@sjcrh/proteinpaint-client 2.198.0 → 2.200.0

package/dist/NumericHandler.unit.spec-X2DAED4O.js

@@ -0,0 +1,219 @@
+import {
+  agedx
+} from "./chunk-32AI7I4C.js";
+import {
+  NumericHandler
+} from "./chunk-NZRMHM76.js";
+import "./chunk-IUBBQPO2.js";
+import {
+  termjson
+} from "./chunk-DHPLHIVP.js";
+import {
+  sleep
+} from "./chunk-ECIBJXFT.js";
+import {
+  require_tape
+} from "./chunk-TUMA63WX.js";
+import {
+  TwRouter
+} from "./chunk-TKW5TW4Z.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-3SHZTAGF.js";
+import "./chunk-HYOEWQ5P.js";
+import "./chunk-6QCYT6G2.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-IIT367QZ.js";
+import "./chunk-RZGEKL77.js";
+import "./chunk-OTTMHVYH.js";
+import "./chunk-GNS6CQMA.js";
+import "./chunk-JVPWIVDT.js";
+import "./chunk-4WF3XDQP.js";
+import "./chunk-7JRDJNLR.js";
+import "./chunk-M3J4MINX.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-MPSLUEI4.js";
+import "./chunk-6PNPHACF.js";
+import "./chunk-WPHUM5S5.js";
+import "./chunk-JNITUVXP.js";
+import "./chunk-2KXLYFAO.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-VQZ2Z5YU.js";
+import "./chunk-UJELJXJG.js";
+import "./chunk-BZTWTH4Y.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import {
+  select_default
+} from "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import "./chunk-DQC5FFGV.js";
+import {
+  __toESM
+} from "./chunk-HFNDKYVF.js";
+
+// termsetting/handlers/test/NumericHandler.unit.spec.ts
+var import_tape = __toESM(require_tape(), 1);
+async function getNumericHandler(_opts = {}) {
+  const term = JSON.parse(JSON.stringify(termjson.agedx));
+  if (term.bins.default.type == "regular-bin") term.bins.default.bin_size = 500;
+  const rawTw = {
+    term,
+    q: {
+      mode: "discrete",
+      //type: 'regular-bin',
+      ...term.bins.default
+    }
+  };
+  const tw = await TwRouter.initRaw(rawTw);
+  const handler = new NumericHandler({
+    termsetting: {
+      tw,
+      term: rawTw.term,
+      q: rawTw.q,
+      opts: {
+        numericEditMenuVersion: ["continuous", "discrete", "binary", "spline"],
+        // _opts will any matching override previous opts key-values
+        ..._opts
+      },
+      api: {
+        async runCallback() {
+          const self = handler.termsetting;
+          const q = handler.editHandler.q;
+          self.tw = await TwRouter.initRaw({ term: self.term, q }, self.opts);
+        }
+      },
+      dom: {
+        tip: {
+          hide() {
+          }
+        }
+      },
+      vocabApi: {
+        getViolinBox() {
+          return agedx;
+        },
+        getPercentile() {
+          return {
+            values: [0.03537315665, 3.13072460515, 8.164619357749999, 17.8726813385]
+          };
+        }
+      }
+    }
+  });
+  const holder = select_default("body").append("div").style("width", "fit-content").style("margin", "20px").style("padding", "5px").style("border", "1px solid #000");
+  return {
+    rawTw,
+    tw,
+    handler,
+    holder,
+    destroy: () => {
+      if (handler.editHandler && "destroy" in handler.editHandler) handler.editHandler.destroy();
+      if (typeof handler.destroy == "function") handler.destroy();
+      holder.remove();
+    }
+  };
+}
+(0, import_tape.default)("\n", (test) => {
+  test.comment("-***- NumericHandler.unit.spec -***-");
+  test.end();
+});
+(0, import_tape.default)("tabs data and pill status", async (test) => {
+  const { handler, destroy } = await getNumericHandler();
+  test.deepEqual(
+    handler.tabs.map((t) => t.label),
+    ["Continuous", "Discrete", "Cubic spline", "Binary"],
+    "sets the expected tab data"
+  );
+  test.deepEqual(handler.getPillStatus(), { text: "bin size=500" }, `should give the expected pill status`);
+  if (test._ok) destroy();
+  test.end();
+});
+(0, import_tape.default)("editHandler", async (test) => {
+  const { handler, destroy } = await getNumericHandler();
+  handler.density_data = { min: 0, max: 100 };
+  await handler.setEditHandler(handler.tabs[0]);
+  test.equal(
+    handler.editHandler.constructor.name,
+    "NumContEditor",
+    `sets the expected editHandler for mode='continuous'`
+  );
+  await handler.setEditHandler(handler.tabs[1]);
+  test.equal(
+    handler.editHandler.constructor.name,
+    "NumDiscreteEditor",
+    `sets the expected editHandler for mode='discrete'`
+  );
+  await handler.setEditHandler(handler.tabs[2]);
