@sjcrh/proteinpaint-client 2.208.0 → 2.210.0

package/dist/geneExpression.unit.spec-XVEJYMPX.js

@@ -0,0 +1,128 @@
+import {
+  SearchHandler
+} from "./chunk-R5PKBL7V.js";
+import {
+  require_tape
+} from "./chunk-PJYCTAMC.js";
+import "./chunk-55FABQU2.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-KV4W2ACA.js";
+import "./chunk-UXD6G6G4.js";
+import "./chunk-ELJX3QIQ.js";
+import "./chunk-3FEP6B5T.js";
+import "./chunk-EEB5VE2A.js";
+import "./chunk-6RRZRISL.js";
+import "./chunk-2KM4PRQM.js";
+import "./chunk-VA57CUC7.js";
+import "./chunk-BK6UDL7F.js";
+import "./chunk-KIAMLQ7S.js";
+import {
+  TermTypes
+} from "./chunk-SB36AUG7.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 {
+  __toESM
+} from "./chunk-HS5PO5ZQ.js";
+
+// termdb/handlers/test/geneExpression.unit.spec.ts
+var import_tape = __toESM(require_tape(), 1);
+(0, import_tape.default)("\n", function(test) {
+  test.comment("-***- termdb/handlers/geneExpression -***-");
+  test.end();
+});
+(0, import_tape.default)("selectGene() should throw when no gene is selected", async (test) => {
+  const handler = new SearchHandler();
+  handler.app = { vocabApi: { termdbConfig: { queries: { geneExpression: {} } } } };
+  handler.callback = () => {
+  };
+  try {
+    await handler.selectGene(void 0);
+    test.fail("Should throw when no gene is selected");
+  } catch (e) {
+    test.match(String(e), /No gene selected/, "Should throw expected message when gene is missing");
+  }
+  test.end();
+});
+(0, import_tape.default)("selectGene() should call callback with configured unit from termdbConfig", async (test) => {
+  const handler = new SearchHandler();
+  let selected;
+  handler.callback = (t) => {
+    selected = t;
+  };
+  handler.app = {
+    vocabApi: {
+      termdbConfig: {
+        queries: {
+          geneExpression: { unit: "log2 TPM" }
+        }
+      }
+    }
+  };
+  handler.sampleTypeSelect = [
+    { property: (key) => key == "checked" ? true : 1 },
+    { property: (key) => key == "checked" ? false : 2 }
+  ];
+  await handler.selectGene({ geneSymbol: "TP53" });
+  test.deepEqual(selected?.sampleTypes, [1], "Should pass selected sampleTypes as array");
+  test.equal(selected?.gene, "TP53", "Should pass selected gene");
+  test.equal(selected?.name, "TP53 log2 TPM", "Should include configured unit in name");
+  test.equal(selected?.type, TermTypes.GENE_EXPRESSION, "Should set type to geneExpression");
+  test.end();
+});
+(0, import_tape.default)("selectGene() should use default unit when not configured", async (test) => {
+  const handler = new SearchHandler();
+  let selected;
+  handler.callback = (t) => {
+    selected = t;
+  };
+  handler.app = {
+    vocabApi: {
+      termdbConfig: {
+        queries: {}
+      }
+    }
+  };
+  await handler.selectGene({ geneSymbol: "BRCA1" });
+  test.equal(selected?.sampleTypes, void 0, "Should include sampleTypes key with undefined value when not provided");
+  test.equal(selected?.gene, "BRCA1", "Should pass selected gene");
+  test.equal(selected?.name, "BRCA1 Gene Expression", "Should use default unit when config unit is not provided");
+  test.equal(selected?.type, TermTypes.GENE_EXPRESSION, "Should set type to geneExpression");
+  test.end();
+});
+(0, import_tape.default)("selectGene() should require at least one sample type when selector is rendered", async (test) => {
+  const handler = new SearchHandler();
+  let called = false;
+  let alertMsg = "";
+  const oldAlert = window.alert;
+  handler.callback = () => {
+    called = true;
+  };
+  handler.app = {
+    vocabApi: {
+      termdbConfig: {
+        queries: {}
+      }
+    }
+  };
+  handler.sampleTypeSelect = [{ property: (key) => key == "checked" ? false : 1 }];
+  window.alert = (msg) => {
+    alertMsg = msg;
+  };
+  await handler.selectGene({ geneSymbol: "BRCA1" });
+  window.alert = oldAlert;
+  test.equal(called, false, "Should not call callback when no sample type is selected");
+  test.equal(alertMsg, "Please select at least one sample type.", "Should notify user to select sample type");
+  test.end();
+});
+//# sourceMappingURL=geneExpression.unit.spec-XVEJYMPX.js.map

