@sjcrh/proteinpaint-client 2.184.0 → 2.185.0

package/dist/chunk-XVDWYTJ6.js

@@ -0,0 +1,676 @@
+import {
+  VolcanoModel
+} from "./chunk-3B7EWIVB.js";
+import {
+  PlotBase,
+  axisstyle,
+  controlsInit,
+  getCombinedTermFilter,
+  getDefaultVolcanoSettings,
+  renderTable,
+  sayerror,
+  table2col
+} from "./chunk-YWUVCXFS.js";
+import {
+  Menu
+} from "./chunk-HYOEWQ5P.js";
+import {
+  dofetch3
+} from "./chunk-6ZCHECOT.js";
+import {
+  copyMerge,
+  getCompInit
+} from "./chunk-MVTCBVSX.js";
+import {
+  roundValueAuto
+} from "./chunk-L4QG7XZE.js";
+import {
+  axisBottom,
+  axisLeft
+} from "./chunk-LOZEKOES.js";
+import {
+  linear
+} from "./chunk-OAWQ6LOO.js";
+
+// plots/gsea.js
+var tip = new Menu();
+var gsea = class _gsea extends PlotBase {
+  static type = "gsea";
+  constructor(opts) {
+    super(opts);
+    this.type = _gsea.type;
+    this.opts = opts;
+    this.components = {
+      controls: {}
+    };
+    const controlsDiv = typeof opts.controls == "object" ? opts.controls : opts.holder.append("div").style("display", "inline-block");
+    const main = opts.holder.append("div").style("display", "inline-block");
+    const actionsDiv = main.append("div").attr("data-testid", "sjpp-gsea-actions").style("margin", "10px").style("text-align", "left");
+    const loadingDiv = main.append("div").attr("data-testid", "sjpp-gsea-loading").style("text-align", "center").style("display", "none").style("margin", "10px").style("text-align", "left").text("Loading...");
+    const holder = main.append("div").style("margin-left", "50px").style("display", "inline-block").attr("data-testid", "sjpp-gsea-holder");
+    const detailsDiv = main.append("div").attr("data-testid", "sjpp-gsea-details").style("display", "inline-block").style("vertical-align", "top").style("margin-top", "50px");
+    const tableDiv = main.append("div").style("margin", "10px").attr("data-testid", "sjpp-gsea-results-table");
+    this.dom = {
+      holder,
+      header: opts.header,
+      actionsDiv,
+      loadingDiv,
+      controlsDiv,
+      detailsDiv,
+      tableDiv
+    };
+  }
+  async setControls() {
+    this.dom.controlsDiv.selectAll("*").remove();
+    const inputs = [
+      {
+        label: "Minimum Gene Set Size Filter Cutoff",
+        type: "number",
+        chartType: "gsea",
+        settingsKey: "min_gene_set_size_cutoff",
+        title: "Minimum Gene set size cutoff. Helps in filtering out small gene sets",
+        min: 0
+      },
+      {
+        label: "Maximum Gene Set Size Filter Cutoff",
+        type: "number",
+        chartType: "gsea",
+        settingsKey: "max_gene_set_size_cutoff",
+        title: "Maximum Gene set size cutoff. Helps in filtering out large gene sets",
+        max: 25e3
+      },
+      {
+        label: "Filter Non-coding Genes",
+        type: "checkbox",
+        chartType: "gsea",
+        settingsKey: "filter_non_coding_genes",
+        title: "Filter non-coding genes",
+        boxLabel: ""
+      },
+      {
+        label: "FDR or Top Gene Sets",
+        type: "radio",
+        chartType: "gsea",
+        settingsKey: "fdr_or_top",
+        title: "Toggle between FDR cutoff and top gene sets in ascending order of FDR",
+        options: [
+          { label: "FDR", value: "fdr" },
+          { label: "Top Gene Sets", value: "top" }
+        ]
+      }
+    ];
+    if (JSON.parse(sessionStorage.getItem("optionalFeatures")).gsea_test) {
+      inputs.push({
+        label: "GSEA method",
+        type: "radio",
+        chartType: "gsea",
+        settingsKey: "gsea_method",
+        title: "Toggle between blitzgsea and CERNO method",
+        options: [
+          { label: "blitzgsea", value: "blitzgsea" },
+          { label: "CERNO", value: "cerno" }
+        ]
+      });
+    }
+    if (this.settings.gsea_method == "blitzgsea") {
+      inputs.push({
+        label: "Number of Permutations",
