@sjcrh/proteinpaint-client 2.219.1 → 2.220.0

package/dist/geneExpression.unit.spec-YV45EZ5O.js

@@ -1,151 +0,0 @@
-import {
-  SearchHandler
-} from "./chunk-SLHXR4BZ.js";
-import {
-  require_tape
-} from "./chunk-PJYCTAMC.js";
-import "./chunk-BKW35Z4U.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-ETXOEP4N.js";
-import "./chunk-CNFTQSNE.js";
-import "./chunk-5NI77Z3O.js";
-import "./chunk-TVJOSRCH.js";
-import "./chunk-3CIL7KH7.js";
-import "./chunk-T4XPCSLP.js";
-import "./chunk-CJHNPYFQ.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-NR6WFCPF.js";
-import "./chunk-GN2A5NL5.js";
-import {
-  TermTypes
-} from "./chunk-ME3HB3V6.js";
-import "./chunk-HBNB5TRH.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-6XKAOSQE.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.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 label a selected sample-type subset", async (test) => {
-  const handler = new SearchHandler();
-  let selected;
-  handler.callback = (t) => {
-    selected = t;
-  };
-  handler.app = {
-    vocabApi: {
-      termdbConfig: {
-        queries: { geneExpression: { sampleTypes: [1, 2] } },
-        sampleTypes: {
-          1: { plural_name: "Primary tumors" },
-          2: { plural_name: "Relapses" }
-        }
-      }
-    }
-  };
-  handler.querySampleTypes = [1, 2];
-  handler.sampleTypeSelect = [
-    { property: (key) => key == "checked" ? false : 1 },
-    { property: (key) => key == "checked" ? true : 2 }
-  ];
-  await handler.selectGene({ geneSymbol: "TP53" });
-  test.equal(selected?.sampleTypeLabel, "Relapses", "Should label the selected sample-type subset");
-  test.equal(selected?.name, "TP53 Gene Expression", "Should preserve the gene expression term name");
-  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-YV45EZ5O.js.map

package/dist/geneORA-R74JPUTC.js

@@ -1,269 +0,0 @@
-import {
-  controlsInit,
-  downloadTable,
-  newSandboxDiv,
-  renderTable,
-  table2col
-} from "./chunk-BKW35Z4U.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-ETXOEP4N.js";
-import {
-  Menu
-} from "./chunk-CNFTQSNE.js";
-import "./chunk-5NI77Z3O.js";
-import "./chunk-TVJOSRCH.js";
-import "./chunk-3CIL7KH7.js";
-import "./chunk-T4XPCSLP.js";
-import {
-  dofetch3
-} from "./chunk-CJHNPYFQ.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-NR6WFCPF.js";
-import "./chunk-GN2A5NL5.js";
-import "./chunk-ME3HB3V6.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-HBNB5TRH.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-6XKAOSQE.js";
-import {
-  roundValueAuto
-} from "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import {
-  select_default
-} from "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.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-R74JPUTC.js.map