+  test.equal(handler.editHandler.constructor.name, "NumSplineEditor", `sets the expected editHandler for mode='binary'`);
+  await handler.setEditHandler(handler.tabs[3]);
+  test.equal(handler.editHandler.constructor.name, "NumBinaryEditor", `sets the expected editHandler for mode='spline'`);
+  if (test._ok) destroy();
+  test.end();
+});
+(0, import_tape.default)("showEditMenu, multiple modes", async (test) => {
+  const { handler, holder, destroy } = await getNumericHandler();
+  await handler.showEditMenu(holder);
+  await sleep(0);
+  test.equal(handler.editHandler.dom.density_div.selectAll("svg").size(), 1, `should render a density plot svg`);
+  test.equal(
+    handler.dom.topBar?.selectAll(".sj-toggle-button").size(),
+    4,
+    `should render 4 tabs, one toggle button for each mode`
+  );
+  test.equal(handler.dom.btnDiv?.selectAll("button").size(), 2, `should render an apply and reset button`);
+  test.deepEqual(handler.getPillStatus(), { text: "bin size=500" }, "should have the expected initial pill status");
+  const tabBtns = handler.dom.topBar.node().querySelectorAll("button");
+  tabBtns[2].click();
+  await sleep(10);
+  handler.dom.btnDiv.select("button").node().click();
+  await sleep(10);
+  test.deepEqual(
+    handler.getPillStatus(),
+    { text: "cubic spline" },
+    "should have a different pill status after switching q.modes"
+  );
+  if (test._ok) destroy();
+  test.end();
+});
+(0, import_tape.default)("showEditMenu, single mode", async (test) => {
+  const { handler, holder, destroy } = await getNumericHandler({ numericEditMenuVersion: ["binary"] });
+  await handler.showEditMenu(holder);
+  await sleep(0);
+  test.equal(handler.editHandler.dom.density_div.selectAll("svg").size(), 1, `should render a density plot svg`);
+  test.equal(
+    handler.dom.topBar?.selectAll(".sj-toggle-button").size(),
+    void 0,
+    `should not render mode toggle buttons`
+  );
+  test.equal(handler.dom.btnDiv?.selectAll("button").size(), 2, `should render an apply and reset button`);
+  if (test._ok) destroy();
+  test.end();
+});
+(0, import_tape.default)("apply and reset", async (test) => {
+  test.timeoutAfter(50);
+  test.plan(2);
+  const { handler, holder, destroy } = await getNumericHandler();
+  handler.editHandler = {
+    getEditedQ() {
+      test.pass("should trigger editHandler.getEditedQ() from applyEdits()");
+      return { mode: "discrete", type: "regular-bin" };
+    },
+    undoEdits() {
+      test.pass("should trigger editHandler.undoEdits() from undoEdits()");
+    }
+  };
+  try {
+    await handler.renderButtons(holder);
+    const btns = holder.node()?.querySelectorAll("button");
+    if (btns?.length) {
+      btns[0].click();
+      btns[1].click();
+    }
+    if (test._ok) destroy();
+    test.end();
+  } catch (e) {
+    test.fail("should trigger editHandler.getEditedQ and .undoEdits(): " + e);
+  }
+});
+//# sourceMappingURL=NumericHandler.unit.spec-X2DAED4O.js.map

package/dist/ProteomeInput-GBVCLNS7.js

@@ -0,0 +1,394 @@
+import {
+  getDefaultGseaSettings
+} from "./chunk-KTKZSYIH.js";
+import {
+  PlotBase,
+  Tabs,
+  getDefaultVolcanoSettings,
+  sayerror,
+  table2col
+} from "./chunk-TKW5TW4Z.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-3SHZTAGF.js";
+import {
+  Menu
+} from "./chunk-HYOEWQ5P.js";
+import "./chunk-6QCYT6G2.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-IIT367QZ.js";
+import "./chunk-RZGEKL77.js";
+import "./chunk-OTTMHVYH.js";
+import "./chunk-GNS6CQMA.js";
+import {
+  dofetch3
+} from "./chunk-JVPWIVDT.js";
+import "./chunk-4WF3XDQP.js";
+import {
+  NumericModes
+} from "./chunk-7JRDJNLR.js";
+import {
+  copyMerge,
+  getCompInit
+} from "./chunk-M3J4MINX.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-MPSLUEI4.js";
+import {
+  PROTEOME_DAP,
+  TermTypeGroups
+} from "./chunk-6PNPHACF.js";
+import "./chunk-WPHUM5S5.js";
+import "./chunk-JNITUVXP.js";
+import "./chunk-2KXLYFAO.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-VQZ2Z5YU.js";
+import "./chunk-UJELJXJG.js";
+import "./chunk-BZTWTH4Y.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-HFNDKYVF.js";
+
+// plots/ProteomeInput.ts
+var ProteomeInput = class _ProteomeInput extends PlotBase {
+  static {
+    this.type = "ProteomeInput";
+  }
+  constructor(opts, api) {
+    super(opts, api);
+    this.type = _ProteomeInput.type;
+    this.opts = opts;
+    this.components = {};
+  }
+  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 {
+      config,