+        type: "number",
+        chartType: "gsea",
+        settingsKey: "num_permutations",
+        title: "Number of permutations to be used for GSEA. Higher number increases accuracy but also compute time.",
+        min: 0,
+        max: 4e4
+        // Setting it to pretty lenient limit for testing
+      });
+    }
+    if (this.settings.fdr_or_top == "fdr") {
+      inputs.push({
+        label: "FDR Filter Cutoff (Linear Scale)",
+        type: "number",
+        chartType: "gsea",
+        settingsKey: "fdr_cutoff",
+        title: "P-value significance",
+        min: 0,
+        max: 1
+      });
+    } else if (this.settings.fdr_or_top == "top") {
+      inputs.push({
+        label: "Number of top Gene Sets by FDR",
+        type: "number",
+        chartType: "gsea",
+        settingsKey: "top_genesets",
+        title: "Number of top gene sets to be displayed in ascending order of FDR",
+        min: 0,
+        max: 5e3
+      });
+    } else {
+      throw "unknown FDR/top option";
+    }
+    this.components.controls = await controlsInit({
+      app: this.app,
+      id: this.id,
+      holder: this.dom.controlsDiv,
+      inputs
+    });
+    this.components.controls.on("downloadClick.gsea", () => {
+      if (!this.imageUrl) return alert("No image to download");
+      const dataUrl = this.imageUrl;
+      const downloadImgName = `${this.state.config.gsea_params.geneset_name || ""}_GSEA_IMG`;
+      const a = document.createElement("a");
+      document.body.appendChild(a);
+      a.addEventListener(
+        "click",
+        () => {
+          a.download = downloadImgName + ".png";
+          a.href = dataUrl;
+          document.body.removeChild(a);
+        },
+        false
+      );
+      a.click();
+    });
+  }
+  getState(appState) {
+    const config = appState.plots.find((p) => p.id === this.id);
+    if (!config) throw `No plot with id='${this.id}' found`;
+    const parentConfig = appState.plots.find((p) => p.id === this.parentId);
+    const termfilter = getCombinedTermFilter(appState, config.filter || parentConfig?.filter);
+    return {
+      config,
+      termfilter
+    };
+  }
+  /** This allows the gsea to run independently. If the DE data
+   * was already requested (e.g. in the DA from the volcano plot),
+   * the cached response returns rather than running the DE
+   * route again.
+   *
+   * Also allows loading the gsea from a mass session file without
+   * error. */
+  async init(appState) {
+    const config = appState.plots.find((p) => p.id === this.id);
+    if (!config.gsea_params) {
+      try {
+        const volcanoSettings = config.settings?.volcano || getDefaultVolcanoSettings({}, { termType: "geneExpression" });
+        const model = new VolcanoModel(this.app, config.termType);
+        const response = await model.getData(config, volcanoSettings);
+        if (!response?.data?.cacheId || response.error) {
+          throw response.error || "No DE cacheId returned from volcano model";
+        }
+        await this.app.save({
+          type: "plot_edit",
+          id: this.id,
+          config: {
+            gsea_params: {
+              cacheId: response.data.cacheId,
+              // Snapshot of the DE request so the server can regenerate
+              // the cache if this GSEA request lands on a peer node or
+              // arrives after the cache TTL has expired.
+              daRequest: response.daRequest,
+              genes_length: response.data.totalRows,
+              genome: this.app.vocabApi.opts.state.vocab.genome,
+              // Sending dslabel at the top level makes the global
+              // auth middleware populate clientAuthResult on this
+              // request the same way it did for the volcano
+              // request, so the server can re-apply the same
+              // auth-filter injection to daRequest before hashing.