package/dist/geneExpression.unit.spec-XVEJYMPX.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../termdb/handlers/test/geneExpression.unit.spec.ts"],
+  "sourcesContent": ["import tape from 'tape'\nimport { SearchHandler } from '../geneExpression.ts'\nimport { TermTypes } from '#types'\n\n/**************\n test sections\n***************/\n\ntape('\\n', function (test) {\n\ttest.comment('-***- termdb/handlers/geneExpression -***-')\n\ttest.end()\n})\n\ntape('selectGene() should throw when no gene is selected', async test => {\n\tconst handler = new SearchHandler()\n\thandler.app = { vocabApi: { termdbConfig: { queries: { geneExpression: {} } } } } as any\n\thandler.callback = () => {}\n\n\ttry {\n\t\tawait handler.selectGene(undefined)\n\t\ttest.fail('Should throw when no gene is selected')\n\t} catch (e) {\n\t\ttest.match(String(e), /No gene selected/, 'Should throw expected message when gene is missing')\n\t}\n\n\ttest.end()\n})\n\ntape('selectGene() should call callback with configured unit from termdbConfig', async test => {\n\tconst handler = new SearchHandler()\n\tlet selected: any\n\n\thandler.callback = t => {\n\t\tselected = t\n\t}\n\thandler.app = {\n\t\tvocabApi: {\n\t\t\ttermdbConfig: {\n\t\t\t\tqueries: {\n\t\t\t\t\tgeneExpression: { unit: 'log2 TPM' }\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t} as any\n\n\thandler.sampleTypeSelect = [\n\t\t{ property: key => (key == 'checked' ? true : 1) },\n\t\t{ property: key => (key == 'checked' ? false : 2) }\n\t] as any\n\n\tawait handler.selectGene({ geneSymbol: 'TP53' })\n\ttest.deepEqual(selected?.sampleTypes, [1], 'Should pass selected sampleTypes as array')\n\ttest.equal(selected?.gene, 'TP53', 'Should pass selected gene')\n\ttest.equal(selected?.name, 'TP53 log2 TPM', 'Should include configured unit in name')\n\ttest.equal(selected?.type, TermTypes.GENE_EXPRESSION, 'Should set type to geneExpression')\n\n\ttest.end()\n})\n\ntape('selectGene() should use default unit when not configured', async test => {\n\tconst handler = new SearchHandler()\n\tlet selected: any\n\n\thandler.callback = t => {\n\t\tselected = t\n\t}\n\thandler.app = {\n\t\tvocabApi: {\n\t\t\ttermdbConfig: {\n\t\t\t\tqueries: {}\n\t\t\t}\n\t\t}\n\t} as any\n\n\tawait handler.selectGene({ geneSymbol: 'BRCA1' })\n\ttest.equal(selected?.sampleTypes, undefined, 'Should include sampleTypes key with undefined value when not provided')\n\ttest.equal(selected?.gene, 'BRCA1', 'Should pass selected gene')\n\ttest.equal(selected?.name, 'BRCA1 Gene Expression', 'Should use default unit when config unit is not provided')\n\ttest.equal(selected?.type, TermTypes.GENE_EXPRESSION, 'Should set type to geneExpression')\n\n\ttest.end()\n})\n\ntape('selectGene() should require at least one sample type when selector is rendered', async test => {\n\tconst handler = new SearchHandler()\n\tlet called = false\n\tlet alertMsg = ''\n\tconst oldAlert = window.alert\n\n\thandler.callback = () => {\n\t\tcalled = true\n\t}\n\thandler.app = {\n\t\tvocabApi: {\n\t\t\ttermdbConfig: {\n\t\t\t\tqueries: {}\n\t\t\t}\n\t\t}\n\t} as any\n\thandler.sampleTypeSelect = [{ property: key => (key == 'checked' ? false : 1) }] as any\n\n\twindow.alert = (msg: any) => {\n\t\talertMsg = msg\n\t}\n\tawait handler.selectGene({ geneSymbol: 'BRCA1' })\n\twindow.alert = oldAlert\n\n\ttest.equal(called, false, 'Should not call callback when no sample type is selected')\n\ttest.equal(alertMsg, 'Please select at least one sample type.', 'Should notify user to select sample type')\n\ttest.end()\n})\n"],
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+  "names": ["tape"]
+}

package/dist/geneORA-6UBS5GSC.js

@@ -0,0 +1,273 @@
+import {
+  controlsInit,
+  downloadTable,
+  newSandboxDiv,
+  renderTable,
+  table2col
+} from "./chunk-55FABQU2.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-KV4W2ACA.js";
+import "./chunk-UXD6G6G4.js";
+import {
+  Menu
+} from "./chunk-ELJX3QIQ.js";
+import "./chunk-3FEP6B5T.js";
+import "./chunk-EEB5VE2A.js";
+import "./chunk-6RRZRISL.js";
+import "./chunk-2KM4PRQM.js";
+import {
+  dofetch3
+} from "./chunk-VA57CUC7.js";
+import "./chunk-BK6UDL7F.js";
+import "./chunk-KIAMLQ7S.js";
+import "./chunk-SB36AUG7.js";
+import {
+  copyMerge,
+  getCompInit
+} from "./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 {
+  roundValueAuto
+} from "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import {
+  select_default
+} from "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-HS5PO5ZQ.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-6UBS5GSC.js.map