@sjcrh/proteinpaint-client 2.181.0 → 2.183.0

package/dist/geneORA-B5UK77KL.js

@@ -0,0 +1,276 @@
+import {
+  controlsInit,
+  downloadTable,
+  newSandboxDiv,
+  renderTable,
+  table2col
+} from "./chunk-OXJ2TWDO.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-V6DLLX4N.js";
+import {
+  dofetch3
+} from "./chunk-7RN3L2BX.js";
+import {
+  Menu
+} from "./chunk-A6TQGNDQ.js";
+import "./chunk-HYZG6OPC.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-5EF5U7MX.js";
+import "./chunk-2K5DSRBJ.js";
+import "./chunk-UCLS2SVB.js";
+import {
+  copyMerge,
+  getCompInit
+} from "./chunk-MVTCBVSX.js";
+import "./chunk-SEQLC4AD.js";
+import {
+  roundValueAuto
+} from "./chunk-L4QG7XZE.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-KQMEJUWI.js";
+import "./chunk-UJU3Q7QJ.js";
+import "./chunk-WGL6FIUE.js";
+import "./chunk-6ITDJ5UR.js";
+import "./chunk-XYFDBYOY.js";
+import "./chunk-TV74I3Y5.js";
+import "./chunk-IH7ILDJS.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-TOU7EVFQ.js";
+import "./chunk-OAWQ6LOO.js";
+import "./chunk-SEEYV6P2.js";
+import {
+  select_default
+} from "./chunk-NDWTN4U5.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-HFNDKYVF.js";
+
+// plots/geneORA.js
+var tip = new Menu();
+var geneORA = class _geneORA {
+  static type = "geneORA";
+  constructor() {
+    this.type = _geneORA.type;
+  }
+  async init(opts) {
+    if (!this.opts.holder || !this.opts.header) {
+      const sandBox = newSandboxDiv(select_default(this.opts.holder.node().parentNode));
+      this.opts.header = sandBox.header;
+      this.opts.holder = sandBox.body;
+    }
+    const controlsDiv = this.opts.holder.append("div").style("display", "inline-block");
+    const mainDiv = this.opts.holder.append("div").style("display", "inline-block").style("margin-left", "50px");
+    const holder = mainDiv.append("div").style("display", "inline-block");
+    const detailsDiv = mainDiv.append("div").style("display", "inline-block").style("vertical-align", "top").style("margin-top", "50px");
+    const tableDiv = this.opts.holder.append("div").style("margin-left", "50px");
+    this.dom = {
+      holder,
+      header: this.opts.header,
+      controlsDiv,
+      detailsDiv,
+      tableDiv
+    };
+  }
+  async setControls() {
+    this.dom.controlsDiv.selectAll("*").remove();
+    const inputs = [
+      {
+        label: "P-value Filter Cutoff (Linear Scale)",
+        type: "number",
+        chartType: "geneORA",
+        settingsKey: "pvalue",
+        title: "P-value significance",
+        min: 0,
+        max: 1
+      },
+      {
+        label: "P-value Filter Type",
+        type: "radio",
+        chartType: "geneORA",
+        settingsKey: "adjusted_original_pvalue",
+        title: "Toggle between original and adjusted pvalues for volcano plot",
+        options: [
+          { label: "Adjusted", value: "adjusted" },
+          { label: "Original", value: "original" }
+        ]
+      },
+      {
+        label: "Gene Set Size Filter Cutoff",
+        type: "number",
+        chartType: "geneORA",
+        settingsKey: "gene_set_size_cutoff",
+        title: "Gene set size cutoff. Helps in filtering out large gene sets",
+        min: 0,
+        max: 2e4
+      },
+      {
+        label: "Filter Non-coding Genes",
+        type: "checkbox",
+        chartType: "geneORA",
+        settingsKey: "filter_non_coding_genes",
+        title: "Filter non-coding genes",
+        boxLabel: ""
+      }
+    ];
+    const geneSet = {
+      label: "Gene Set Group",
+      type: "dropdown",
+      chartType: "geneORA",
+      settingsKey: "pathway",
+      title: "Display table showing original and adjusted pvalues corresponding to each significant pathway",
+      boxLabel: ""
+    };
+    geneSet.options = this.app.opts.genome.termdbs.msigdb.analysisGenesetGroups;
+    if (!this.settings.pathway) {