+              dslabel: this.app.vocabApi.vocab.dslabel
+            }
+          }
+        });
+      } catch (e) {
+        if (e instanceof Error) console.error(e.message || e);
+        else if (e.stack) console.log(e.stack);
+        throw e;
+      }
+    }
+  }
+  reactsTo(action) {
+    if (action.type.startsWith("plot_")) {
+      return (action.id === this.id || action.id == this.parentId) && (!action.config?.childType || action.config?.childType == this.type);
+    }
+  }
+  async main() {
+    const config = this.app.getState().plots.find((p) => p.id === this.id);
+    this.config = structuredClone(config);
+    if (this.config.chartType != this.type && this.config.childType != this.type) return;
+    this.settings = this.config.settings.gsea;
+    this.imageUrl = null;
+    await this.setControls();
+    if (this.dom.header) {
+      const geneCount = this.config.gsea_params.genes_length ?? this.config.gsea_params.genes?.length ?? 0;
+      this.dom.header.html(
+        geneCount + ' genes <span style="font-size:.8em;opacity:.7">GENE SET ENRICHMENT ANALYSIS</span>'
+      );
+    }
+    render_gsea(this);
+  }
+};
+async function renderPathwayDropdown(self) {
+  const settings = structuredClone(self.settings);
+  const pathwayOpts = structuredClone(self.app.opts.genome.termdbs.msigdb.analysisGenesetGroups);
+  if (JSON.parse(sessionStorage.getItem("optionalFeatures")).gsea_test && self.settings.gsea_method == "blitzgsea") {
+    pathwayOpts.push(
+      { label: "REACTOME (blitzgsea)", value: "REACTOME--blitzgsea" },
+      { label: "KEGG (blitzgsea)", value: "KEGG--blitzgsea" },
+      { label: "WikiPathways (blitzgsea)", value: "WikiPathways--blitzgsea" }
+    );
+  }
+  if (settings.pathway) {
+    pathwayOpts.shift();
+    pathwayOpts.find((opt) => opt.value == settings.pathway).selected = true;
+  }
+  self.dom.actionsDiv.append("span").attr("data-testid", "sjpp-gsea-pathway").style("margin-right", "10px").text("Select a gene set group:");
+  const dropdown = self.dom.actionsDiv.append("select").on("change", (event) => {
+    if (!settings.pathway) {
+      const placeholder = dropdown.select('option[value="-"]');
+      placeholder.remove();
+      pathwayOpts.shift();
+    }
+    const idx = event.target.selectedIndex;
+    settings.pathway = pathwayOpts[idx].value;
+    self.app.dispatch({
+      type: "plot_edit",
+      id: self.id,
+      config: {
+        //Need to clear the gsea_params completely
+        gsea_params: {
+          geneset_name: null,
+          pathway: pathwayOpts[idx].value
+        },
+        highlightGenes: [],
+        settings: {
+          gsea: settings
+        }
+      }
+    });
+  });
+  for (const opt of pathwayOpts) {
+    dropdown.append("option").text(opt.label).attr("value", opt.value).attr("selected", opt.selected ? true : null);
+  }
+}
+async function render_gsea(self) {
+  self.dom.actionsDiv.selectAll("*").remove();
+  renderPathwayDropdown(self);
+  if (self.settings.pathway == "-" || self.settings.pathway == void 0) return;
+  self.dom.detailsDiv.selectAll("*").remove();
+  self.dom.holder.selectAll("*").remove();
+  self.dom.tableDiv.selectAll("*").remove();
+  self.config.gsea_params.geneSetGroup = self.settings.pathway;
+  self.config.gsea_params.filter_non_coding_genes = self.settings.filter_non_coding_genes;
+  self.config.gsea_params.num_permutations = self.settings.num_permutations;
+  let output;
+  try {
+    const p = self.config.gsea_params;
+    const body = {
+      genome: p.genome,
+      geneSetGroup: self.settings.pathway,
+      filter_non_coding_genes: self.settings.filter_non_coding_genes,
+      method: self.settings.gsea_method