+      activeCohort: appState.activeCohort,
+      termdbConfig: appState.termdbConfig
+    };
+  }
+  async init(appState) {
+    const state = this.getState(appState);
+    const proteomeDetails = state.config.proteomeDetails;
+    const { organism, assay, cohort } = proteomeDetails;
+    const organisms = state.termdbConfig?.queries?.proteome?.organisms || {};
+    const cohortConfig = organisms[organism]?.assays?.[assay]?.cohorts?.[cohort];
+    this.dom = this.initDom(proteomeDetails);
+    this.tabs = [
+      {
+        label: "Single protein",
+        isVisible: () => true,
+        callback: async (_event, tab) => {
+          await this.renderSingleProtein(tab, proteomeDetails, state.activeCohort);
+          delete tab.callback;
+        }
+      },
+      {
+        label: "Two proteins",
+        isVisible: () => true,
+        callback: async (_event, tab) => {
+          await this.renderTwoProteinSelect(tab, proteomeDetails, state.activeCohort);
+          delete tab.callback;
+        }
+      },
+      {
+        label: "Hierarchical clustering",
+        isVisible: () => true,
+        callback: async (_event, tab) => {
+          await this.renderMultiProteinSelect(tab, proteomeDetails, state.activeCohort);
+          delete tab.callback;
+        }
+      },
+      {
+        label: "DAP Volcano",
+        isVisible: () => !!cohortConfig?.DAPfile,
+        callback: async (_event, tab) => {
+          await this.renderDapVolcano(tab, proteomeDetails);
+          delete tab.callback;
+        }
+      }
+    ];
+    const chartTabs = new Tabs({
+      holder: this.dom.tabs,
+      tabs: this.tabs,
+      tabsPosition: "vertical"
+    });
+    await chartTabs.main();
+  }
+  initDom(proteomeDetails) {
+    const { organism, assay, cohort } = proteomeDetails;
+    this.opts.header.append("span").style("padding-right", "5px").text(`${organism} ${assay}: ${cohort}`);
+    this.opts.header.append("span").text("PROTEOME").style("font-size", "0.7em").style("opacity", "0.6");
+    return {
+      tabs: this.opts.holder.append("div").style("margin", "10px").attr("data-testid", "sjpp-proteome-input-tabs-wrapper")
+    };
+  }
+  getUsecase(proteomeDetails) {
+    const { organism, assay, cohort } = proteomeDetails;
+    return {
+      target: "proteomeAbundance",
+      detail: "term",
+      proteomeDetails: { organism, assay, cohort },
+      label: `Organism: ${organism}; Assay: ${assay}; Sample set: ${cohort}`
+    };
+  }
+  async renderSingleProtein(tab, proteomeDetails, activeCohort) {
+    const { organism, assay, cohort } = proteomeDetails;
+    const row = tab.contentHolder.style("padding", "15px");
+    row.append("div").style("padding", "5px").style("margin-bottom", "5px").text("Select a protein:");
+    const treeHolder = row.append("div");
+    const termdb = await import("./app-O64TGDFH.js");
+    termdb.appInit({
+      vocabApi: this.app.vocabApi,
+      holder: treeHolder,
+      state: {
+        activeCohort,
+        nav: { header_mode: "search_only" },
+        tree: { usecase: this.getUsecase(proteomeDetails) }
+      },
+      tree: {
+        click_term: (term) => {
+          const t = structuredClone(term.term || term);
+          t.dataTypeDetails = { organism, assay, cohort };
+          const config = {
+            chartType: "summary",
+            term: { term: t, q: { mode: NumericModes.continuous } },
+            assayCohortTitle: `${organism} ${assay}: ${cohort}`,
+            proteomeDetails: { organism, assay, cohort }
+          };
+          const overlayTerm = this.getState(this.app.getState()).termdbConfig?.queries?.proteome?.organisms?.[organism]?.overlayTerm;
+          if (overlayTerm) config.term2 = { term: structuredClone(overlayTerm), q: {} };
+          this.dispatchEdits(config);
+        }
+      }
+    });
+  }
+  addProteinSearchbox(row, proteomeDetails, onSelect) {
+    const usecase = this.getUsecase(proteomeDetails);
+    const tip = new Menu({ padding: "0px" });
+    const searchbox = row.append("input").attr("type", "search").attr("placeholder", "Protein").attr("class", "sja_genesearchinput").style("width", "200px");
+    const mark = row.append("span").style("margin-left", "5px");
+    const word = row.append("span").style("margin-left", "5px").style("font-size", ".8em").style("opacity", 0.6);
+    let debounceTimer;
+    const doSearch = async () => {
+      const v = searchbox.property("value").trim();
+      if (v.length < 2) {
