@sjcrh/proteinpaint-client 2.209.0 → 2.210.1-0

package/dist/DE-BI7DHHW4.js

@@ -0,0 +1,89 @@
+import {
+  appInit
+} from "./chunk-GPY6SBCX.js";
+import "./chunk-NJWNKBRC.js";
+import "./chunk-FJ3JD7B3.js";
+import "./chunk-GWHIKECP.js";
+import "./chunk-BSWPONNA.js";
+import "./chunk-WTQQWFV4.js";
+import "./chunk-X46YA4CB.js";
+import "./chunk-SKMFMGCD.js";
+import "./chunk-3ELYMSGO.js";
+import "./chunk-PRZWSBMA.js";
+import "./chunk-CSAS3PVJ.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-KV4W2ACA.js";
+import "./chunk-T4RYLTR3.js";
+import "./chunk-ELJX3QIQ.js";
+import "./chunk-Y3SDMRDX.js";
+import "./chunk-EEB5VE2A.js";
+import "./chunk-6RRZRISL.js";
+import "./chunk-2KM4PRQM.js";
+import "./chunk-VTHZGUSZ.js";
+import "./chunk-3TV5WWUN.js";
+import "./chunk-4Y5W26UF.js";
+import "./chunk-UYKJOBRO.js";
+import "./chunk-WINIL2KN.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-7X6NF7NI.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-Z2ZITHT4.js";
+import "./chunk-4OLM3KSB.js";
+import "./chunk-FXQXCOII.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-HS5PO5ZQ.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" },
+      // an embedder may supply prebuilt groups, see config.groups[] in plots/DEinput.ts
+      plots: arg.state?.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-BI7DHHW4.js.map

package/dist/DEinput-W66CT4U2.js

@@ -0,0 +1,501 @@
+import {
+  rehydrateFilter
+} from "./chunk-SKMFMGCD.js";
+import {
+  PlotBase,
+  Tabs,
+  excludeFilterByTag,
+  filterInit,
+  filterJoin,
+  filterPromptInit,
+  getNormalRoot,
+  make_radios,
+  negateFilter,
+  renderPreAnalysisData,
+  renderTable
+} from "./chunk-CSAS3PVJ.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-KV4W2ACA.js";
+import "./chunk-T4RYLTR3.js";
+import "./chunk-ELJX3QIQ.js";
+import "./chunk-Y3SDMRDX.js";
+import "./chunk-EEB5VE2A.js";
+import "./chunk-6RRZRISL.js";
+import "./chunk-2KM4PRQM.js";
+import {
+  dofetch3
+} from "./chunk-VTHZGUSZ.js";
+import "./chunk-3TV5WWUN.js";
+import {
+  termType2label
+} from "./chunk-4Y5W26UF.js";
+import {
+  TermTypeGroups,
+  TermTypes,
+  getColors
+} from "./chunk-UYKJOBRO.js";
+import {
+  copyMerge,
+  getCompInit
+} from "./chunk-WINIL2KN.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-7X6NF7NI.js";
+import {
+  uiLabel
+} from "./chunk-W5J3LTYS.js";
+import "./chunk-Z2ZITHT4.js";
+import "./chunk-4OLM3KSB.js";
+import "./chunk-FXQXCOII.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import "./chunk-I6Y4O3RR.js";
+import {
+  color,
+  rgb
+} from "./chunk-Q5RDQNIT.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-HS5PO5ZQ.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.dom = this.getDom();
+    this.groups = [];
+  }
+  static {
+    this.type = "DEinput";
+  }
+  get isGE() {
+    return this.termType == TermTypes.GENE_EXPRESSION;
+  }
+  getDom() {
+    const header = this.opts?.header || 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(appState) {
+    const state = this.getState(appState);
+    this.termType = state.config.termType || TermTypes.GENE_EXPRESSION;
+    this.dom.header?.html(`Differential ${termType2label(this.termType)}`);
+    await this.renderExpressionSourceUI();
+  }
+  // TODO: handle errors
+  async main() {
+    if (!this.state) return;
+    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.maySeedGroups();
+    this.hasCohort0 = this.groups.some((g) => g.filter.lst.some((item) => item.tvs?.term.type == "cohort"));
+    await this.makeGroupsUI();
+    this.mayRenderSubmit();
+    await this.mayAutoSubmit();
+  }
+  /* config.groups[] lets a caller launch this ui with prebuilt groups, each defined by a mass
+  filter, instead of requiring the user to build both groups by hand. seeded only once: main() reruns
+  on every state change, and a seeded group is editable like any other, so a rerun must not undo a
+  rename, edit, or deletion */
+  maySeedGroups() {
+    if (this.groupsSeeded) return;
