@sjcrh/proteinpaint-client 2.206.0 → 2.207.0

package/dist/DE-2J7DSRPC.js

@@ -1,89 +0,0 @@
-import {
-  appInit
-} from "./chunk-NSRGYBDM.js";
-import "./chunk-HJSGHFJ6.js";
-import "./chunk-ZWCVRVV4.js";
-import "./chunk-BMQDU7KN.js";
-import "./chunk-WPDM57B5.js";
-import "./chunk-5UO7MKCO.js";
-import "./chunk-X46YA4CB.js";
-import "./chunk-SKMFMGCD.js";
-import "./chunk-ANGLZ4XR.js";
-import "./chunk-PRZWSBMA.js";
-import "./chunk-Q5SK3U2T.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-54KC7DAB.js";
-import "./chunk-N7DVQTPC.js";
-import "./chunk-ELJX3QIQ.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-RPDVFM7E.js";
-import "./chunk-M4XXKTH2.js";
-import "./chunk-5ILEFNXJ.js";
-import "./chunk-IZUYLFOX.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-2J7DSRPC.js.map

package/dist/DEinput-I7JWNOSD.js

@@ -1,499 +0,0 @@
-import {
-  rehydrateFilter
-} from "./chunk-SKMFMGCD.js";
-import {
-  PlotBase,
-  Tabs,
-  excludeFilterByTag,
-  filterInit,
-  filterJoin,
-  filterPromptInit,
-  getNormalRoot,
-  make_radios,
-  negateFilter,
-  renderPreAnalysisData,
-  renderTable
-} from "./chunk-Q5SK3U2T.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-54KC7DAB.js";
-import "./chunk-N7DVQTPC.js";
-import "./chunk-ELJX3QIQ.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import {
-  dofetch3
-} from "./chunk-RPDVFM7E.js";
-import "./chunk-M4XXKTH2.js";
-import {
-  termType2label
-} from "./chunk-5ILEFNXJ.js";
-import {
-  TermTypeGroups,
-  TermTypes,
-  getColors
-} from "./chunk-IZUYLFOX.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;
-    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,
-        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-I7JWNOSD.js.map

package/dist/DM-NQ46YPGF.js

@@ -1,90 +0,0 @@
-import {
-  appInit
-} from "./chunk-NSRGYBDM.js";
-import "./chunk-HJSGHFJ6.js";
-import "./chunk-ZWCVRVV4.js";
-import "./chunk-BMQDU7KN.js";
-import "./chunk-WPDM57B5.js";
-import "./chunk-5UO7MKCO.js";
-import "./chunk-X46YA4CB.js";
-import "./chunk-SKMFMGCD.js";
-import "./chunk-ANGLZ4XR.js";
-import "./chunk-PRZWSBMA.js";
-import "./chunk-Q5SK3U2T.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-54KC7DAB.js";
-import "./chunk-N7DVQTPC.js";
-import "./chunk-ELJX3QIQ.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-RPDVFM7E.js";
-import "./chunk-M4XXKTH2.js";
-import "./chunk-5ILEFNXJ.js";
-import "./chunk-IZUYLFOX.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/DM.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({
-    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.
-      // DEinput is the group-building submission ui, shared with DE and switched by termType;
-      // it launches the 'differentialAnalysis' results chart once groups are submitted
-      plots: arg.state?.plots || [{ chartType: "DEinput", termType: "dnaMethylation" }]
-    },
-    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=DM-NQ46YPGF.js.map