+        tip.hide();
+        return;
+      }
+      try {
+        const data = await this.app.vocabApi.findTerm(v, "", usecase, TermTypeGroups.PROTEOME_ABUNDANCE);
+        if (!data.lst?.length) {
+          mark.style("color", "red").html("&cross;");
+          word.text("No match");
+          tip.hide();
+        } else {
+          tip.clear().showunder(searchbox.node());
+          for (const term of data.lst) {
+            tip.d.append("div").attr("class", "sja_menuoption").style("border-radius", "0px").text(term.name).on("click", () => {
+              tip.hide();
+              searchbox.property("value", term.name);
+              mark.style("color", "green").html("&check;");
+              word.text(term.name);
+              onSelect(term);
+            });
+          }
+        }
+      } catch (e) {
+        mark.style("color", "red").html("&cross;");
+        word.text(e.message || "Error");
+      }
+    };
+    searchbox.on("keyup", async (event) => {
+      if (event.key === "Escape") {
+        tip.hide();
+        return;
+      }
+      clearTimeout(debounceTimer);
+      mark.html("");
+      word.text("");
+      debounceTimer = setTimeout(doSearch, 300);
+    });
+    return { searchbox, mark, word };
+  }
+  async renderTwoProteinSelect(tab, proteomeDetails, _activeCohort) {
+    const { organism, assay, cohort } = proteomeDetails;
+    const holder = tab.contentHolder.style("padding", "10px");
+    let selectedTerm1 = null;
+    let selectedTerm2 = null;
+    const gene1row = holder.append("div").style("padding", "5px");
+    const gene2row = holder.append("div").style("padding", "5px").style("display", "none");
+    const submitBtn = holder.append("button").attr("type", "button").attr("disabled", true);
+    gene1row.append("span").text("Select the first protein:");
+    this.addProteinSearchbox(gene1row, proteomeDetails, (term) => {
+      selectedTerm1 = term;
+      gene2row.style("display", "block");
+    });
+    gene2row.append("span").text("Select the second protein:");
+    this.addProteinSearchbox(gene2row, proteomeDetails, (term) => {
+      selectedTerm2 = term;
+      submitBtn.attr("disabled", null);
+    });
+    submitBtn.text("Submit").style("border", "none").style("border-radius", "20px").style("padding", "10px 15px").style("margin-top", "10px").on("click", async () => {
+      if (!selectedTerm1 || !selectedTerm2) {
+        sayerror(holder, "Please select two proteins.");
+        return;
+      }
+      const t1 = structuredClone(selectedTerm1);
+      const t2 = structuredClone(selectedTerm2);
+      t1.dataTypeDetails = { organism, assay, cohort };
+      t2.dataTypeDetails = { organism, assay, cohort };
+      await this.dispatchEdits({
+        chartType: "summary",
+        term: { term: t1, q: { mode: NumericModes.continuous } },
+        term2: { term: t2, q: { mode: NumericModes.continuous } },
+        assayCohortTitle: `${organism} ${assay}: ${cohort}`,
+        proteomeDetails: { organism, assay, cohort }
+      });
+    });
+  }
+  async renderMultiProteinSelect(tab, proteomeDetails, activeCohort) {
+    const { organism, assay, cohort } = proteomeDetails;
+    const holder = tab.contentHolder.style("padding", "10px");
+    const usecase = this.getUsecase(proteomeDetails);
+    const termdb = await import("./app-O64TGDFH.js");
+    const treeHolder = holder.append("div");
+    termdb.appInit({
+      vocabApi: this.app.vocabApi,
+      holder: treeHolder,
+      state: {
+        activeCohort,
+        nav: { header_mode: "search_only" },
+        tree: { usecase }
+      },
+      tree: {
+        submit_lst: (termlst) => {
+          const twlst = termlst.map((term) => {
+            const t = structuredClone(term);
+            t.dataTypeDetails = { organism, assay, cohort };
+            return { term: t, q: { mode: NumericModes.continuous } };
+          });
+          if (twlst.length < 3) {
+            alert("At least three proteins are required for hierarchical clustering. Please select more proteins.");
+            return;
+          }
+          this.dispatchEdits({
+            chartType: "hierCluster",
+            dataType: "proteomeAbundance",
+            termgroups: [{ name: "Protein Abundance Cluster", lst: twlst, type: "hierCluster" }],
+            assayCohortTitle: `${organism} ${assay}: ${cohort}`,
+            proteomeDetails: { organism, assay, cohort }
+          });
+        }
+      }
