@sjcrh/proteinpaint-client 2.196.0 → 2.197.0

package/dist/chunk-JFRSVFWO.js

@@ -1,736 +0,0 @@
-import {
-  VolcanoModel
-} from "./chunk-6MQWYMPB.js";
-import {
-  PlotBase,
-  axisstyle,
-  controlsInit,
-  getCombinedTermFilter,
-  getDefaultVolcanoSettings,
-  renderTable,
-  sayerror,
-  table2col
-} from "./chunk-WY2PGUVX.js";
-import {
-  Menu
-} from "./chunk-HYOEWQ5P.js";
-import {
-  dofetch3
-} from "./chunk-LYVLF6HO.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-M3J4MINX.js";
-import {
-  PROTEOME_DAP,
-  SINGLECELL_CELLTYPE
-} from "./chunk-NNFAUP2I.js";
-import {
-  axisBottom,
-  axisLeft
-} from "./chunk-LOZEKOES.js";
-import {
-  linear
-} from "./chunk-SOTB4FRE.js";
-import {
-  roundValueAuto
-} from "./chunk-TLT4YIG3.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 {
-        if (config.termType === PROTEOME_DAP) {
-          await this.app.save({
-            type: "plot_edit",
-            id: this.id,
-            config: {
-              gsea_params: {
-                dapParams: config.proteomeDetails,
-                genome: this.app.vocabApi.opts.state.vocab.genome,
-                dslabel: this.app.vocabApi.vocab.dslabel
-              }
-            }
-          });
-        } else if (config.termType === SINGLECELL_CELLTYPE) {
-          const body = {
-            genome: this.app.vocabApi.vocab.genome,
-            dslabel: this.app.vocabApi.vocab.dslabel,
-            sample: config.sample,
-            termId: config.termId,
-            categoryName: config.categoryName
-          };
-          const response = await dofetch3("termdb/singlecellDEgenes", { body, signal: this.api?.getAbortSignal() });
-          if (response.error) throw response.error;
-          if (!Array.isArray(response.data) || response.data.length === 0) throw "No DE genes returned for this cluster";
-          const genes = [];
-          const fold_change = [];
-          for (const g of response.data) {
-            genes.push(g.gene_name);
-            fold_change.push(g.fold_change);
-          }
-          await this.app.save({
-            type: "plot_edit",
-            id: this.id,
-            config: {
-              gsea_params: {
-                genes,
-                fold_change,
-                genes_length: genes.length,
-                genome: this.app.vocabApi.opts.state.vocab.genome
-              }
-            }
-          });
-        } else {
-          const volcanoSettings = config.settings?.volcano || getDefaultVolcanoSettings({}, { termType: "geneExpression" });
-          const model = new VolcanoModel(this, 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 if (p.dapParams) {
-      body.dapParams = p.dapParams;
-      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 Object.assign(new Error(output.error), { code: output.code });
-    }
-  } catch (e) {
-    self.dom.holder.selectAll("*").remove();
-    const msg = String(e?.message || e);
-    if (e?.code === "CACHE_BUSY") {
-      if (window.confirm(msg)) render_gsea(self);
-      return;
-    }
-    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;
-  }
-  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 || self.config.gsea_params.dapParams)) {
-          const fetchBody = {
-            genome: self.config.gsea_params.genome,
-            dslabel: self.config.gsea_params.dslabel,
-            fetchDE: true,
-            geneSetGroup: "-",
-            filter_non_coding_genes: false,
-            method: "cerno"
-          };
-          if (self.config.gsea_params.cacheId) {
-            fetchBody.cacheId = self.config.gsea_params.cacheId;
-            fetchBody.daRequest = self.config.gsea_params.daRequest;
-          } else if (self.config.gsea_params.dapParams) {
-            fetchBody.dapParams = self.config.gsea_params.dapParams;
-          }
-          const deResp = await dofetch3("genesetEnrichment", {
-            body: fetchBody
-          });
-          if (deResp.error) throw Object.assign(new Error(deResp.error), { code: deResp.code });
-          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);
-      if (e?.code === "CACHE_BUSY") {
-        if (window.confirm(msg)) render_gsea(self);
-        return;
-      }
-      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-JFRSVFWO.js.map