@sjcrh/proteinpaint-client 2.221.0 → 2.223.0

package/dist/GSEA-ZEJB3QZQ.js

@@ -1,870 +0,0 @@
-import {
-  VolcanoModel
-} from "./chunk-RV335DF2.js";
-import {
-  getDefaultGseaSettings
-} from "./chunk-NX5IB4IY.js";
-import {
-  PlotBase,
-  axisstyle,
-  controlsInit,
-  getCombinedTermFilter,
-  getDefaultVolcanoSettings,
-  renderTable,
-  sayerror,
-  table2col
-} from "./chunk-WD7FZ5EE.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-WXSMUSU7.js";
-import "./chunk-CNFTQSNE.js";
-import "./chunk-RIHO7ZD5.js";
-import "./chunk-TVJOSRCH.js";
-import "./chunk-3CIL7KH7.js";
-import "./chunk-T4XPCSLP.js";
-import {
-  dofetch3
-} from "./chunk-4TJO2DGU.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-MHWYRNGA.js";
-import "./chunk-JHLF2ZC2.js";
-import {
-  DMR_SCAN_ELEMENT_TYPE,
-  PROTEOME_DAP,
-  SINGLECELL_CELLTYPE,
-  axisBottom,
-  axisLeft
-} from "./chunk-WJLRU5OF.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-HBNB5TRH.js";
-import "./chunk-PF4DSFDR.js";
-import {
-  linear
-} from "./chunk-4OLM3KSB.js";
-import "./chunk-PWYMHUXY.js";
-import {
-  roundValueAuto
-} from "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-HS5PO5ZQ.js";
-
-// plots/gsea/model/GseaParams.ts
-function isValidGseaParams(value) {
-  return isProteomeDAPGseaParams(value) || isScctGseaParams(value) || isOtherTermTypesGseaParams(value);
-}
-function isProteomeDAPGseaParams(value) {
-  if (!value || typeof value !== "object") return false;
-  const p = value;
-  const d = p.dapParams;
-  return typeof p.genome === "string" && typeof p.dslabel === "string" && d && typeof d.organism === "string" && typeof d.assay === "string" && typeof d.cohort === "string";
-}
-function isScctGseaParams(value) {
-  if (!value || typeof value !== "object") return false;
-  const p = value;
-  return typeof p.genome === "string" && Array.isArray(p.genes) && p.genes.every((g) => typeof g === "string") && Array.isArray(p.fold_change) && p.fold_change.every((fc) => typeof fc === "number") && typeof p.genes_length === "number";
-}
-function isOtherTermTypesGseaParams(value) {
-  if (!value || typeof value !== "object") return false;
-  const p = value;
-  return typeof p.genome === "string" && typeof p.cacheId === "string" && "daRequest" in p && typeof p.genes_length === "number" && typeof p.dslabel === "string";
-}
-
-// plots/gsea/model/GSEAModel.ts
-var GSEAModel = class {
-  constructor(gsea) {
-    this.gsea = gsea;
-    this.app = gsea.app;
-  }
-  async getGseaParams(_params, state, config) {
-    if (!this.termType) this.termType = config.termType;
-    const params = structuredClone(_params);
-    if (!params.genome) params.genome = state.genome;
-    if (!params.dslabel) params.dslabel = state.dslabel;
-    if (this.termType === PROTEOME_DAP) this.getProteomeDAPParams(params);
-    else if (this.termType === SINGLECELL_CELLTYPE) await this.getScctParams(params, state, config);
-    else await this.getOtherTermTypesParams(params, config);
-    return params;
-  }
-  getProteomeDAPParams(params) {
-    if (isProteomeDAPGseaParams(params)) return;
-    if (!params.dapParams) params.dapParams = this.gsea.state.config.proteomeDetails;
-  }
-  async getScctParams(params, state, config) {
-    if (isScctGseaParams(params)) return;
-    let response;
-    try {
-      response = await this.getDEGenes(state, config);
-      if (response.error) throw new Error(response.error);
-      if (!Array.isArray(response.data) || response.data.length === 0) {
-        throw new Error("No DE genes returned for this cluster");
-      }
-    } catch (e) {
-      if (e instanceof Error) console.error(e.message || e);
-      else if (e.stack) console.log(e.stack);