+    });
+    const enforceMinAndLayout = () => {
+      const submitBtn = treeHolder.select("button").node();
+      if (submitBtn) {
+        const selectedCount = treeHolder.selectAll('.sja_menuoption[aria-label="Click to delete"]').size();
+        submitBtn.disabled = selectedCount < 3;
+      }
+      const node = treeHolder.node();
+      const divs = node.querySelectorAll("div");
+      for (const div of divs) {
+        if (div.style.flexWrap === "wrap" && div.style.display === "inline-block") {
+          div.style.display = "flex";
+        }
+      }
+    };
+    const observer = new MutationObserver(enforceMinAndLayout);
+    observer.observe(treeHolder.node(), {
+      childList: true,
+      subtree: true,
+      attributes: true,
+      attributeFilter: ["style"]
+    });
+  }
+  async renderDapVolcano(tab, proteomeDetails) {
+    const { organism, assay, cohort } = proteomeDetails;
+    const holder = tab.contentHolder.style("padding", "15px");
+    const countsDiv = holder.append("div");
+    countsDiv.append("span").text("Loading sample counts...");
+    try {
+      const result = await dofetch3("termdb/dapVolcano", {
+        body: {
+          genome: this.app.vocabApi.vocab.genome,
+          dslabel: this.app.vocabApi.vocab.dslabel,
+          organism,
+          assay,
+          cohort,
+          countsOnly: true
+        }
+      });
+      countsDiv.selectAll("*").remove();
+      if (result.error) throw result.error;
+      const table = table2col({ holder: countsDiv });
+      table.table.style("margin-left", "5px").style("padding", "5px 10px");
+      {
+        const [c1, c2] = table.addRow();
+        c1.html(`<span style="font-size:.8em;font-weight:bold">CONTROL</span>`);
+        c2.html(`${result.sample_size1} samples`);
+      }
+      {
+        const [c1, c2] = table.addRow();
+        c1.html(`<span style="font-size:.8em;font-weight:bold">CASE</span>`);
+        c2.html(`${result.sample_size2} samples`);
+      }
+    } catch (e) {
+      countsDiv.selectAll("*").remove();
+      countsDiv.append("span").style("color", "#999").text("Sample counts unavailable");
+      console.error(e.stack);
+    }
+    holder.append("button").attr("class", "sjpp_apply_btn sja_filter_tag_btn sja_sharp_border").text("Launch Volcano").on("click", async () => {
+      await this.dispatchEdits({
+        chartType: "differentialAnalysis",
+        childType: "volcano",
+        termType: PROTEOME_DAP,
+        headerText: `${organism} ${assay}: ${cohort}`,
+        proteomeDetails: { organism, assay, cohort },
+        settings: {
+          volcano: {
+            ...getDefaultVolcanoSettings({}, { termType: PROTEOME_DAP }),
+            pValueType: "original"
+          },
+          gsea: getDefaultGseaSettings({})
+        },
+        highlightedData: [],
+        hidePlotFilter: true
+      });
+    });
+  }
+  async dispatchEdits(config) {
+    await this.app.dispatch({
+      type: "app_refresh",
+      subactions: [
+        { type: "plot_create", config },
+        { type: "plot_delete", id: this.id }
+      ]
+    });
+  }
+  async main() {
+  }
+};
+var proteomeInputInit = getCompInit(ProteomeInput);
+var componentInit = proteomeInputInit;
+function getPlotConfig(opts) {
+  const config = {
+    chartType: "ProteomeInput",
+    hidePlotFilter: true
+  };
+  return copyMerge(config, opts);
+}
+export {
+  ProteomeInput,
+  componentInit,
+  getPlotConfig,
+  proteomeInputInit
+};
+//# sourceMappingURL=ProteomeInput-GBVCLNS7.js.map

package/dist/ProteomeInput-GBVCLNS7.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/ProteomeInput.ts"],
+  "sourcesContent": ["import { PlotBase } from './PlotBase.ts'\nimport { getCompInit, copyMerge, type ComponentApi, type RxComponent } from '#rx'\nimport { NumericModes } from '#shared/terms.js'\nimport { sayerror, Tabs, Menu, table2col } from '#dom'\nimport { TermTypeGroups } from '#shared/common.js'\nimport { getDefaultVolcanoSettings } from './volcano/settings/defaults.ts'\nimport { getDefaultGseaSettings } from './gsea/settings/defaults.ts'\nimport { dofetch3 } from '#common/dofetch'\nimport { PROTEOME_DAP, type ProteomeDetails } from '#types'\n\nexport class ProteomeInput extends PlotBase implements RxComponent {\n\tstatic type = 'ProteomeInput'\n\n\ttype: string\n\tdom!: { [index: string]: any }\n\ttabs!: any\n\n\tconstructor(opts: any, api: ComponentApi) {\n\t\tsuper(opts, api)\n\t\tthis.type = ProteomeInput.type\n\t\tthis.opts = opts\n\t\tthis.components = {}\n\t}\n\n\tgetState(appState: any) {\n\t\tconst config = appState.plots.find((p: any) => 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\tconfig,\n\t\t\tactiveCohort: appState.activeCohort,\n\t\t\ttermdbConfig: appState.termdbConfig\n\t\t}\n\t}\n\n\tasync init(appState: any) {\n\t\tconst state = this.getState(appState)\n\t\tconst proteomeDetails: ProteomeDetails = state.config.proteomeDetails\n\t\tconst { organism, assay, cohort } = proteomeDetails\n\t\tconst organisms = state.termdbConfig?.queries?.proteome?.organisms || {}\n\t\tconst cohortConfig = organisms[organism]?.assays?.