+    };
+    if (p.cacheId) {
+      body.cacheId = p.cacheId;
+      if (p.daRequest) body.daRequest = p.daRequest;
+      if (p.dslabel) body.dslabel = p.dslabel;
+    } else {
+      body.genes = p.genes;
+      body.fold_change = p.fold_change;
+    }
+    if (self.settings.gsea_method == "blitzgsea") {
+      body.num_permutations = self.settings.num_permutations;
+    }
+    output = await rungsea(body, self.dom);
+    if (output.error) {
+      throw output.error;
+    }
+  } catch (e) {
+    alert("Error: " + e);
+    return;
+  }
+  if (self.config.gsea_params.geneset_name != null) {
+    try {
+      if (self.settings.gsea_method == "blitzgsea") {
+        self.config.gsea_params.method = self.settings.gsea_method;
+        const image = await rungsea(self.config.gsea_params, self.dom);
+        if (image.error) throw image.error;
+        self.imageUrl = URL.createObjectURL(image);
+        const png_width = 600;
+        const png_height = 400;
+        self.dom.holder.append("img").attr("width", png_width).attr("height", png_height).attr("src", self.imageUrl);
+      } else if (self.settings.gsea_method == "cerno") {
+        if (!self.rankedDE && self.config.gsea_params.cacheId) {
+          const deResp = await dofetch3("genesetEnrichment", {
+            body: {
+              genome: self.config.gsea_params.genome,
+              cacheId: self.config.gsea_params.cacheId,
+              // Also send daRequest so the server can recompute
+              // the cache on miss (same farm-safety reason as
+              // the primary enrichment call).
+              daRequest: self.config.gsea_params.daRequest,
+              // Top-level dslabel so the auth middleware populates
+              // clientAuthResult for the server's auth-filter
+              // adjustment of daRequest.
+              dslabel: self.config.gsea_params.dslabel,
+              fetchDE: true,
+              geneSetGroup: "-",
+              filter_non_coding_genes: false,
+              method: "cerno"
+            }
+          });
+          if (deResp.error) throw deResp.error;
+          self.rankedDE = deResp.data;
+        }
+        render_cerno_plot(self, output);
+      } else {
+        throw "Unknown method:" + self.settings.gsea_method;
+      }
+    } catch (e) {
+      self.dom.holder.selectAll("*").remove();
+      const msg = String(e?.message || e);
+      const userMsg = /daCacheMissing|ENOENT|no such file/i.test(msg) ? "The differential-analysis cache for this GSEA is no longer available. Reopen the volcano plot to regenerate it." : msg;
+      sayerror(self.dom.holder, userMsg);
+      return;
+    }
+  }
+  const table_stats = table2col({ holder: self.dom.detailsDiv.attr("data-testid", "sjpp-gsea-stats") });
+  const [t1, t2] = table_stats.addRow();
+  t2.style("text-align", "center").style("font-size", "0.8em").style("opacity", "0.8").text("COUNT");
+  let addStats;
+  if (self.settings.gsea_method == "blitzgsea") {
+    addStats = [
+      {
+        label: "Gene sets analyzed",
+        values: Object.keys(output.data).length
+      }
+    ];
+  } else if (self.settings.gsea_method == "cerno") {
+    addStats = [
+      {
+        label: "Gene sets analyzed",
+        values: Object.keys(output).length
+      }
+    ];
+  } else {
+    throw "Unknown method:" + self.settings.gsea_method;
+  }
+  for (const dataRow of addStats) {
+    const [td1, td2] = table_stats.addRow();
+    td1.text(dataRow.label);
+    td2.style("text-align", "end").text(dataRow.values);
+  }
+  self.gsea_table_rows = [];
+  let output_keys;
+  if (self.settings.gsea_method == "blitzgsea") {
+    output_keys = Object.entries(output.data).map(([key, value]) => {