-      throw new Error(e.message || e);
-    }
-    const genes = [];
-    const fold_change = [];
-    for (const g of response.data) {
-      genes.push(g.gene_name);
-      fold_change.push(g.fold_change);
-    }
-    params.genes = genes;
-    params.fold_change = fold_change;
-    params.genes_length = genes.length;
-  }
-  async getDEGenes(state, config) {
-    const body = {
-      genome: state.genome,
-      dslabel: state.dslabel,
-      sample: config.sample,
-      termId: config.termId,
-      categoryName: config.categoryName
-    };
-    return await dofetch3("termdb/singlecellDEgenes", { body });
-  }
-  async getOtherTermTypesParams(params, config) {
-    if (isOtherTermTypesGseaParams(params)) return;
-    let response;
-    try {
-      response = await this.getCachedResponse(config);
-      if (!response?.data?.cacheId || response.error) {
-        throw new Error(response.error || "No DE cacheId returned from volcano model");
-      }
-    } catch (e) {
-      if (e instanceof Error) console.error(e.message || e);
-      else if (e.stack) console.log(e.stack);
-      throw new Error(e.message || e);
-    }
-    params.cacheId = response.data.cacheId;
-    params.daRequest = response.daRequest;
-    params.genes_length = response.data.totalRows;
-    if (response.daRequest?.element_type === DMR_SCAN_ELEMENT_TYPE) {
-      const ranked = await dofetch3("genesetEnrichment", {
-        body: {
-          genome: params.genome,
-          dslabel: params.dslabel,
-          cacheId: params.cacheId,
-          daRequest: params.daRequest,
-          fetchDE: true,
-          method: "blitzgsea",
-          geneSetGroup: "",
-          filter_non_coding_genes: false
-        }
-      });
-      if (ranked?.error) throw new Error(ranked.error);
-      params.genes_length = ranked?.data?.genes?.length ?? 0;
-    }
-  }
-  async getCachedResponse(config) {
-    const volcanoSettings = config.settings?.volcano || getDefaultVolcanoSettings({}, { termType: config.termType });
-    const model = new VolcanoModel(this.gsea, config.termType);
-    return await model.getData(config, volcanoSettings);
-  }
-  async runEnrichment(body) {
-    this.toggleLoading(true);
-    try {
-      return await dofetch3("genesetEnrichment", { body });
-    } finally {
-      this.toggleLoading(false);
-    }
-  }
-  toggleLoading(isLoading) {
-    this.gsea.dom.actionsDiv.style("display", isLoading ? "none" : "block");
-    this.gsea.dom.loadingDiv.style("display", isLoading ? "block" : "none");
-  }
-};
-
-// plots/gsea/view/GSEAControls.ts
-async function setControls(controlsDiv, gsea) {
-  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" }
-      ]
-    },
-    {
-      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" }
-      ],
-      getDisplayStyle: () => {
-        return gsea.testEnabled ? "" : "none";
-      }
-    },
-    {
-      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
-      getDisplayStyle: (plot) => {
-        const settings = plot.settings.gsea;
-        return settings.gsea_method === "blitzgsea" ? "" : "none";
-      }
-    },
-    {
-      label: "FDR Filter Cutoff (Linear Scale)",
-      type: "number",
-      chartType: "gsea",
-      settingsKey: "fdr_cutoff",
-      title: "P-value significance",
-      min: 0,
-      max: 1,
-      getDisplayStyle: (plot) => {
-        const settings = plot.settings.gsea;
-        return settings.fdr_or_top == "fdr" ? "" : "none";
-      }
-    },
-    {
-      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,
-      getDisplayStyle: (plot) => {
-        const settings = plot.settings.gsea;
-        return settings.fdr_or_top == "top" ? "" : "none";
-      }
