@sjcrh/proteinpaint-client 2.204.0 → 2.206.0

package/dist/DE-VANPWKZI.js

@@ -1,88 +0,0 @@
-import {
-  appInit
-} from "./chunk-GI3RVOO4.js";
-import "./chunk-DUGOFIQS.js";
-import "./chunk-GF6CKFXE.js";
-import "./chunk-6SKLD7JU.js";
-import "./chunk-GTMHDSOQ.js";
-import "./chunk-SKMFMGCD.js";
-import "./chunk-KWLBPOPE.js";
-import "./chunk-X46YA4CB.js";
-import "./chunk-ZU47ERPU.js";
-import "./chunk-PRZWSBMA.js";
-import "./chunk-7RX5UEF3.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-L42F5J5C.js";
-import "./chunk-HKQDZKSF.js";
-import "./chunk-ELJX3QIQ.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-FUSTNOQZ.js";
-import "./chunk-VSPUFGDX.js";
-import "./chunk-WVPFLPWB.js";
-import "./chunk-S5SOLLGM.js";
-import "./chunk-WINIL2KN.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-D6G64XPJ.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-YLJOZP4P.js";
-import "./chunk-HDTFYTEL.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" },
-      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-VANPWKZI.js.map

package/dist/DE-VANPWKZI.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../gdc/DE.ts"],
-  "sourcesContent": ["import { appInit } from '#mass/app'\n\n/*\nlaunches submission UI for differental gene expression\n*/\n\ninterface InitArg {\n\tdebugmode?: true\n\tgenome?: string\n\tdslabel?: string\n\tfilter0?: object\n\tstate?: {\n\t\tplots?: Array<{ chartType: string; [key: string]: any }>\n\t}\n\topts?: {\n\t\tapp?: Record<string, any>\n\t}\n}\n\ninterface UpdateArg {\n\tfilter0?: object\n\t[key: string]: any\n}\n\nexport async function init(\n\targ: InitArg,\n\tholder: HTMLElement,\n\tgenomes: any\n): Promise<{ update: (updateArg: UpdateArg) => Promise<void> }> {\n\tconst useGenome = arg.genome || 'hg38'\n\tconst useDslabel = arg.dslabel || 'GDC'\n\tconst genome = genomes[useGenome]\n\tconst massApi = await appInit({\n\t\t//debug: arg.debugmode, // is debug accepted?\n\t\tgenome,\n\t\tholder,\n\t\tstate: {\n\t\t\tgenome: useGenome,\n\t\t\tdslabel: useDslabel,\n\t\t\ttermfilter: { filter0: arg.filter0 },\n\t\t\tnav: { activeTab: 1, header_mode: 'hidden' },\n\t\t\tplots: [{ chartType: 'DEinput' }]\n\t\t},\n\t\topts: Object.assign(\n\t\t\t{\n\t\t\t\t// todo additional customizations\n\t\t\t\t// dictionary:{header:'Select a variable to build Correlation Plot'}\n\t\t\t\t// some way to make gene exp violin/boxplot to use log scale by default, but numeric dict term should not\n\t\t\t},\n\t\t\targ.opts || {}\n\t\t),\n\t\tapp: arg.opts?.app || {}\n\t})\n\tconst api = {\n\t\tupdate: async (updateArg: UpdateArg) => {\n\t\t\tif (!massApi) return\n\n\t\t\t// NOTE: changes inside the mass app (nav tabs, sandbox, etc) are handled internally\n\t\t\t// within the mass app instance; only embedder portal-dispatched changes, such as filter0,\n\t\t\t// should be handled below\n\n\t\t\tif ('filter0' in updateArg) {\n\t\t\t\tmassApi.dispatch({\n\t\t\t\t\ttype: 'app_refresh',\n\t\t\t\t\tsubactions: [\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\ttype: 'filter_replace',\n\t\t\t\t\t\t\tfilter0: updateArg.filter0\n\t\t\t\t\t\t}\n\t\t\t\t\t]\n\t\t\t\t})\n\t\t\t}\n\t\t},\n\t\ttriggerAbort: (reason = '') => massApi.triggerAbort(reason)\n\t}\n\n\treturn api\n}\n"],
-  "mappings": ";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAwBA,eAAsB,KACrB,KACA,QACA,SAC+D;AAC/D,QAAM,YAAY,IAAI,UAAU;AAChC,QAAM,aAAa,IAAI,WAAW;AAClC,QAAM,SAAS,QAAQ,SAAS;AAChC,QAAM,UAAU,MAAM,QAAQ;AAAA;AAAA,IAE7B;AAAA,IACA;AAAA,IACA,OAAO;AAAA,MACN,QAAQ;AAAA,MACR,SAAS;AAAA,MACT,YAAY,EAAE,SAAS,IAAI,QAAQ;AAAA,MACnC,KAAK,EAAE,WAAW,GAAG,aAAa,SAAS;AAAA,MAC3C,OAAO,CAAC,EAAE,WAAW,UAAU,CAAC;AAAA,IACjC;AAAA,IACA,MAAM,OAAO;AAAA,MACZ;AAAA;AAAA;AAAA;AAAA,MAIA;AAAA,MACA,IAAI,QAAQ,CAAC;AAAA,IACd;AAAA,IACA,KAAK,IAAI,MAAM,OAAO,CAAC;AAAA,EACxB,CAAC;AACD,QAAM,MAAM;AAAA,IACX,QAAQ,OAAO,cAAyB;AACvC,UAAI,CAAC,QAAS;AAMd,UAAI,aAAa,WAAW;AAC3B,gBAAQ,SAAS;AAAA,UAChB,MAAM;AAAA,UACN,YAAY;AAAA,YACX;AAAA,cACC,MAAM;AAAA,cACN,SAAS,UAAU;AAAA,YACpB;AAAA,UACD;AAAA,QACD,CAAC;AAAA,MACF;AAAA,IACD;AAAA,IACA,cAAc,CAAC,SAAS,OAAO,QAAQ,aAAa,MAAM;AAAA,EAC3D;AAEA,SAAO;AACR;",
-  "names": []
-}