+      return { key, value };
+    });
+  } else if (self.settings.gsea_method == "cerno") {
+    output_keys = Object.entries(output).map(([key, value]) => {
+      return { key, value };
+    });
+  } else {
+    throw "Unknown method:" + self.settings.gsea_method;
+  }
+  if (self.settings.fdr_or_top == "top") {
+    output_keys.sort((i, j) => Number(i.value.fdr) - Number(j.value.fdr));
+    const top_genesets = Math.min(self.settings.top_genesets, output_keys.length);
+    for (let iter = 0; iter < top_genesets; iter++) {
+      if (self.settings.max_gene_set_size_cutoff >= output_keys[iter].value.geneset_size && self.settings.min_gene_set_size_cutoff <= output_keys[iter].value.geneset_size) {
+        setResultsRows(output_keys, iter, self);
+      }
+    }
+  } else if (self.settings.fdr_or_top == "fdr") {
+    for (let iter = 0; iter < output_keys.length; iter++) {
+      if (self.settings.fdr_cutoff >= output_keys[iter].value.fdr && self.settings.max_gene_set_size_cutoff >= output_keys[iter].value.geneset_size && self.settings.min_gene_set_size_cutoff <= output_keys[iter].value.geneset_size) {
+        setResultsRows(output_keys, iter, self);
+      }
+    }
+  }
+  self.dom.tableDiv.selectAll("*").remove();
+  const d_gsea = self.dom.tableDiv.append("div");
+  self.gsea_table_cols = [];
+  if (self.settings.gsea_method == "blitzgsea") {
+    self.gsea_table_cols = [
+      { label: "Gene Set", sortable: true },
+      //{ label: 'Enrichment Score' },
+      { label: "Normalized Enrichment Score", barplot: { axisWidth: 200 }, sortable: true },
+      { label: "Gene Set Size", sortable: true },
+      { label: "P value", sortable: true },
+      //{ label: 'Sidak' },
+      { label: "FDR", sortable: true },
+      { label: "Leading Edge" }
+    ];
+  } else if (self.settings.gsea_method == "cerno") {
+    self.gsea_table_cols = [
+      { label: "Gene Set", sortable: true },
+      { label: "Area Under Curve", barplot: { axisWidth: 200 }, sortable: true },
+      { label: "Enrichment Score", barplot: { axisWidth: 200 }, sortable: true },
+      { label: "Total Gene Set Size", sortable: true },
+      { label: "P value", sortable: true },
+      { label: "FDR", sortable: true },
+      { label: "Gene Set Hits" }
+    ];
+  } else {
+    throw "Unknown method:" + self.settings.gsea_method;
+  }
+  let download = {};
+  if (self.config.chartType == "differentialAnalysis") {
+    self.dom.detailsDiv.append("button").style("margin-left", "10px").style(
+      "display",
+      self.config.chartType == "differentialAnalysis" && self.config.gsea_params.geneset_name == null ? "none" : "block"
+    ).attr("aria-label", "Highlight genes in the volcano plot").text("Highlight genes").on("click", () => {
+      self.app.dispatch({
+        type: "plot_edit",
+        id: self.id,
+        config: {
+          childType: "volcano",
+          highlightedData: self.config.highlightGenes
+        }
+      });
+    });
+  }
+  if (self.state.config.downloadFilename) download.fileName = self.state.config.downloadFilename;
+  const geneSetIdx = self.gsea_table_rows.findIndex((row) => row[0].value == self.config.gsea_params.geneset_name);
+  const selectedRows = geneSetIdx > -1 ? [geneSetIdx] : [];
+  renderTable({
+    download,
+    columns: self.gsea_table_cols,
+    rows: self.gsea_table_rows,
+    div: d_gsea,
+    showLines: true,
+    maxHeight: "30vh",
+    singleMode: true,
+    resize: true,
+    header: { allowSort: true },
+    selectedRows,
+    noButtonCallback: async (index) => {
+      const config = {
+        gsea_params: {
+          geneset_name: self.gsea_table_rows[index][0].value
+        }