+    this.groupsSeeded = true;
+    if (!this.state.config.groups?.length) return;
+    const massFilter = getNormalRoot(excludeFilterByTag(structuredClone(this.state.termfilter.filter), "cohortFilter"));
+    for (const g of this.state.config.groups) {
+      this.addNewGroup(filterJoin([massFilter, getNormalRoot(g.filter)]), this.groups, g.name, g.color);
+    }
+  }
+  /* config.autoSubmit runs the analysis on the seeded groups without waiting for a click, for a caller
+  that already knows the groups to compare. runs only once: main() reruns on every state change, and
+  each run is a round trip to termdb/DE */
+  async mayAutoSubmit() {
+    if (!this.state.config.autoSubmit || this.autoSubmitted) return;
+    if (this.dom.submit.style("display") == "none") return;
+    this.autoSubmitted = true;
+    await this.clickSubmit(this.getSubmitGroups());
+  }
+  /** the groups as compared by the analysis: a lone group is compared against all other samples */
+  getSubmitGroups() {
+    if (this.groups.length != 1) return this.groups;
+    const group = this.groups[0];
+    return [
+      group,
+      {
+        name: "Not in " + group.name,
+        color: "#ccc",
+        filter: negateFilter(group.filter)
+      }
+    ];
+  }
+  async renderExpressionSourceUI() {
+    const config = this.app.vocabApi.termdbConfig;
+    if (!this.isGE) {
+      const dm = config.queries?.dnaMethylation;
+      if (!dm?.promoter && !dm?.elementTypes?.length)
+        throw new Error("No DNA methylation data configured for differential analysis");
+      this.expressionSource = "bulk";
+      return;
+    }
+    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",
+        header_mode: this.opts?.header_mode,
+        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 ${newName} already exists`);
+              await this.main();
+            } else {
+              this.groups[i].name = newName;
+              await this.main();
+            }
+          }
+        },
+        {
+          label: "COLOR",
+          editCallback: async (i, cell) => {
+            this.groups[i].color = cell.color;
+            this.main();
+          }
+        },
+        // dataset may rename what a row counts (GDC: cases, not samples)
+        { label: `#${uiLabel(this.app.vocabApi.termdbConfig?.uiLabels, "Sample", "Sample").toUpperCase()}` },
+        { 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: "" },
+        // filled in asynchronously below, so one slow count does not hold up the table
+        {}
+        // 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();
+      });
+      this.app.vocabApi.getFilteredSampleCount(this.groups[i].filter, this.hasCohort0 ? null : this.state.termfilter.filter0).then((n) => row[3].__td.text(n)).catch((e) => row[3].__td.text("n/a").attr("title", e?.message || e));
+      const group = this.groups[i];
+      filterInit({
+        holder: row[4].__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, color2) {
+    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: color2 || 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 (${this.groups[0].name} vs others)`);
+      this.dom.submit.on("click", async () => {
+        await this.clickSubmit(this.getSubmitGroups());
+      });
+    } else if (this.groups.length == 2) {
+      this.dom.addGroup.select(".sja_new_filter_btn").style("pointer-events", "none").style("opacity", 0.5);
+      this.dom.submit.text(`Submit (${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;
+    const mapParent2Children = true;
+    for (const g of groups) {
+      const samples = await this.vocabApi.getFilteredSampleList(
+        filterJoin([g.filter, this.state.termfilter.filter]),
+        filter0,
+        mapParent2Children
+      );
+      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,
+        list: sampleIds
+        //samples need to be passed for the samplelst filter to work
+      };
+    }