[assay]?.cohorts?.[cohort]\n\n\t\tthis.dom = this.initDom(proteomeDetails)\n\n\t\tthis.tabs = [\n\t\t\t{\n\t\t\t\tlabel: 'Single protein',\n\t\t\t\tisVisible: () => true,\n\t\t\t\tcallback: async (_event: any, tab: any) => {\n\t\t\t\t\tawait this.renderSingleProtein(tab, proteomeDetails, state.activeCohort)\n\t\t\t\t\tdelete tab.callback\n\t\t\t\t}\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Two proteins',\n\t\t\t\tisVisible: () => true,\n\t\t\t\tcallback: async (_event: any, tab: any) => {\n\t\t\t\t\tawait this.renderTwoProteinSelect(tab, proteomeDetails, state.activeCohort)\n\t\t\t\t\tdelete tab.callback\n\t\t\t\t}\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Hierarchical clustering',\n\t\t\t\tisVisible: () => true,\n\t\t\t\tcallback: async (_event: any, tab: any) => {\n\t\t\t\t\tawait this.renderMultiProteinSelect(tab, proteomeDetails, state.activeCohort)\n\t\t\t\t\tdelete tab.callback\n\t\t\t\t}\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'DAP Volcano',\n\t\t\t\tisVisible: () => !!cohortConfig?.DAPfile,\n\t\t\t\tcallback: async (_event: any, tab: any) => {\n\t\t\t\t\tawait this.renderDapVolcano(tab, proteomeDetails)\n\t\t\t\t\tdelete tab.callback\n\t\t\t\t}\n\t\t\t}\n\t\t]\n\n\t\tconst chartTabs = new Tabs({\n\t\t\tholder: this.dom.tabs,\n\t\t\ttabs: this.tabs,\n\t\t\ttabsPosition: 'vertical'\n\t\t})\n\t\tawait chartTabs.main()\n\t}\n\n\tinitDom(proteomeDetails: ProteomeDetails) {\n\t\tconst { organism, assay, cohort } = proteomeDetails\n\t\tthis.opts.header.append('span').style('padding-right', '5px').text(`${organism} ${assay}: ${cohort}`)\n\t\tthis.opts.header.append('span').text('PROTEOME').style('font-size', '0.7em').style('opacity', '0.6')\n\n\t\treturn {\n\t\t\ttabs: this.opts.holder\n\t\t\t\t.append('div')\n\t\t\t\t.style('margin', '10px')\n\t\t\t\t.attr('data-testid', 'sjpp-proteome-input-tabs-wrapper')\n\t\t}\n\t}\n\n\tprivate getUsecase(proteomeDetails: ProteomeDetails) {\n\t\tconst { organism, assay, cohort } = proteomeDetails\n\t\treturn {\n\t\t\ttarget: 'proteomeAbundance',\n\t\t\tdetail: 'term',\n\t\t\tproteomeDetails: { organism, assay, cohort },\n\t\t\tlabel: `Organism: ${organism}; Assay: ${assay}; Sample set: ${cohort}`\n\t\t}\n\t}\n\n\tasync renderSingleProtein(tab: any, proteomeDetails: ProteomeDetails, activeCohort: number) {\n\t\tconst { organism, assay, cohort } = proteomeDetails\n\t\tconst row = tab.contentHolder.style('padding', '15px')\n\t\trow.append('div').style('padding', '5px').style('margin-bottom', '5px').text('Select a protein:')\n\n\t\tconst treeHolder = row.append('div')\n\t\tconst termdb = await import('../termdb/app')\n\t\ttermdb.appInit({\n\t\t\tvocabApi: this.app.vocabApi,\n\t\t\tholder: treeHolder,\n\t\t\tstate: {\n\t\t\t\tactiveCohort,\n\t\t\t\tnav: { header_mode: 'search_only' },\n\t\t\t\ttree: { usecase: this.getUsecase(proteomeDetails) }\n\t\t\t},\n\t\t\ttree: {\n\t\t\t\tclick_term: (term: any) => {\n\t\t\t\t\tconst t = structuredClone(term.term || term)\n\t\t\t\t\tt.dataTypeDetails = { organism, assay, cohort }\n\t\t\t\t\tconst config: any = {\n\t\t\t\t\t\tchartType: 'summary',\n\t\t\t\t\t\tterm: { term: t, q: { mode: NumericModes.continuous } },\n\t\t\t\t\t\tassayCohortTitle: `${organism} ${assay}: ${cohort}`,\n\t\t\t\t\t\tproteomeDetails: { organism, assay, cohort }\n\t\t\t\t\t}\n\t\t\t\t\tconst overlayTerm = this.getState(this.app.getState()).termdbConfig?.queries?.proteome?.organisms?.