+      };
+      if (self.config.chartType == "differentialAnalysis") {
+        let genes;
+        if (self.settings.gsea_method == "blitzgsea") {
+          genes = [...self.gsea_table_rows[index][5].value.split(",")];
+        } else if (self.settings.gsea_method == "cerno") {
+          genes = [...self.gsea_table_rows[index][6].value.split(",")];
+        } else {
+          throw "Unknown method:" + self.settings.gsea_method;
+        }
+        if (genes) config.highlightGenes = genes;
+      }
+      await self.app.dispatch({
+        type: "plot_edit",
+        id: self.id,
+        config
+      });
+    }
+  });
+}
+function setResultsRows(output_keys, iter, self) {
+  const pathway_name = output_keys[iter].key;
+  const pval = output_keys[iter].value.pval ? roundValueAuto(output_keys[iter].value.pval) : output_keys[iter].value.pval;
+  const fdr = output_keys[iter].value.fdr ? roundValueAuto(output_keys[iter].value.fdr) : output_keys[iter].value.fdr;
+  if (self.settings.gsea_method == "blitzgsea") {
+    const nes = output_keys[iter].value.nes ? roundValueAuto(output_keys[iter].value.nes) : output_keys[iter].value.nes;
+    self.gsea_table_rows.push([
+      { value: pathway_name },
+      { value: nes },
+      { value: output_keys[iter].value.geneset_size },
+      { value: pval },
+      //{ value: sidak },
+      { value: fdr },
+      { value: output_keys[iter].value.leading_edge }
+    ]);
+  } else if (self.settings.gsea_method == "cerno") {
+    const auc = output_keys[iter].value.auc ? roundValueAuto(output_keys[iter].value.auc) : output_keys[iter].value.auc;
+    const es = output_keys[iter].value.es ? roundValueAuto(output_keys[iter].value.es) : output_keys[iter].value.es;
+    self.gsea_table_rows.push([
+      { value: pathway_name },
+      { value: auc },
+      { value: es },
+      { value: output_keys[iter].value.geneset_size },
+      { value: pval },
+      { value: fdr },
+      { value: output_keys[iter].value.leading_edge }
+    ]);
+  } else {
+    throw "Unknown method:" + self.settings.gsea_method;
+  }
+}
+function render_cerno_plot(self, cerno_output) {
+  const holder = self.dom.holder;
+  holder.selectAll("*").remove();
+  const svg_width = 400;
+  const svg_height = 400;
+  const svg = holder.append("svg").attr("width", svg_width).attr("height", svg_height);
+  const toppad = 20;
+  const rightpad = 5;
+  const yaxisw = 50;
+  const xaxish = 50;
+  const yaxisg = svg.append("g");
+  const xaxisg = svg.append("g");
+  const xpad = 50;
+  const ypad = 100;
+  const rankedDE = self.rankedDE || self.config.gsea_params;
+  const DE_output = [];
+  for (let i = 0; i < rankedDE.genes.length; i++) {
+    const item = { gene: rankedDE.genes[i], fold_change: rankedDE.fold_change[i] };
+    DE_output.push(item);
+  }
+  DE_output.sort((i, j) => j.fold_change - i.fold_change);
+  const xscale = linear().domain([0, DE_output.length]).range([xpad, svg_width - rightpad]);
+  const yscale = linear().domain([100, 0]).range([toppad, svg_height - ypad]);
+  yaxisg.attr("transform", "translate(" + xpad + ",0)");
+  xaxisg.attr("transform", "translate(0," + (svg_height - ypad) + ")");
+  const xlab = svg.append("text").text("Gene list").attr("fill", "black").attr("text-anchor", "start").attr("transform", "translate(" + xscale(DE_output.length / 3) + "," + (svg_height - ypad + 2 * toppad) + ")");
+  const ylab = svg.append("text").text("Percentage of gene set").attr("fill", "black").attr("text-anchor", "middle").attr("y", xpad / 2).attr("x", -svg_width / 2.5).attr("transform", "rotate(-90)");
+  let fontSize = 30;