+    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(this.isGE ? "termdb/DE" : "termdb/diffMeth", { body });
+    this.dom.loading.style("display", "none");
+    this.dom.preAnalysis.style("display", "block").selectAll("*").remove();
+    renderPreAnalysisData({
+      preAnalysisData,
+      samplelstTW,
+      groups: samplelstTW.q.groups,
+      holder: this.dom.preAnalysis,
+      termType: this.termType,
+      self: this
+    });
+  }
+};
+var DEinputInit = getCompInit(DEinputPlot);
+var componentInit = DEinputInit;
+var supportedTermTypes = /* @__PURE__ */ new Set([TermTypes.GENE_EXPRESSION, TermTypes.DNA_METHYLATION]);
+async function getPlotConfig(opts, app) {
+  if (opts.termType && !supportedTermTypes.has(opts.termType))
+    throw new Error(`termType='${opts.termType}' is not supported by DEinput`);
+  const config = {
+    chartType: "DEinput",
+    // default keeps every existing caller on gene expression without passing anything
+    termType: opts.termType || TermTypes.GENE_EXPRESSION,
+    settings: {}
+  };
+  const c = copyMerge(config, opts);
+  if (c.groups) c.groups = await getValidGroups(c.groups, app);
+  return c;
+}
+async function getValidGroups(groups, app) {
+  if (!Array.isArray(groups)) throw "config.groups must be an array";
+  if (groups.length > 2) throw "config.groups[] cannot exceed 2 groups";
+  const names = /* @__PURE__ */ new Set();
+  for (const g of groups) {
+    if (!g?.filter) throw "config.groups[] entry is missing .filter{}";
+    if ("name" in g && typeof g.name != "string") throw "config.groups[].name must be a string";
+    if (!g.name) continue;
+    if (names.has(g.name)) throw `duplicate config.groups[].name='${g.name}'`;
+    names.add(g.name);
+  }
+  const validated = [];
+  for (const g of groups) {
+    const filter = getNormalRoot(g.filter);
+    if (!filter.lst.length) throw "config.groups[] entry has a blank .filter{}";
+    if (app?.vocabApi) await Promise.all(rehydrateFilter(filter, app.vocabApi));
+    const name = g.name || getUnusedGroupName(names);
+    names.add(name);
+    const valid = Object.assign({}, g, { filter, name });
+    if ("color" in g) {
+      const c = color(g.color);
+      if (!c) throw `invalid config.groups[].color='${g.color}'`;
+      valid.color = c.formatHex();
+    }
+    validated.push(valid);
+  }
+  return validated;
+}
+function getUnusedGroupName(names) {
+  const base = "New group";
+  for (let i = 0; ; i++) {
+    const name = base + (i === 0 ? "" : " " + i);
+    if (!names.has(name)) return name;
+  }
+}
+export {
+  DEinputInit,
+  componentInit,
+  getPlotConfig
+};
+//# sourceMappingURL=DEinput-W66CT4U2.js.map

package/dist/DEinput-W66CT4U2.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 { rehydrateFilter } from '#filter/rehydrateFilter'\nimport { getColors } from '#shared/common.js'\nimport { color as d3color, 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'\nimport { TermTypes } from '#types'\nimport { uiLabel } from '#shared'\n\nconst colorScale = getColors(5)\n\n/* Group-building submission UI for a two-group differential analysis.\n\nServes both differential gene expression and differential DNA methylation, selected by\nconfig.termType (default gene expression, so existing callers are unchanged). The two differ\nin only three places, all branched on `isGE` below: which ds query proves the assay exists,\nwhich server route the pre-analysis hits, and the expression-source tabs (methylation has no\npseudobulk counterpart). The group table, filter prompt and submit flow are shared.\n\nThe results view is a separate chart, 'differentialAnalysis'; this plot only builds groups\nand hands them over via renderPreAnalysisData(). */\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\t/** set once config.groups[] has been copied into this.groups[] */\n\tgroupsSeeded?: boolean\n\t/** set once config.autoSubmit has triggered clickSubmit() */\n\tautoSubmitted?: boolean\n\t/** geneExpression (default) or dnaMethylation. Resolved in init() from state.config, NOT from\n\t * opts: mass/plot.js hands the component only {app, holder, header, id, ...