.vocabApi.vocab.genome,\n\t\t\tdslabel: this.app.vocabApi.vocab.dslabel,\n\t\t\tsamplelst: { groups: samplelstTW.q.groups },\n\t\t\tfilter: this.state.termfilter.filter,\n\t\t\tfilter0,\n\t\t\tpreAnalysis: true\n\t\t}\n\t\tif (this.expressionSource === 'pseudobulk') body.pseudobulk = this.pseudobulk\n\t\tconst preAnalysisData = await dofetch3('termdb/DE', { body })\n\n\t\tthis.dom.loading.style('display', 'none')\n\n\t\t// render sample counts\n\t\tthis.dom.preAnalysis.style('display', 'block').selectAll('*').remove()\n\t\tthis.dom.preAnalysis.append('div').style('font-weight', 'bold').text('Samples with gene expression data:')\n\n\t\trenderPreAnalysisData({\n\t\t\tpreAnalysisData,\n\t\t\tsamplelstTW,\n\t\t\tgroups: samplelstTW.q.groups,\n\t\t\tholder: this.dom.preAnalysis,\n\t\t\tself: this\n\t\t})\n\t}\n}\n\nexport const DEinputInit = getCompInit(DEinputPlot)\nexport const componentInit = DEinputInit\n\nexport async function getPlotConfig(opts) {\n\tconst config = {\n\t\tchartType: 'DEinput',\n\t\tsettings: {}\n\t}\n\n\t// may apply term-specific changes to the default object\n\treturn copyMerge(config, opts)\n}\n"],
+  "mappings": 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+  "names": ["term", "filter", "i"]
+}