package/dist/DEinput-MONPHDB2.js

@@ -1,405 +0,0 @@
-import {
-  PlotBase,
-  Tabs,
-  excludeFilterByTag,
-  filterInit,
-  filterJoin,
-  filterPromptInit,
-  getNormalRoot,
-  make_radios,
-  negateFilter,
-  renderPreAnalysisData,
-  renderTable
-} from "./chunk-7RX5UEF3.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-L42F5J5C.js";
-import "./chunk-HKQDZKSF.js";
-import "./chunk-ELJX3QIQ.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import {
-  dofetch3
-} from "./chunk-FUSTNOQZ.js";
-import "./chunk-VSPUFGDX.js";
-import {
-  termType2label
-} from "./chunk-WVPFLPWB.js";
-import {
-  TermTypeGroups,
-  getColors
-} from "./chunk-S5SOLLGM.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-WINIL2KN.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-D6G64XPJ.js";
-import {
-  uiLabel
-} from "./chunk-W5J3LTYS.js";
-import "./chunk-YLJOZP4P.js";
-import "./chunk-HDTFYTEL.js";
-import "./chunk-FXQXCOII.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-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";
-  }
-  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",
-        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) {
-    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.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();
-    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-MONPHDB2.js.map

package/dist/DEinput-MONPHDB2.js.map

@@ -1,7 +0,0 @@
-{
-  "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'\nimport { uiLabel } from '#shared'\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: 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\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\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) {\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.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. renderPreAnalysisData writes its own header, using the ds vocabulary\n\t\tthis.dom.preAnalysis.style('display', 'block').selectAll('*').remove()\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"],
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