+      this.settings.pathway = "-";
+    }
+    inputs.push(geneSet);
+    this.components = {
+      controls: await controlsInit({
+        app: this.app,
+        id: this.id,
+        holder: this.dom.controlsDiv,
+        inputs
+      })
+    };
+    this.components.controls.on("downloadClick.geneORA", () => {
+      downloadTable(this.gene_ora_table_rows, this.gene_ora_table_cols);
+    });
+  }
+  getState(appState) {
+    const config = appState.plots.find((p) => p.id === this.id);
+    if (!config) throw `No plot with id='${this.id}' found`;
+    return {
+      config
+    };
+  }
+  async main() {
+    this.config = JSON.parse(JSON.stringify(this.state.config));
+    this.settings = this.config.settings.geneORA;
+    await this.setControls();
+    this.dom.header.html(
+      this.config.geneORAparams.sample_genes.split(",").length + ' genes <span style="font-size:.8em;opacity:.7">GENE SET OVERREPRESENTATION ANALYSIS</span>'
+    );
+    render_geneORA(this);
+  }
+};
+async function render_geneORA(self) {
+  if (self.settings.pathway != "-") {
+    self.dom.detailsDiv.selectAll("*").remove();
+    self.dom.tableDiv.selectAll("*").remove();
+    self.config.geneORAparams.geneSetGroup = self.settings.pathway;
+    self.config.geneORAparams.filter_non_coding_genes = self.settings.filter_non_coding_genes;
+    const wait = self.dom.detailsDiv.append("div").text("Loading...");
+    let output;
+    try {
+      output = await rungeneORA(self.config.geneORAparams);
+      wait.remove();
+      if (output.error) {
+        throw output.error;
+      }
+    } catch (e) {
+      alert("Error: " + e);
+      return;
+    }
+    const table_stats = table2col({ holder: self.dom.detailsDiv });
+    const [t1, t2] = table_stats.addRow();
+    t2.style("text-align", "center").style("font-size", "0.8em").style("opacity", "0.8").text("COUNT");
+    const addStats = [
+      //{
+      //	label: 'Sample genes',
+      //	values: self.config.geneORAparams.sample_genes.split(',').length
+      //},
+      {
+        label: "Gene sets analyzed",
+        values: output.num_pathways
+      }
+    ];
+    if (self.config.geneORAparams.background_genes) {
+      addStats.push({
+        label: "Background genes",
+        values: self.config.geneORAparams.background_genes.split(",").length
+      });
+    }
+    for (const dataRow of addStats) {
+      const [td1, td2] = table_stats.addRow();
+      td1.text(dataRow.label);
+      td2.style("text-align", "end").text(dataRow.values);
+    }
+    self.gene_ora_table_cols = [
+      { label: "Gene set group" },
+      { label: "Original p-value (linear scale)" },
+      { label: "Adjusted p-value (linear scale)" },
+      { label: "Gene set size" },
+      { label: "Gene set hits" }
+    ];
+    self.gene_ora_table_rows = [];
+    for (const pathway of output.pathways) {
+      if (self.settings.adjusted_original_pvalue == "adjusted" && self.settings.pvalue >= pathway.p_value_adjusted && self.settings.gene_set_size_cutoff > pathway.gene_set_size) {
+        self.gene_ora_table_rows.push([
+          { value: pathway.pathway_name },
+          { value: roundValueAuto(pathway.p_value_original) },
+          { value: roundValueAuto(pathway.p_value_adjusted) },
+          { value: pathway.gene_set_size },
+          { value: pathway.gene_set_hits }
+        ]);
+      } else if (self.settings.adjusted_original_pvalue == "original" && self.settings.pvalue >= pathway.p_value_original && self.settings.gene_set_size_cutoff > pathway.gene_set_size) {
+        self.gene_ora_table_rows.push([
+          { value: pathway.pathway_name },
+          { value: roundValueAuto(pathway.p_value_original) },
+          { value: roundValueAuto(pathway.p_value_adjusted) },
+          { value: pathway.gene_set_size },
+          { value: pathway.gene_set_hits }
+        ]);
+      }
+    }
+    const d_ora = self.dom.tableDiv.append("div");