}, so config fields\n\t * are not on opts and reading it in the constructor would silently always be undefined. */\n\ttermType!: string\n\n\tconstructor(opts: any, api: ComponentApi) {\n\t\tsuper(opts, api)\n\t\tthis.type = DEinputPlot.type\n\t\tthis.dom = this.getDom()\n\t\tthis.groups = []\n\t}\n\n\tget isGE() {\n\t\treturn this.termType == TermTypes.GENE_EXPRESSION\n\t}\n\n\tgetDom() {\n\t\t// header text is set in init(), once state.config.termType is known\n\t\tconst header = this.opts?.header || 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(appState) {\n\t\tconst state = this.getState(appState)\n\t\tthis.termType = state.config.termType || TermTypes.GENE_EXPRESSION\n\t\tthis.dom.header?.html(`Differential ${termType2label(this.termType)}`)\n\t\tawait this.renderExpressionSourceUI()\n\t}\n\n\t// TODO: handle errors\n\tasync main() {\n\t\t/* The expression-source tabs are built during init(), and Tabs.main() fires the active tab's\n\t\tcallback immediately -- which calls main() before rx has assigned this.state. Bail out here\n\t\trather than let maySeedGroups() throw on this.state.config: it sets groupsSeeded=true first,\n\t\tso the throw permanently skips seeding and config.groups[] silently never appears. The\n\t\tframework calls main() again right after init(), so nothing is lost by returning. */\n\t\tif (!this.state) return\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.maySeedGroups()\n\t\t// set before makeGroupsUI(), which uses it when requesting each group's sample count\n\t\tthis.hasCohort0 = this.groups.some(g => g.filter.lst.some(item => item.tvs?.term.type == 'cohort'))\n\t\t// awaited: on the first run makeGroupsUI() awaits the filter prompt, and it re-enables the add\n\t\t// group button at its end, which would otherwise undo the button state set by mayRenderSubmit()\n\t\tawait this.makeGroupsUI()\n\t\tthis.mayRenderSubmit()\n\t\tawait this.mayAutoSubmit()\n\t}\n\n\t/* config.groups[] lets a caller launch this ui with prebuilt groups, each defined by a mass\n\tfilter, instead of requiring the user to build both groups by hand. seeded only once: main() reruns\n\ton every state change, and a seeded group is editable like any other, so a rerun must not undo a\n\trename, edit, or deletion */\n\tmaySeedGroups() {\n\t\tif (this.groupsSeeded) return\n\t\tthis.groupsSeeded = true\n\t\tif (!this.state.config.groups?.length) return\n\t\t/* a group built by the filter prompt embeds the mass filter, since the prompt is seeded with it\n\t\tin makeGroupsUI(); rebase the prebuilt groups the same way. without this, the sample count in the\n\t\tgroup table, which uses the group filter alone, would not match the sample set that clickSubmit()\n\t\tanalyzes, which joins in the mass filter. the cohort filter is excluded to match the prompt, and\n\t\tto not flip hasCohort0, and thus drop filter0, for a group that did not ask for a cohort */\n\t\tconst massFilter = getNormalRoot(excludeFilterByTag(structuredClone(this.state.termfilter.filter), 'cohortFilter'))\n\t\tfor (const g of this.state.config.groups) {\n\t\t\tthis.addNewGroup(filterJoin([massFilter, getNormalRoot(g.filter)]), this.groups, g.name, g.color)\n\t\t}\n\t}\n\n\t/* config.autoSubmit runs the analysis on the seeded groups without waiting for a click, for a caller\n\tthat already knows the groups to compare. runs only once: main() reruns on every state change, and\n\teach run is a round trip to termdb/DE */\n\tasync mayAutoSubmit() {\n\t\tif (!this.state.config.autoSubmit || this.autoSubmitted) return\n\t\t// mayRenderSubmit() hides the button when the groups cannot be compared, such as a lone group\n\t\t// under a cohort filter that cannot be negated\n\t\tif (this.dom.submit.style('display') == 'none') return\n\t\tthis.autoSubmitted = true\n\t\tawait