-    }
-  ];
-  gsea.components.controls = await controlsInit({
-    app: gsea.app,
-    id: gsea.id,
-    holder: controlsDiv,
-    inputs
-  });
-  gsea.components.controls.on("downloadClick.gsea", () => {
-    if (!gsea.imageUrl) return alert("No image to download");
-    const dataUrl = gsea.imageUrl;
-    const downloadImgName = `${gsea.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();
-  });
-}
-
-// plots/gsea/viewModel/GSEAViewModel.ts
-function formatStat(v) {
-  if (v == null) return v;
-  if (v === "Infinity") return "\u221E";
-  if (v === "-Infinity") return "\u2212\u221E";
-  return typeof v == "number" ? roundValueAuto(v) : v;
-}
-var GSEAViewModel = class {
-  constructor(gsea) {
-    this.rankedDE = null;
-    this.rankedDEKey = "";
-    this.gsea = gsea;
-    this.initPathwayOpts = structuredClone(gsea.app.opts.genome.termdbs.msigdb.analysisGenesetGroups);
-  }
-  async processData() {
-    const settings = this.gsea.state.config.settings.gsea;
-    const viewData = {
-      pathwayOpts: this.getPathwayOpts(settings)
-    };
-    if (!settings.pathway || settings.pathway == "-") {
-      this.viewData = viewData;
-      return;
-    }
-    let outputMap;
-    try {
-      const output = await this.gsea.model.runEnrichment(this.getRequestBody(settings));
-      if (output?.error) throw Object.assign(new Error(output.error), { code: output.code });
-      outputMap = this.getOutputMap(output, settings.gsea_method);
-    } catch (e) {
-      const msg = String(e?.message || e);
-      if (e?.code === "CACHE_BUSY") {
-        if (window.confirm(msg)) {
-          await this.processData();
-          return;
-        }
-        this.viewData = viewData;
-        return;
-      }
-      viewData.error = /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;
-      this.viewData = viewData;
-      return;
-    }
-    viewData.statsData = this.getStatsData(outputMap);
-    viewData.tableData = this.getTableData(outputMap, settings);
-    viewData.selectedRows = this.getSelectedRows(viewData.tableData.rowItems);
-    viewData.showHighlightButton = this.gsea.state.config.chartType == "differentialAnalysis" && this.gsea.state.config.gsea_params?.geneset_name != null;
-    const selectedGeneset = this.gsea.state.config.gsea_params?.geneset_name;
-    if (selectedGeneset) {
-      if (settings.gsea_method == "blitzgsea") {
-        try {
-          viewData.detailImage = await this.getDetailImage(settings, selectedGeneset);
-        } catch (e) {
-          const msg = String(e?.message || e);
-          if (e?.code === "CACHE_BUSY") {
-            if (window.confirm(msg)) {
-              await this.processData();
-              return;
-            }
-          } else {
-            viewData.detailError = /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;
-          }
-        }
-      } else {
-        viewData.cernoPlotData = await this.getCernoPlotData(outputMap, selectedGeneset);
-      }
-    }
-    this.viewData = viewData;
-  }
-  getPathwayOpts(settings) {
-    const pathwayOpts = structuredClone(this.initPathwayOpts);
-    if (this.gsea.testEnabled && 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();
-      const opt = pathwayOpts.find((opt2) => opt2.value == settings.pathway);
-      if (!opt) console.warn(`Selected pathway ${settings.pathway} not found in pathway options.`);
-      else opt.selected = true;
-    }
-    return pathwayOpts;
-  }
-  getRequestBody(settings, geneset_name) {
-    const p = this.gsea.gsea_params;
-    const body = {
-      genome: p.genome,
-      geneSetGroup: settings.pathway,
-      filter_non_coding_genes: settings.filter_non_coding_genes,