+    renderTable({
+      columns: self.gene_ora_table_cols,
+      rows: self.gene_ora_table_rows,
+      div: d_ora,
+      showLines: true,
+      maxHeight: "30vh",
+      resize: true
+    });
+  }
+}
+async function getPlotConfig(opts, app) {
+  try {
+    const config = {
+      //idea for fixing nav button
+      //samplelst: { groups: app.opts.state.groups}
+      settings: {
+        geneORA: {
+          pvalue: 0.05,
+          adjusted_original_pvalue: "adjusted",
+          pathway: void 0,
+          gene_set_size_cutoff: 2e3,
+          filter_non_coding_genes: true
+        },
+        controls: { isOpen: true }
+      }
+    };
+    return copyMerge(config, opts);
+  } catch (e) {
+    throw `${e} [geneORA getPlotConfig()]`;
+  }
+}
+var geneORAInit = getCompInit(geneORA);
+var componentInit = geneORAInit;
+function makeChartBtnMenu(holder, chartsInstance) {
+  chartsInstance.prepPlot({
+    config: {
+      chartType: "geneORA"
+    }
+  });
+}
+async function rungeneORA(body) {
+  return await dofetch3("genesetOverrepresentation", { body });
+}
+export {
+  componentInit,
+  geneORAInit,
+  getPlotConfig,
+  makeChartBtnMenu
+};
+//# sourceMappingURL=geneORA-B5UK77KL.js.map

package/dist/geneVariant-7MGUAIZ6.js

@@ -0,0 +1,39 @@
+import {
+  SearchHandler,
+  addParentTerm,
+  getChildTerms
+} from "./chunk-OXJ2TWDO.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-V6DLLX4N.js";
+import "./chunk-7RN3L2BX.js";
+import "./chunk-A6TQGNDQ.js";
+import "./chunk-HYZG6OPC.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-5EF5U7MX.js";
+import "./chunk-2K5DSRBJ.js";
+import "./chunk-UCLS2SVB.js";
+import "./chunk-MVTCBVSX.js";
+import "./chunk-SEQLC4AD.js";
+import "./chunk-L4QG7XZE.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-KQMEJUWI.js";
+import "./chunk-UJU3Q7QJ.js";
+import "./chunk-WGL6FIUE.js";
+import "./chunk-6ITDJ5UR.js";
+import "./chunk-XYFDBYOY.js";
+import "./chunk-TV74I3Y5.js";
+import "./chunk-IH7ILDJS.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-TOU7EVFQ.js";
+import "./chunk-OAWQ6LOO.js";
+import "./chunk-SEEYV6P2.js";
+import "./chunk-NDWTN4U5.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-HFNDKYVF.js";
+export {
+  SearchHandler,
+  addParentTerm,
+  getChildTerms
+};
+//# sourceMappingURL=geneVariant-7MGUAIZ6.js.map

package/dist/geneVariant-FK3KZJ2K.js

@@ -0,0 +1,37 @@
+import {
+  getDtsFromGroups,
+  getHandler
+} from "./chunk-OXJ2TWDO.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-V6DLLX4N.js";
+import "./chunk-7RN3L2BX.js";
+import "./chunk-A6TQGNDQ.js";
+import "./chunk-HYZG6OPC.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-5EF5U7MX.js";
+import "./chunk-2K5DSRBJ.js";
+import "./chunk-UCLS2SVB.js";
+import "./chunk-MVTCBVSX.js";
+import "./chunk-SEQLC4AD.js";
+import "./chunk-L4QG7XZE.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-KQMEJUWI.js";
+import "./chunk-UJU3Q7QJ.js";
+import "./chunk-WGL6FIUE.js";
+import "./chunk-6ITDJ5UR.js";
+import "./chunk-XYFDBYOY.js";
+import "./chunk-TV74I3Y5.js";
+import "./chunk-IH7ILDJS.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-TOU7EVFQ.js";
+import "./chunk-OAWQ6LOO.js";
+import "./chunk-SEEYV6P2.js";
+import "./chunk-NDWTN4U5.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-HFNDKYVF.js";
+export {
+  getDtsFromGroups,
+  getHandler
+};
+//# sourceMappingURL=geneVariant-FK3KZJ2K.js.map

package/dist/geneVariant.integration.spec-C6TYWKIC.js

@@ -0,0 +1,196 @@
+import {
+  hg38
+} from "./chunk-7VB2BKXW.js";
+import {
+  sleep
+} from "./chunk-ZIBWLDQI.js";
+import {
+  require_tape
+} from "./chunk-QWOE5YTB.js";
+import {
+  SearchHandler,
+  vocabInit
+} from "./chunk-OXJ2TWDO.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-V6DLLX4N.js";
+import "./chunk-7RN3L2BX.js";
+import "./chunk-A6TQGNDQ.js";
+import "./chunk-HYZG6OPC.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-5EF5U7MX.js";