+  const title = svg.append("text").text(self.config.gsea_params.geneset_name).attr("fill", "black").attr("text-anchor", "start").attr("font-size", fontSize + "px").attr("transform", "translate(" + xpad + "," + toppad / 2 + ")");
+  let title_bbox = title.node().getBBox();
+  while (title_bbox.width > svg_width - xpad || title_bbox.height > toppad * 3.5 / 5) {
+    fontSize -= 1;
+    title.node().setAttribute("font-size", fontSize + "px");
+    title_bbox = title.node().getBBox();
+  }
+  const auc = cerno_output[self.config.gsea_params.geneset_name].auc;
+  if (typeof auc === "number") {
+    let auc_pos;
+    if (auc >= 0.5) {
+      auc_pos = xscale(DE_output.length * 3 / 3.5) + "," + (svg_height - ypad * 1.5);
+    } else {
+      auc_pos = xscale(DE_output.length * 0.8 / 4.5) + "," + (svg_height - ypad * 3);
+    }
+    const auc_text = svg.append("text").text("AUC=" + roundValueAuto(auc)).attr("fill", "black").attr("text-anchor", "middle").attr("transform", "translate(" + auc_pos + ")");
+  } else {
+    throw "AUC not a number:" + auc;
+  }
+  axisstyle({
+    axis: yaxisg.call(axisLeft().scale(yscale)),
+    color: "black",
+    showline: true,
+    fontsize: "10"
+  });
+  axisstyle({
+    axis: xaxisg.call(axisBottom().scale(xscale)),
+    color: "black",
+    showline: true,
+    fontsize: "10"
+  });
+  if (Object.keys(cerno_output).includes(self.config.gsea_params.geneset_name)) {
+    const hit_genes = cerno_output[self.config.gsea_params.geneset_name].leading_edge.split(",");
+    const y_increment = 100 / hit_genes.length;
+    const lines = svg.append("g");
+    let y_iter = 100;
+    for (let i = 0; i < DE_output.length; i++) {
+      const y_old = y_iter;
+      if (hit_genes.includes(DE_output[i].gene)) {
+        y_iter = y_iter - y_increment;
+        lines.append("line").style("stroke", "red").attr("x1", xscale(i)).attr("y1", svg_height).attr("x2", xscale(i)).attr("y2", svg_height - ypad + 2.5 * toppad);
+      }
+      lines.append("line").style("stroke", "red").attr("x1", xscale(i)).attr("y1", yscale(100 - y_old)).attr("x2", xscale(i + 1)).attr("y2", yscale(100 - y_iter));
+    }
+  } else {
+    throw "${self.config.gsea_params.geneset_name} not found";
+  }
+}
+function getDefaultGseaSettings(overrides = {}) {
+  const defaults = {
+    fdr_cutoff: 0.05,
+    num_permutations: 1e3,
+    top_genesets: 40,
+    pathway: void 0,
+    geneset_name: null,
+    min_gene_set_size_cutoff: 0,
+    max_gene_set_size_cutoff: 2e4,
+    filter_non_coding_genes: true,
+    fdr_or_top: "top",
+    gsea_method: "blitzgsea"
+  };
+  if (JSON.parse(sessionStorage.getItem("optionalFeatures")).gsea_test) {
+    defaults.gsea_method = "cerno";
+  }
+  return Object.assign(defaults, overrides);
+}
+async function getPlotConfig(opts, app) {
+  try {
+    const config = {
+      //idea for fixing nav button
+      //samplelst: { groups: app.opts.state.groups}
+      settings: {
+        gsea: getDefaultGseaSettings(opts.overrides)
+      }
+    };
+    return copyMerge(config, opts);
+  } catch (e) {
+    throw `${e} [gsea getPlotConfig()]`;
+  }
+}
+var gseaInit = getCompInit(gsea);
+var componentInit = gseaInit;
+function makeChartBtnMenu(holder, chartsInstance) {
+  chartsInstance.prepPlot({
+    config: {
+      chartType: "gsea"
+    }
+  });
+}
+async function rungsea(body, dom) {
+  dom.actionsDiv.style("display", "none");
+  dom.loadingDiv.style("display", "block");
+  const data = await dofetch3("genesetEnrichment", { body });
+  dom.loadingDiv.style("display", "none");
+  dom.actionsDiv.style("display", "block");
+  return data;
+}
+
+export {
+  getDefaultGseaSettings,
+  getPlotConfig,
+  gseaInit,
+  componentInit,
+  makeChartBtnMenu
+};
+//# sourceMappingURL=chunk-XVDWYTJ6.js.map