-      method: 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 (settings.gsea_method == "blitzgsea") {
-      body.num_permutations = settings.num_permutations;
-    }
-    if (geneset_name) body.geneset_name = geneset_name;
-    return body;
-  }
-  getOutputMap(output, method) {
-    if (method == "blitzgsea") {
-      if (!output?.data || typeof output.data != "object") throw new Error("Invalid blitzgsea response");
-      return output.data;
-    }
-    if (output?.data && !Array.isArray(output.data) && !output.data.genes && !output.data.fold_change) {
-      return output.data;
-    }
-    if (output && typeof output == "object" && !Array.isArray(output)) return output;
-    throw new Error("Invalid cerno response");
-  }
-  getStatsData(outputMap) {
-    return [{ label: "Gene sets analyzed", value: Object.keys(outputMap).length }];
-  }
-  getTableData(outputMap, settings) {
-    const entries = Object.entries(outputMap).map(([genesetName, result]) => ({ genesetName, result }));
-    const rowItems = [];
-    if (settings.fdr_or_top == "top") {
-      entries.sort((a, b) => Number(a.result.fdr ?? Infinity) - Number(b.result.fdr ?? Infinity));
-      for (let index = 0; index < Math.min(settings.top_genesets, entries.length); index++) {
-        const item = entries[index];
-        if (this.withinSizeCutoff(item.result, settings)) rowItems.push(this.makeRowItem(item, settings.gsea_method));
-      }
-    } else {
-      for (const item of entries) {
-        if (!this.withinSizeCutoff(item.result, settings)) continue;
-        if (Number(item.result.fdr ?? Infinity) > settings.fdr_cutoff) continue;
-        rowItems.push(this.makeRowItem(item, settings.gsea_method));
-      }
-    }
-    return {
-      columns: this.getTableColumns(settings.gsea_method),
-      rows: rowItems.map((item) => item.row),
-      rowItems
-    };
-  }
-  withinSizeCutoff(result, settings) {
-    return settings.max_gene_set_size_cutoff >= result.geneset_size && settings.min_gene_set_size_cutoff <= result.geneset_size;
-  }
-  makeRowItem(item, method) {
-    const pvalue = formatStat(item.result.pval);
-    const fdr = formatStat(item.result.fdr);
-    const leadingEdge = item.result.leading_edge;
-    const genes = leadingEdge ? leadingEdge.split(",").map((gene) => gene.trim()).filter(Boolean) : [];
-    if (method == "blitzgsea") {
-      const nes = formatStat(item.result.nes);
-      return {
-        genesetName: item.genesetName,
-        genes,
-        row: [
-          { value: item.genesetName },
-          { value: nes },
-          { value: item.result.geneset_size },
-          { value: pvalue },
-          { value: fdr },
-          { value: leadingEdge }
-        ]
-      };
-    }
-    const auc = formatStat(item.result.auc);
-    const es = formatStat(item.result.es);
-    return {
-      genesetName: item.genesetName,
-      genes,
-      row: [
-        { value: item.genesetName },
-        { value: auc },
-        { value: es },
-        { value: item.result.geneset_size },
-        { value: pvalue },
-        { value: fdr },
-        { value: leadingEdge }
-      ]
-    };
-  }
-  getTableColumns(method) {
-    if (method == "blitzgsea") {
-      return [
-        { label: "Gene Set", sortable: true },
-        {
-          label: "Normalized Enrichment Score",
-          barplot: { axisWidth: 200 },
-          sortable: true,
-          tooltip: "Normal quantile of the permutation p-value. \xB1\u221E means the p-value underflowed the permutation model, so the enrichment is beyond what the null distribution can score \u2014 the P value column reads 0 for the same reason. Rank these by enrichment score, not by how far off the scale they are."
