@sjcrh/proteinpaint-client 2.203.0 → 2.203.1

package/dist/DE-HUQLQ2Z3.js

@@ -0,0 +1,87 @@
+import {
+  appInit
+} from "./chunk-TSK4ZTFK.js";
+import "./chunk-QJ6SO7CF.js";
+import "./chunk-HIWTGMTE.js";
+import "./chunk-WPDJCEX2.js";
+import "./chunk-F4PMOAQK.js";
+import "./chunk-SKMFMGCD.js";
+import "./chunk-IHU55O2R.js";
+import "./chunk-UILBQKQ6.js";
+import "./chunk-L26EQ4PZ.js";
+import "./chunk-PRZWSBMA.js";
+import "./chunk-D5PX2UDG.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-XFAL46LZ.js";
+import "./chunk-OPMMU6DQ.js";
+import "./chunk-ELJX3QIQ.js";
+import "./chunk-7BLXK3GI.js";
+import "./chunk-VSSZJHOR.js";
+import "./chunk-5RUVBYLK.js";
+import "./chunk-6X7PP7A4.js";
+import "./chunk-EO6M3LY3.js";
+import "./chunk-DXLO4OAB.js";
+import "./chunk-4QBRVM4V.js";
+import "./chunk-H6INPPUC.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-IMYSFDE5.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-4ZL6IBXM.js";
+import "./chunk-OZVWP4ZR.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-HFNDKYVF.js";
+
+// gdc/DE.ts
+async function init(arg, holder, genomes) {
+  const useGenome = arg.genome || "hg38";
+  const useDslabel = arg.dslabel || "GDC";
+  const genome = genomes[useGenome];
+  const massApi = await appInit({
+    //debug: arg.debugmode, // is debug accepted?
+    genome,
+    holder,
+    state: {
+      genome: useGenome,
+      dslabel: useDslabel,
+      termfilter: { filter0: arg.filter0 },
+      nav: { activeTab: 1, header_mode: "hidden" },
+      plots: [{ chartType: "DEinput" }]
+    },
+    opts: Object.assign(
+      {
+        // todo additional customizations
+        // dictionary:{header:'Select a variable to build Correlation Plot'}
+        // some way to make gene exp violin/boxplot to use log scale by default, but numeric dict term should not
+      },
+      arg.opts || {}
+    ),
+    app: arg.opts?.app || {}
+  });
+  const api = {
+    update: async (updateArg) => {
+      if (!massApi) return;
+      if ("filter0" in updateArg) {
+        massApi.dispatch({
+          type: "app_refresh",
+          subactions: [
+            {
+              type: "filter_replace",
+              filter0: updateArg.filter0
+            }
+          ]
+        });
+      }
+    },
+    triggerAbort: (reason = "") => massApi.triggerAbort(reason)
+  };
+  return api;
+}
+export {
+  init
+};
+//# sourceMappingURL=DE-HUQLQ2Z3.js.map

package/dist/DEinput-WWUISAF2.js

@@ -0,0 +1,404 @@
+import {
+  PlotBase,
+  Tabs,
+  excludeFilterByTag,
+  filterInit,
+  filterJoin,
+  filterPromptInit,
+  getNormalRoot,
+  make_radios,
+  negateFilter,
+  renderPreAnalysisData,
+  renderTable
+} from "./chunk-D5PX2UDG.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-XFAL46LZ.js";
+import "./chunk-OPMMU6DQ.js";
+import "./chunk-ELJX3QIQ.js";
+import "./chunk-7BLXK3GI.js";
+import "./chunk-VSSZJHOR.js";
+import "./chunk-5RUVBYLK.js";
+import {
+  dofetch3
+} from "./chunk-6X7PP7A4.js";
+import "./chunk-EO6M3LY3.js";
+import {
+  termType2label
+} from "./chunk-DXLO4OAB.js";
+import {
+  TermTypeGroups,
+  getColors
+} from "./chunk-4QBRVM4V.js";
+import {
+  copyMerge,
+  getCompInit
+} from "./chunk-H6INPPUC.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-IMYSFDE5.js";
+import {
+  uiLabel
+} from "./chunk-W5J3LTYS.js";
+import "./chunk-4ZL6IBXM.js";
+import "./chunk-OZVWP4ZR.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-HFNDKYVF.js";
+
+// plots/DEinput.ts
+var colorScale = getColors(5);
+var DEinputPlot = class _DEinputPlot extends PlotBase {
+  constructor(opts, api) {
+    super(opts, api);
+    this.components = {};
+    this.type = _DEinputPlot.type;
+    this.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-WWUISAF2.js.map