[organism]\n\t\t\t\t\t\t?.overlayTerm\n\t\t\t\t\tif (overlayTerm) config.term2 = { term: structuredClone(overlayTerm), q: {} }\n\t\t\t\t\tthis.dispatchEdits(config)\n\t\t\t\t}\n\t\t\t}\n\t\t})\n\t}\n\n\tprivate addProteinSearchbox(row: any, proteomeDetails: ProteomeDetails, onSelect: (term: any) => void) {\n\t\tconst usecase = this.getUsecase(proteomeDetails)\n\t\tconst tip = new Menu({ padding: '0px' })\n\t\tconst searchbox = row\n\t\t\t.append('input')\n\t\t\t.attr('type', 'search')\n\t\t\t.attr('placeholder', 'Protein')\n\t\t\t.attr('class', 'sja_genesearchinput')\n\t\t\t.style('width', '200px')\n\t\tconst mark = row.append('span').style('margin-left', '5px')\n\t\tconst word = row.append('span').style('margin-left', '5px').style('font-size', '.8em').style('opacity', 0.6)\n\n\t\tlet debounceTimer: ReturnType<typeof setTimeout>\n\t\tconst doSearch = async () => {\n\t\t\tconst v = searchbox.property('value').trim()\n\t\t\tif (v.length < 2) {\n\t\t\t\ttip.hide()\n\t\t\t\treturn\n\t\t\t}\n\t\t\ttry {\n\t\t\t\tconst data = await this.app.vocabApi.findTerm(v, '', usecase, TermTypeGroups.PROTEOME_ABUNDANCE)\n\t\t\t\tif (!data.lst?.length) {\n\t\t\t\t\tmark.style('color', 'red').html('&cross;')\n\t\t\t\t\tword.text('No match')\n\t\t\t\t\ttip.hide()\n\t\t\t\t} else {\n\t\t\t\t\ttip.clear().showunder(searchbox.node())\n\t\t\t\t\tfor (const term of data.lst) {\n\t\t\t\t\t\ttip.d\n\t\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t\t\t\t\t.style('border-radius', '0px')\n\t\t\t\t\t\t\t.text(term.name)\n\t\t\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\t\t\ttip.hide()\n\t\t\t\t\t\t\t\tsearchbox.property('value', term.name)\n\t\t\t\t\t\t\t\tmark.style('color', 'green').html('&check;')\n\t\t\t\t\t\t\t\tword.text(term.name)\n\t\t\t\t\t\t\t\tonSelect(term)\n\t\t\t\t\t\t\t})\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t} catch (e: any) {\n\t\t\t\tmark.style('color', 'red').html('&cross;')\n\t\t\t\tword.text(e.message || 'Error')\n\t\t\t}\n\t\t}\n\n\t\tsearchbox.on('keyup', async (event: any) => {\n\t\t\tif (event.key === 'Escape') {\n\t\t\t\ttip.hide()\n\t\t\t\treturn\n\t\t\t}\n\t\t\tclearTimeout(debounceTimer)\n\t\t\tmark.html('')\n\t\t\tword.text('')\n\t\t\tdebounceTimer = setTimeout(doSearch, 300)\n\t\t})\n\n\t\treturn { searchbox, mark, word }\n\t}\n\n\tasync renderTwoProteinSelect(tab: any, proteomeDetails: ProteomeDetails, _activeCohort: number) {\n\t\tconst { organism, assay, cohort } = proteomeDetails\n\t\tconst holder = tab.contentHolder.style('padding', '10px')\n\t\tlet selectedTerm1: any = null\n\t\tlet selectedTerm2: any = null\n\n\t\tconst gene1row = holder.append('div').style('padding', '5px')\n\t\tconst gene2row = holder.append('div').style('padding', '5px').style('display', 'none')\n\t\tconst submitBtn = holder.append('button').attr('type', 'button').attr('disabled', true)\n\n\t\tgene1row.append('span').text('Select the first protein:')\n\t\tthis.addProteinSearchbox(gene1row, proteomeDetails, (term: any) => {\n\t\t\tselectedTerm1 = term\n\t\t\tgene2row.style('display', 'block')\n\t\t})\n\n\t\tgene2row.append('span').text('Select the second protein:')\n\t\tthis.addProteinSearchbox(gene2row, proteomeDetails, (term: any) => {\n\t\t\tselectedTerm2 = term\n\t\t\tsubmitBtn.attr('disabled', null)\n\t\t})\n\n\t\tsubmitBtn\n\t\t\t.text('Submit')\n\t\t\t.style('border', 'none')\n\t\t\t.style('border-radius', '20px')\n\t\t\t.style('padding', '10px 15px')\n\t\t\t.style('margin-top', '10px')\n\t\t\t.on('click', async () => {\n\t\t\t\tif (!selectedTerm1 || !selectedTerm2) {\n\t\t\t\t\tsayerror(holder, 'Please select two proteins.')\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tconst t1 = structuredClone(selectedTerm1)\n\t\t\t\tconst t2 = structuredClone(selectedTerm2)\n\t\t\t\tt1.dataTypeDetails = { organism, assay, cohort }\n\t\t\t\tt2.dataTypeDetails = { organism, assay, cohort }\n\t\t\t\tawait this.dispatchEdits({\n\t\t\t\t\tchartType: 'summary',\n\t\t\t\t\tterm: { term: t1, q: { mode: NumericModes.continuous } },\n\t\t\t\t\tterm2: { term: t2, q: { mode: NumericModes.continuous } },\n\t\t\t\t\tassayCohortTitle: `${organism} ${assay}: ${cohort}`,\n\t\t\t\t\tproteomeDetails: { organism, assay, cohort }\n\t\t\t\t})\n\t\t\t})\n\t}\n\n\tasync renderMultiProteinSelect(tab: any, proteomeDetails: ProteomeDetails, activeCohort: number) {\n\t\tconst { organism, assay, cohort } = proteomeDetails\n\t\tconst holder = tab.contentHolder.style('padding', '10px')\n\n\t\tconst usecase = this.getUsecase(proteomeDetails)\n\t\tconst termdb = await import('../termdb/app')\n\n\t\tconst treeHolder = holder.append('div')\n\n\t\ttermdb.appInit({\n\t\t\tvocabApi: this.app.vocabApi,\n\t\t\tholder: treeHolder,\n\t\t\tstate: {\n\t\t\t\tactiveCohort,\n\t\t\t\tnav: { header_mode: 'search_only' },\n\t\t\t\ttree: { usecase }\n\t\t\t},\n\t\t\ttree: {\n\t\t\t\tsubmit_lst: (termlst: any[]) => {\n\t\t\t\t\tconst twlst = termlst.map((term: any) => {\n\t\t\t\t\t\tconst t = structuredClone(term)\n\t\t\t\t\t\tt.dataTypeDetails = { organism, assay, cohort }\n\t\t\t\t\t\treturn { term: t, q: { mode: NumericModes.continuous } }\n\t\t\t\t\t})\n\n\t\t\t\t\tif (twlst.length < 3) {\n\t\t\t\t\t\talert('At least three proteins are required for hierarchical clustering. Please select more proteins.')