-        },
-        { label: "Gene Set Size", sortable: true },
-        { label: "P value", sortable: true },
-        { label: "FDR", sortable: true },
-        { label: "Leading Edge" }
-      ];
-    }
-    return [
-      { 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" }
-    ];
-  }
-  getSelectedRows(rowItems) {
-    const selectedGeneset = this.gsea.state.config.gsea_params?.geneset_name;
-    const selectedIndex = rowItems.findIndex((item) => item.genesetName == selectedGeneset);
-    return selectedIndex > -1 ? [selectedIndex] : [];
-  }
-  async getDetailImage(settings, genesetName) {
-    const image = await this.gsea.model.runEnrichment(this.getRequestBody(settings, genesetName));
-    if (image?.error) throw Object.assign(new Error(image.error), { code: image.code });
-    if (this.gsea.imageUrl) URL.revokeObjectURL(this.gsea.imageUrl);
-    this.gsea.imageUrl = URL.createObjectURL(image);
-    return {
-      src: this.gsea.imageUrl,
-      width: 600,
-      height: 400
-    };
-  }
-  async getCernoPlotData(outputMap, genesetName) {
-    const selected = outputMap[genesetName];
-    if (!selected) throw new Error(`${genesetName} not found`);
-    const rankedDE = await this.getRankedDE();
-    const rankedGenes = rankedDE.genes.map((gene, index) => ({ gene, fold_change: rankedDE.fold_change[index] }));
-    rankedGenes.sort((a, b) => b.fold_change - a.fold_change);
-    return {
-      auc: selected.auc,
-      genesetName,
-      leadingEdgeGenes: selected.leading_edge.split(",").map((gene) => gene.trim()).filter(Boolean),
-      rankedGenes
-    };
-  }
-  async getRankedDE() {
-    const cacheKey = this.getRankedDECacheKey();
-    if (this.rankedDE && this.rankedDEKey == cacheKey) return this.rankedDE;
-    if (!this.gsea.gsea_params.cacheId && !this.gsea.gsea_params.dapParams) {
-      const rankedDE2 = {
-        genes: this.gsea.gsea_params.genes,
-        fold_change: this.gsea.gsea_params.fold_change
-      };
-      this.rankedDE = rankedDE2;
-      this.rankedDEKey = cacheKey;
-      return rankedDE2;
-    }
-    const response = await this.gsea.model.runEnrichment({
-      genome: this.gsea.gsea_params.genome,
-      dslabel: this.gsea.gsea_params.dslabel,
-      fetchDE: true,
-      geneSetGroup: "-",
-      filter_non_coding_genes: false,
-      method: "cerno",
-      ...this.gsea.gsea_params.cacheId ? {
-        cacheId: this.gsea.gsea_params.cacheId,
-        daRequest: this.gsea.gsea_params.daRequest
-      } : { dapParams: this.gsea.gsea_params.dapParams }
-    });
-    if (response?.error) throw Object.assign(new Error(response.error), { code: response.code });
-    const rankedDE = response.data;
-    this.rankedDE = rankedDE;
-    this.rankedDEKey = cacheKey;
-    return rankedDE;
-  }
-  getRankedDECacheKey() {
-    if (this.gsea.gsea_params.cacheId) return `cache:${this.gsea.gsea_params.cacheId}`;
-    if (this.gsea.gsea_params.dapParams) return `dap:${JSON.stringify(this.gsea.gsea_params.dapParams)}`;
-    const genes = this.gsea.gsea_params.genes || [];
-    return `inline:${genes.length}:${genes[0] || ""}:${genes[genes.length - 1] || ""}`;
-  }
-};
-
-// plots/gsea/view/GSEAView.ts
-var GSEAView = class {
-  constructor(gsea) {
-    this.gsea = gsea;
-    this.dom = gsea.dom;
-  }
-  initRender() {
-    this.renderActions();
-  }
-  renderActions() {
-    this.dom.actionsDiv.append("span").attr("data-testid", "sjpp-gsea-pathway").style("margin-right", "10px").style("display", "inline-block").text("Select a gene set group:");
-    this.pathwayDropDown = this.dom.actionsDiv.append("select").style("display", "inline-block").on("change", async () => {