this.clickSubmit(this.getSubmitGroups())\n\t}\n\n\t/** the groups as compared by the analysis: a lone group is compared against all other samples */\n\tgetSubmitGroups() {\n\t\tif (this.groups.length != 1) return this.groups\n\t\tconst group = this.groups[0]\n\t\treturn [\n\t\t\tgroup,\n\t\t\t{\n\t\t\t\tname: 'Not in ' + group.name,\n\t\t\t\tcolor: '#ccc',\n\t\t\t\tfilter: negateFilter(group.filter)\n\t\t\t}\n\t\t]\n\t}\n\n\tasync renderExpressionSourceUI() {\n\t\tconst config = this.app.vocabApi.termdbConfig\n\n\t\t/* methylation has one source, the element matrices, and no pseudobulk counterpart, so there\n\t\tis nothing to choose -- skip the tabs entirely. the ds gate mirrors the one the Groups menu\n\t\tapplies (mass/groups.js): a promoter matrix OR any element type is enough, so a ds offering\n\t\tonly non-promoter classes is still reachable. */\n\t\tif (!this.isGE) {\n\t\t\tconst dm = config.queries?.dnaMethylation\n\t\t\tif (!dm?.promoter && !dm?.elementTypes?.length)\n\t\t\t\tthrow new Error('No DNA methylation data configured for differential analysis')\n\t\t\tthis.expressionSource = 'bulk'\n\t\t\treturn\n\t\t}\n\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\theader_mode: this.opts?.header_mode,\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 ${newName} already exists`)\n\t\t\t\t\t\t\tawait this.main()\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\tthis.groups[i].name = newName\n\t\t\t\t\t\t\tawait this.main()\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\tlabel: 'COLOR',\n\t\t\t\t\teditCallback: async (i, cell) => {\n\t\t\t\t\t\tthis.groups[i].color = cell.color\n\t\t\t\t\t\tthis.main()\n\t\t\t\t\t}\n\t\t\t\t},\n\t\t\t\t// dataset may rename what a row counts (GDC: cases, not samples)\n\t\t\t\t{ label: `#${uiLabel(this.app.vocabApi.termdbConfig?.uiLabels, 'Sample', 'Sample').toUpperCase()}` },\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: '' }, // filled in asynchronously below, so one slow count does not hold up the table\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// fill the #SAMPLE cell. not awaited: the table is already rendered, and on gdc each count\n\t\t\t// is a /cases round trip\n\t\t\tthis.app.vocabApi\n\t\t\t\t.getFilteredSampleCount(this.groups[i].filter, this.hasCohort0 ? null : this.state.termfilter.filter0)\n\t\t\t\t.then(n => row[3].__td.text(n))\n\t\t\t\t.catch(e => row[3].__td.text('n/a').attr('title', e?.message || e))\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[4].__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, color?: 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: color || 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 (${this.groups[0].name} vs others)`)\n\t\t\tthis.dom.submit.on('click', async () => {\n\t\t\t\tawait this.clickSubmit(this.getSubmitGroups())\n\t\t\t})\n\t\t} else if (this.groups.length == 2) {\n\t\t\t// two groups of samples, compare these groups\n\t\t\tthis.dom.addGroup.select('.sja_new_filter_btn').style('pointer-events', 'none').style('opacity', 0.5)\n\t\t\tthis.dom.submit.text(`Submit (${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\tconst mapParent2Children = true // DE/DM data assumed to be at sample-level so map parent samples to child samples\n\t\tfor (const g of groups) {\n\t\t\tconst samples = await this.vocabApi!.getFilteredSampleList(\n\t\t\t\tfilterJoin([g.filter, this.state.termfilter.filter]),\n\t\t\t\tfilter0,\n\t\t\t\tmapParent2Children\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\tlist: sampleIds //samples need to be passed for the samplelst filter to work\n\t\t\t}\n\t\t}\n\n\t\t// get actual numbers of samples with data for this assay\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\t// both routes accept the same preAnalysis body and answer with the same {data:{groupName:n}}\n\t\tconst preAnalysisData = await dofetch3(this.isGE ? 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+  "names": ["term", "filter", "i", "color"]
+}