\n\t\t\t\t\t\treturn\n\t\t\t\t\t}\n\n\t\t\t\t\tthis.dispatchEdits({\n\t\t\t\t\t\tchartType: 'hierCluster',\n\t\t\t\t\t\tdataType: 'proteomeAbundance',\n\t\t\t\t\t\ttermgroups: [{ name: 'Protein Abundance Cluster', lst: twlst, type: 'hierCluster' }],\n\t\t\t\t\t\tassayCohortTitle: `${organism} ${assay}: ${cohort}`,\n\t\t\t\t\t\tproteomeDetails: { organism, assay, cohort }\n\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t}\n\t\t})\n\n\t\tconst enforceMinAndLayout = () => {\n\t\t\tconst submitBtn = treeHolder.select('button').node() as HTMLButtonElement | null\n\t\t\tif (submitBtn) {\n\t\t\t\tconst selectedCount = treeHolder.selectAll('.sja_menuoption[aria-label=\"Click to delete\"]').size()\n\t\t\t\tsubmitBtn.disabled = selectedCount < 3\n\t\t\t}\n\n\t\t\tconst node = treeHolder.node() as HTMLElement\n\t\t\tconst divs = node.querySelectorAll('div')\n\t\t\tfor (const div of divs) {\n\t\t\t\tif (div.style.flexWrap === 'wrap' && div.style.display === 'inline-block') {\n\t\t\t\t\tdiv.style.display = 'flex'\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\tconst observer = new MutationObserver(enforceMinAndLayout)\n\t\tobserver.observe(treeHolder.node(), {\n\t\t\tchildList: true,\n\t\t\tsubtree: true,\n\t\t\tattributes: true,\n\t\t\tattributeFilter: ['style']\n\t\t})\n\t}\n\n\tasync renderDapVolcano(tab: any, proteomeDetails: ProteomeDetails) {\n\t\tconst { organism, assay, cohort } = proteomeDetails\n\t\tconst holder = tab.contentHolder.style('padding', '15px')\n\n\t\tconst countsDiv = holder.append('div')\n\t\tcountsDiv.append('span').text('Loading sample counts...')\n\n\t\ttry {\n\t\t\tconst result = await dofetch3('termdb/dapVolcano', {\n\t\t\t\tbody: {\n\t\t\t\t\tgenome: this.app.vocabApi.vocab.genome,\n\t\t\t\t\tdslabel: this.app.vocabApi.vocab.dslabel,\n\t\t\t\t\torganism,\n\t\t\t\t\tassay,\n\t\t\t\t\tcohort,\n\t\t\t\t\tcountsOnly: true\n\t\t\t\t}\n\t\t\t})\n\t\t\tcountsDiv.selectAll('*').remove()\n\t\t\tif (result.error) throw result.error\n\t\t\tconst table = table2col({ holder: countsDiv })\n\t\t\ttable.table.style('margin-left', '5px').style('padding', '5px 10px')\n\t\t\t{\n\t\t\t\tconst [c1, c2] = table.addRow()\n\t\t\t\tc1.html(`<span style=\"font-size:.8em;font-weight:bold\">CONTROL</span>`)\n\t\t\t\tc2.html(`${result.sample_size1} samples`)\n\t\t\t}\n\t\t\t{\n\t\t\t\tconst [c1, c2] = table.addRow()\n\t\t\t\tc1.html(`<span style=\"font-size:.8em;font-weight:bold\">CASE</span>`)\n\t\t\t\tc2.html(`${result.sample_size2} samples`)\n\t\t\t}\n\t\t} catch (e: any) {\n\t\t\tcountsDiv.selectAll('*').remove()\n\t\t\tcountsDiv.append('span').style('color', '#999').text('Sample counts unavailable')\n\t\t\tconsole.error(e.stack)\n\t\t}\n\n\t\tholder\n\t\t\t.append('button')\n\t\t\t.attr('class', 'sjpp_apply_btn sja_filter_tag_btn sja_sharp_border')\n\t\t\t.text('Launch Volcano')\n\t\t\t.on('click', async () => {\n\t\t\t\tawait this.dispatchEdits({\n\t\t\t\t\tchartType: 'differentialAnalysis',\n\t\t\t\t\tchildType: 'volcano',\n\t\t\t\t\ttermType: PROTEOME_DAP,\n\t\t\t\t\theaderText: `${organism} ${assay}: ${cohort}`,\n\t\t\t\t\tproteomeDetails: { organism, assay, cohort },\n\t\t\t\t\tsettings: {\n\t\t\t\t\t\tvolcano: {\n\t\t\t\t\t\t\t...getDefaultVolcanoSettings({}, { termType: PROTEOME_DAP }),\n\t\t\t\t\t\t\tpValueType: 'original'\n\t\t\t\t\t\t},\n\t\t\t\t\t\tgsea: getDefaultGseaSettings({})\n\t\t\t\t\t},\n\t\t\t\t\thighlightedData: [],\n\t\t\t\t\thidePlotFilter: true\n\t\t\t\t})\n\t\t\t})\n\t}\n\n\tasync dispatchEdits(config: any) {\n\t\tawait this.app.dispatch({\n\t\t\ttype: 'app_refresh',\n\t\t\tsubactions: [\n\t\t\t\t{ type: 'plot_create', config },\n\t\t\t\t{ type: 'plot_delete', id: this.id }\n\t\t\t]\n\t\t})\n\t}\n\n\tasync main() {}\n}\n\nexport const proteomeInputInit = getCompInit(ProteomeInput)\nexport const componentInit = proteomeInputInit\n\nexport function getPlotConfig(opts: any) {\n\tconst config = {\n\t\tchartType: 'ProteomeInput',\n\t\thidePlotFilter: true\n\t}\n\treturn copyMerge(config, opts)\n}\n"],
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