-      const value = this.pathwayDropDown.node().value;
-      const settings = structuredClone(this.gsea.state.config.settings.gsea);
-      settings.pathway = value;
-      await this.gsea.app.dispatch({
-        type: "plot_edit",
-        id: this.gsea.id,
-        config: {
-          //Need to clear the gsea_params completely
-          gsea_params: {
-            geneset_name: null,
-            pathway: value
-          },
-          highlightGenes: [],
-          settings: {
-            gsea: settings
-          }
-        }
-      });
-    });
-  }
-  update() {
-    const viewData = this.gsea.viewModel.viewData;
-    this.renderPathwayOptions(viewData.pathwayOpts);
-    this.dom.detailsDiv.selectAll("*").remove();
-    this.dom.holder.selectAll("*").remove();
-    this.dom.tableDiv.selectAll("*").remove();
-    if (viewData.error) {
-      sayerror(this.dom.holder, viewData.error);
-      return;
-    }
-    if (!viewData.tableData) return;
-    this.dom.actionsDiv.selectAll(".sjpp-gsea-ranking-note").remove();
-    const da = this.gsea.gsea_params?.daRequest;
-    if (da?.element_type === DMR_SCAN_ELEMENT_TYPE) {
-      this.dom.actionsDiv.append("span").attr("class", "sjpp-gsea-ranking-note").style("margin-left", "14px").style("font-size", ".9em").style("color", "#555").text(
-        da.scan?.backgroundCorrection ? "Genes ranked by gene-body \u0394\u03B2 in excess of matched intergenic background (case \u2212 control); negative is gene-body methylation loss" : "Genes ranked by gene-body \u0394\u03B2 (case \u2212 control); negative is gene-body methylation loss"
-      );
-    }
-    this.renderStats(viewData.statsData);
-    if (viewData.detailImage) this.renderImage(viewData.detailImage);
-    if (viewData.cernoPlotData) this.renderCernoPlot(viewData.cernoPlotData);
-    if (viewData.detailError) sayerror(this.dom.holder, viewData.detailError);
-    if (viewData.showHighlightButton) this.renderHighlightButton();
-    this.renderResultsTable(viewData);
-  }
-  renderPathwayOptions(pathwayOpts) {
-    this.pathwayDropDown.selectAll("option").remove();
-    this.pathwayDropDown.selectAll("option").data(pathwayOpts).enter().append("option").text((d) => d.label).property("value", (d) => d.value).property("selected", (d) => d.selected);
-  }
-  renderStats(statsData) {
-    const tableStats = table2col({ holder: this.dom.detailsDiv.attr("data-testid", "sjpp-gsea-stats") });
-    const [, countHeader] = tableStats.addRow();
-    countHeader.style("text-align", "center").style("font-size", "0.8em").style("opacity", "0.8").text("COUNT");
-    for (const row of statsData) {
-      const [labelCell, valueCell] = tableStats.addRow();
-      labelCell.text(row.label);
-      valueCell.style("text-align", "end").text(row.value);
-    }
-  }
-  renderImage(detailImage) {
-    this.dom.holder.append("img").attr("width", detailImage.width).attr("height", detailImage.height).attr("src", detailImage.src);
-  }
-  renderHighlightButton() {
-    this.dom.detailsDiv.append("button").style("margin-left", "10px").style("display", "block").attr("aria-label", "Highlight genes in the volcano plot").text("Highlight genes").on("click", () => {
-      this.gsea.app.dispatch({
-        type: "plot_edit",
-        id: this.gsea.id,
-        config: {
-          childType: "volcano",
-          highlightedData: this.gsea.state.config.highlightGenes
-        }
-      });
-    });
-  }
-  renderResultsTable(viewData) {
-    const tableDiv = this.dom.tableDiv.append("div");
-    renderTable({
-      download: {