+import "./chunk-2K5DSRBJ.js";
+import "./chunk-UCLS2SVB.js";
+import "./chunk-MVTCBVSX.js";
+import "./chunk-SEQLC4AD.js";
+import "./chunk-L4QG7XZE.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-KQMEJUWI.js";
+import "./chunk-UJU3Q7QJ.js";
+import "./chunk-WGL6FIUE.js";
+import "./chunk-6ITDJ5UR.js";
+import "./chunk-XYFDBYOY.js";
+import "./chunk-TV74I3Y5.js";
+import "./chunk-IH7ILDJS.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-TOU7EVFQ.js";
+import "./chunk-OAWQ6LOO.js";
+import "./chunk-SEEYV6P2.js";
+import {
+  select_default
+} from "./chunk-NDWTN4U5.js";
+import "./chunk-OMR2DT66.js";
+import {
+  __toESM
+} from "./chunk-HFNDKYVF.js";
+
+// termdb/handlers/test/geneVariant.integration.spec.ts
+var import_tape = __toESM(require_tape(), 1);
+async function getVocabApi() {
+  const vocabApi2 = vocabInit({ state: { vocab: { genome: "hg38-test", dslabel: "TermdbTest" } } });
+  if (!vocabApi2) throw "vocabApi is missing";
+  await vocabApi2.getTermdbConfig();
+  return vocabApi2;
+}
+var vocabApi = await getVocabApi();
+var handler = new SearchHandler();
+function getHolder() {
+  const holder = select_default("body").append("div");
+  return holder;
+}
+async function initializeSearchHandler(opts) {
+  const callback = opts.callback || (() => {
+  });
+  await handler.init({
+    holder: opts.holder,
+    app: { vocabApi },
+    genomeObj: hg38,
+    callback
+  });
+}
+(0, import_tape.default)("\n", function(test) {
+  test.comment("-***- geneVariant search handler -***-");
+  test.end();
+});
+(0, import_tape.default)("Search handler layout", async (test) => {
+  const holder = getHolder();
+  await initializeSearchHandler({ holder });
+  const mutationTypeRadiosDiv = holder.select('[data-testid="sjpp-genevariant-mutationTypeRadios"]');
+  test.ok(
+    mutationTypeRadiosDiv.selectAll('input[type="radio"]').size() > 0,
+    "Mutation type radio buttons should be present"
+  );
+  const inputTypeRadiosDiv = holder.select('[data-testid="sjpp-genevariant-genesetTypeRadios"]');
+  test.equal(
+    inputTypeRadiosDiv.selectAll('input[type="radio"]').size(),
+    2,
+    "Input type radio buttons should be present"
+  );
+  const searchDiv = holder.select('[data-testid="sjpp-genevariant-geneSearchDiv"]');
+  test.equal(searchDiv.selectAll('input[type="search"]').size(), 1, "Gene search input should be present");
+  if (test["_ok"]) holder.remove();
+  test.end();
+});
+(0, import_tape.default)("Single gene input", async (test) => {
+  let tw;
+  const callback = (_tw) => {
+    tw = _tw;
+  };
+  const holder = getHolder();
+  await initializeSearchHandler({ holder, callback });
+  const geneSearchInput = holder.select('[data-testid="sjpp-genevariant-geneSearchDiv"]').select('input[type="search"]').node();
+  geneSearchInput.value = "TP53";
+  geneSearchInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter", code: "Enter", bubbles: true }));
+  await sleep(100);
+  test.equal(tw.term.type, "geneVariant", "term.type should be geneVariant");
+  test.equal(tw.q.type, "predefined-groupset", "q.type should be predefined-groupset");
+  test.equal(tw.q.predefined_groupset_idx, 0, "q.predefined_groupset_idx should be 0");
+  test.equal(tw.term.genes.length, 1, "term.genes[] should have length of 1");
+  test.deepEqual(
+    tw.term.genes[0],
+    { kind: "gene", id: "TP53", gene: "TP53", name: "TP53", type: "geneVariant" },
+    "term.genes[0] should have expected structure"
+  );
+  if (test["_ok"]) holder.remove();
+  test.end();
+});
+(0, import_tape.default)("Change mutation type", async (test) => {
+  let tw;
+  const callback = (_tw) => {
+    tw = _tw;
+  };
+  const holder = getHolder();
+  await initializeSearchHandler({ holder, callback });
+  const mutationTypeRadiosDiv = holder.select('[data-testid="sjpp-genevariant-mutationTypeRadios"]');