-        fileName: this.gsea.state.config.downloadFilename || ""
-      },
-      columns: viewData.tableData.columns,
-      rows: viewData.tableData.rows,
-      div: tableDiv,
-      showLines: true,
-      maxHeight: "30vh",
-      singleMode: true,
-      resize: true,
-      header: { allowSort: true },
-      selectedRows: viewData.selectedRows,
-      noButtonCallback: async (index) => {
-        const rowItem = viewData.tableData.rowItems[index];
-        const config = {
-          gsea_params: {
-            geneset_name: rowItem.genesetName
-          }
-        };
-        if (this.gsea.state.config.chartType == "differentialAnalysis" && rowItem.genes.length) {
-          config.highlightGenes = rowItem.genes;
-        }
-        await this.gsea.app.dispatch({
-          type: "plot_edit",
-          id: this.gsea.id,
-          config
-        });
-      }
-    });
-  }
-  renderCernoPlot(cernoPlotData) {
-    const holder = this.dom.holder;
-    const svgWidth = 400;
-    const svgHeight = 400;
-    const svg = holder.append("svg").attr("width", svgWidth).attr("height", svgHeight);
-    const topPad = 20;
-    const rightPad = 5;
-    const xPad = 50;
-    const yPad = 100;
-    const yAxis = svg.append("g");
-    const xAxis = svg.append("g");
-    const xScale = linear().domain([0, cernoPlotData.rankedGenes.length]).range([xPad, svgWidth - rightPad]);
-    const yScale = linear().domain([100, 0]).range([topPad, svgHeight - yPad]);
-    yAxis.attr("transform", `translate(${xPad},0)`);
-    xAxis.attr("transform", `translate(0,${svgHeight - yPad})`);
-    svg.append("text").text("Gene list").attr("fill", "black").attr("text-anchor", "start").attr("transform", `translate(${xScale(cernoPlotData.rankedGenes.length / 3)},${svgHeight - yPad + 2 * topPad})`);
-    svg.append("text").text("Percentage of gene set").attr("fill", "black").attr("text-anchor", "middle").attr("y", xPad / 2).attr("x", -svgWidth / 2.5).attr("transform", "rotate(-90)");
-    let fontSize = 30;
-    const title = svg.append("text").text(cernoPlotData.genesetName).attr("fill", "black").attr("text-anchor", "start").attr("font-size", `${fontSize}px`).attr("transform", `translate(${xPad},${topPad / 2})`);
-    let titleBox = title.node().getBBox();
-    while (titleBox.width > svgWidth - xPad || titleBox.height > topPad * 3.5 / 5) {
-      fontSize -= 1;
-      title.node().setAttribute("font-size", `${fontSize}px`);
-      titleBox = title.node().getBBox();
-    }
-    if (typeof cernoPlotData.auc === "number") {
-      const aucPos = cernoPlotData.auc >= 0.5 ? `${xScale(cernoPlotData.rankedGenes.length * 3 / 3.5)},${svgHeight - yPad * 1.5}` : `${xScale(cernoPlotData.rankedGenes.length * 0.8 / 4.5)},${svgHeight - yPad * 3}`;
-      svg.append("text").text(`AUC=${roundValueAuto(cernoPlotData.auc)}`).attr("fill", "black").attr("text-anchor", "middle").attr("transform", `translate(${aucPos})`);
-    }
-    axisstyle({
-      axis: yAxis.call(axisLeft(yScale)),
-      color: "black",
-      showline: true,
-      fontsize: "10"
-    });
-    axisstyle({
-      axis: xAxis.call(axisBottom(xScale)),
-      color: "black",
-      showline: true,
-      fontsize: "10"
-    });
-    const hitGenes = new Set(cernoPlotData.leadingEdgeGenes);
-    const yIncrement = 100 / Math.max(hitGenes.size, 1);
-    const lines = svg.append("g");
-    let yIter = 100;
-    for (let index = 0; index < cernoPlotData.rankedGenes.length; index++) {
-      const rankedGene = cernoPlotData.rankedGenes[index];
-      const yOld = yIter;
-      if (hitGenes.has(rankedGene.gene)) {
-        yIter -= yIncrement;
-        lines.append("line").style("stroke", "red").attr("x1", xScale(index)).attr("y1", svgHeight).attr("x2", xScale(index)).attr("y2", svgHeight - yPad + 2.5 * topPad);
-      }
-      lines.append("line").style("stroke", "red").attr("x1", xScale(index)).attr("y1", yScale(100 - yOld)).attr("x2", xScale(index + 1)).attr("y2", yScale(100 - yIter));
-    }
-  }
-};
-
-// plots/gsea/GSEA.ts
-var GSEA = class _GSEA extends PlotBase {
-  static {
-    this.type = "gsea";
-  }
-  constructor(opts, api) {
-    super(opts, api);
-    this.type = _GSEA.type;
-    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
-    };
-    this.testEnabled = JSON.parse(sessionStorage.getItem("optionalFeatures") || "{}")?.gsea_test;
-  }
-  getState(appState) {
-    const config = appState.plots.find((p) => p.id === this.id);
-    if (!config) throw new Error(`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,
-      genome: appState.vocab.genome,
-      dslabel: appState.vocab.dslabel
-    };
-  }
-  async init(appState) {
-    const state = this.getState(appState);
-    const config = structuredClone(state.config);
-    this.model = new GSEAModel(this);
-    validateConfigByTermType(config);
-    if (!isValidGseaParams(config.gsea_params)) {
-      this.gsea_params = await this.model.getGseaParams(config.gsea_params, state, config);
-    } else {
-      this.gsea_params = config.gsea_params;
-    }
-    await setControls(this.dom.controlsDiv, this);
-    this.viewModel = new GSEAViewModel(this);
-    this.view = new GSEAView(this);
-    this.view.initRender();
-  }
-  async main() {
-    const state = structuredClone(this.state);
-    if (state.config.chartType != this.type && state.config.childType != this.type) return;
-    if (this.dom.header) {
-      const geneCount = this.gsea_params.genes_length ?? this.gsea_params.genes?.length ?? 0;
-      this.dom.header.html(
-        geneCount + ' genes <span style="font-size:.8em;opacity:.7">GENE SET ENRICHMENT ANALYSIS</span>'
-      );
-    }
-    if (this.imageUrl) URL.revokeObjectURL(this.imageUrl);
-    this.imageUrl = null;
-    await this.viewModel.processData();
-    this.view.update();
-  }
-};
-var gseaInit = getCompInit(GSEA);
-var componentInit = gseaInit;
-async function getPlotConfig(opts, app) {
-  if (!opts.termType) throw new Error("No termType provided [gsea getPlotConfig()]");
-  try {
-    const config = {
-      gsea_params: {
-        genome: app.opts.state.vocab.genome
-      },
-      //idea for fixing nav button
-      //samplelst: { groups: app.opts.state.groups}
-      settings: {
-        gsea: getDefaultGseaSettings(opts.overrides, opts)
-      }
-    };
-    copyMerge(config, opts);
-    validateConfigByTermType(config);
-    return config;
-  } catch (e) {
-    throw `${e} [gsea getPlotConfig()]`;
-  }
-}
-function validateConfigByTermType(config) {
-  if (!config.gsea_params) config.gsea_params = {};
-  if (config.termType === PROTEOME_DAP) {
-    if (!config.proteomeDetails) throw new Error("No proteomeDetails provided for DAP GSEA");
-    config.gsea_params.dapParams = config.proteomeDetails;
-  } else if (config.termType === SINGLECELL_CELLTYPE) {
-    if (!config.sample || !config.termId || !config.categoryName)
-      throw new Error("Missing sample, termId, or categoryName for single cell cluster GSEA");
-  }
-}
-function makeChartBtnMenu(holder, chartsInstance) {
-  chartsInstance.prepPlot({
-    config: {
-      chartType: "gsea"
-    }
-  });
-}
-export {
-  GSEA,
-  componentInit,
-  getPlotConfig,
-  gseaInit,
-  makeChartBtnMenu
-};
-//# sourceMappingURL=GSEA-ZEJB3QZQ.js.map