+  const mutationTypeRadios = mutationTypeRadiosDiv.selectAll('input[type="radio"]');
+  const thirdRadio = mutationTypeRadios.nodes()[2];
+  thirdRadio.click();
+  const inputTypeRadiosDiv = holder.select('[data-testid="sjpp-genevariant-genesetTypeRadios"]');
+  const geneSetDiv = inputTypeRadiosDiv.selectAll("div").filter((d) => d.value == "geneset");
+  test.equal(geneSetDiv.style("display"), "none", "Gene set option should be hidden for CNV");
+  const geneSearchInput = holder.select('[data-testid="sjpp-genevariant-geneSearchDiv"]').select('input[type="search"]').node();
+  geneSearchInput.value = "TP53";
+  geneSearchInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter", code: "Enter", bubbles: true }));
+  await sleep(100);
+  test.equal(tw.q.predefined_groupset_idx, 2, "q.predefined_groupset_idx should be 2 upon selecting third radio button");
+  if (test["_ok"]) holder.remove();
+  test.end();
+});
+(0, import_tape.default)("Gene set input", async (test) => {
+  let tw;
+  const callback = (_tw) => {
+    tw = _tw;
+  };
+  const holder = getHolder();
+  await initializeSearchHandler({ holder, callback });
+  const inputTypeRadiosDiv = holder.select('[data-testid="sjpp-genevariant-genesetTypeRadios"]');
+  const inputTypeRadios = inputTypeRadiosDiv.selectAll('input[type="radio"]');
+  const secondRadio = inputTypeRadios.nodes()[1];
+  secondRadio.click();
+  const geneSearchInput = holder.select('[data-testid="sjpp-genevariant-geneSearchDiv"]').select('input[type="search"]').node();
+  geneSearchInput.value = "TP53";
+  geneSearchInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter", code: "Enter", bubbles: true }));
+  await sleep(100);
+  geneSearchInput.value = "KRAS";
+  geneSearchInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter", code: "Enter", bubbles: true }));
+  const buttons = holder.select('[data-testid="sjpp-genevariant-geneSearchDiv"]').selectAll("button").nodes();
+  const submitButton = buttons.find((btn) => btn.textContent.trim() === "Submit");
+  await sleep(100);
+  submitButton.click();
+  await sleep(100);
+  test.equal(tw.term.genes.length, 2, "term.genes[] should have length of 2");
+  test.equal(tw.term.name, "TP53, KRAS", "term.name should concatenate gene names");
+  if (test["_ok"]) holder.remove();
+  test.end();
+});
+(0, import_tape.default)("Gene set input - custom name", async (test) => {
+  let tw;
+  const callback = (_tw) => {
+    tw = _tw;
+  };
+  const holder = getHolder();
+  await initializeSearchHandler({ holder, callback });
+  const inputTypeRadiosDiv = holder.select('[data-testid="sjpp-genevariant-genesetTypeRadios"]');
+  const inputTypeRadios = inputTypeRadiosDiv.selectAll('input[type="radio"]');
+  const secondRadio = inputTypeRadios.nodes()[1];
+  secondRadio.click();
+  const geneSearchInput = holder.select('[data-testid="sjpp-genevariant-geneSearchDiv"]').select('input[type="search"]').node();
+  geneSearchInput.value = "TP53";
+  geneSearchInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter", code: "Enter", bubbles: true }));
+  await sleep(100);
+  geneSearchInput.value = "KRAS";
+  geneSearchInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter", code: "Enter", bubbles: true }));
+  await sleep(100);
+  const nameInput = holder.select('[data-testid="sja_genesetinput_name"]').node();
+  nameInput.value = "Test gene set";
+  const buttons = holder.select('[data-testid="sjpp-genevariant-geneSearchDiv"]').selectAll("button").nodes();
+  const submitButton = buttons.find((btn) => btn.textContent.trim() === "Submit");
+  await sleep(100);
+  submitButton.click();
+  await sleep(100);
+  test.equal(tw.term.genes.length, 2, "term.genes[] should have length of 2");
+  test.equal(tw.term.name, "Test gene set", "term.name should be custom name");
+  if (test["_ok"]) holder.remove();
+  test.end();
+});
+//# sourceMappingURL=geneVariant.integration.spec-C6TYWKIC.js.map