@sjcrh/proteinpaint-client 2.207.1 → 2.209.0

package/dist/chunk-FNW6BKOA.js

@@ -0,0 +1,480 @@
+import {
+  renderTable
+} from "./chunk-C3HEDQPT.js";
+import {
+  clusterMethodLst,
+  distanceMethodLst
+} from "./chunk-OBDIJ4QS.js";
+import {
+  termType2label
+} from "./chunk-3XBG5HIV.js";
+import {
+  select_default
+} from "./chunk-I6Y4O3RR.js";
+import {
+  __export
+} from "./chunk-HS5PO5ZQ.js";
+
+// plots/matrix/hierCluster.interactivity.js
+var hierCluster_interactivity_exports = {};
+__export(hierCluster_interactivity_exports, {
+  addSelectedRowsOptions: () => addSelectedRowsOptions,
+  addSelectedSamplesOptions: () => addSelectedSamplesOptions,
+  getAllChildrenClusterIds: () => getAllChildrenClusterIds,
+  getClusterFromLeftDendrogram: () => getClusterFromLeftDendrogram,
+  getClusterFromTopDendrogram: () => getClusterFromTopDendrogram,
+  setClusteringBtn: () => setClusteringBtn,
+  showTable4selectedRows: () => showTable4selectedRows,
+  showTable4selectedSamples: () => showTable4selectedSamples,
+  triggerZoomBranch: () => triggerZoomBranch
+});
+function getAllChildrenClusterIds(clickedClusterId, left) {
+  const mergedClusters = left ? this.hierClusterData.clustering.row.mergedClusters : this.hierClusterData.clustering.col.mergedClusters;
+  const children = mergedClusters.get(clickedClusterId).childrenClusters || [];
+  let allChildren = [...children];
+  for (const child of children) {
+    allChildren = allChildren.concat(this.getAllChildrenClusterIds(child, left));
+  }
+  return allChildren;
+}
+function addSelectedSamplesOptions(clickedSampleNames, event) {
+  const l = this.settings.matrix.controlLabels;
+  const ss = this.opts.allow2selectSamples;
+  const optionArr = [
+    {
+      label: "Zoom in",
+      callback: () => {
+        this.triggerZoomBranch(this, clickedSampleNames);
+      }
+    },
+    {
+      label: `List ${clickedSampleNames.length} ${l.samples}`,
+      callback: () => this.showTable4selectedSamples(clickedSampleNames)
+    }
+  ];
+  if (ss) {
+    optionArr.push({
+      label: ss.buttonText || `Select ${l.samples}`,
+      callback: async () => {
+        const samples = clickedSampleNames.map((c) => this.data.samples[c]);
+        ss.callback({
+          samples: await this.app.vocabApi.convertSampleId(samples, ss.attributes),
+          source: ss.defaultSelectionLabel || `Selected ${l.samples} from gene expression`
+        });
+      }
+    });
+  } else {
+    if (this.state.nav && this.state.nav.header_mode !== "hidden") {
+      const samples = clickedSampleNames.map((c) => this.sampleOrder.find((s) => s.row.sample == c).row);
+      for (const s of samples) {
+        if (!s.sampleId) s.sampleId = s.sample;
+      }
+      optionArr.push({
+        label: "Add to a group",
+        callback: async () => {
+          const group = {
+            name: "Group",
+            items: samples
+          };
+          this.addGroup(group);
+        }
+      });
+    }
+  }
+  this.mouseout();
+  this.dom.tip.hide();
+  this.dom.dendroClickMenu.d.selectAll("*").remove();
+  this.dom.dendroClickMenu.d.selectAll("div").data(optionArr).enter().append("div").attr("class", "sja_menuoption").style("border-radius", "0px").html((d) => d.label).attr("data-testid", (d) => `hierCluster_dendro_menu_${d.label.split(" ")[0]}`).on("click", (event2) => {
+    this.dom.dendroClickMenu.d.selectAll("*").remove();
+    event2.target.__data__.callback();
+  });
+  this.dom.dendroClickMenu.show(event.clientX, event.clientY);
+}
+function addSelectedRowsOptions(clickedRowNames, event) {
+  const rowType = this.config.settings.matrix.controlLabels.terms;
+  const optionArr = [
+    {
+      label: `List ${clickedRowNames.length} ${rowType}`,
+      callback: () => this.showTable4selectedRows(clickedRowNames, rowType)
+    }
+  ];
+  if (this.config.dataType == "geneExpression" && this.app.opts.genome.termdbs) {
+    const minGeneCutoff = this.app.opts.genome.termdbs.msigdb.geneORAparam.minCutoff;
+    const maxGeneCutoff = this.app.opts.genome.termdbs.msigdb.geneORAparam.maxCutoff;
+    optionArr.push({
+      label: `Gene set overrepresentation analysis`,
+      disabled: clickedRowNames.length < minGeneCutoff || clickedRowNames.length > maxGeneCutoff,
+      callback: () => {
+        if (clickedRowNames.length < minGeneCutoff || clickedRowNames.length > maxGeneCutoff) return;
+        this.dom.dendroClickMenu.d.selectAll("*").remove();
+        const lst = [];
+        for (const x of clickedRowNames) {
+          const j = this.terms?.find?.((t) => t.tw.$id == x);
+          if (j) {
+            const n = j.tw?.term?.gene;
+            if (n) lst.push(n);
+          }
+        }
+        const config = {
+          chartType: "geneORA",
+          geneORAparams: {
+            sample_genes: lst.join(","),
+            genome: this.app.vocabApi.opts.state.vocab.genome
+          }
+        };
+        this.app.dispatch({
+          type: "plot_create",
+          config
+        });
+      }
+    });
+  }
+  this.mouseout();
+  this.dom.tip.hide();
+  this.dom.dendroClickMenu.d.selectAll("*").remove();
+  this.dom.dendroClickMenu.d.selectAll("div").data(optionArr).enter().append("div").attr("class", (d) => d.disabled ? "sja_menuoption_not_interactive" : "sja_menuoption").style("opacity", (d) => d.disabled ? 0.5 : 1).style("border-radius", "0px").html(
+    (d) => d.disabled ? `${d.label} <span style="font-size: 0.6em; display: block; margin-left: 2px; margin-top: 2px;">Only available when 15 - 500 genes selected</span>` : d.label
+  ).attr("data-testid", (d) => `hierCluster_dendro_menu_${d.label.split(" ")[0]}`).on("click", (event2) => {
+    if (event2.target.__data__?.callback) event2.target.__data__.callback();
+  });
+  this.dom.dendroClickMenu.show(event.clientX, event.clientY);
+}
+function triggerZoomBranch(self, clickedSampleNames) {
+  if (self.zoomArea) {
+    self.zoomArea.remove();
+    delete self.zoomArea;
+  }
+  const c = {
+    startCell: self.serieses[0].cells.find((d2) => d2.sample == clickedSampleNames[0]),
+    endCell: self.serieses[0].cells.find((d2) => d2.sample == clickedSampleNames[clickedSampleNames.length - 1])
+  };
+  const s = self.settings.matrix;
+  const d = self.dimensions;
+  const start = c.startCell.totalIndex < c.endCell.totalIndex ? c.startCell : c.endCell;
+  const zoomIndex = Math.floor(start.totalIndex + Math.abs(c.endCell.totalIndex - c.startCell.totalIndex) / 2);
+  const centerCell = self.sampleOrder[zoomIndex];
+  const colw = self.computedSettings.colw || self.settings.matrix.colw;
+  const maxZoomLevel = s.colwMax / colw;
+  const minZoomLevel = s.colwMin / colw;
+  const tentativeZoomLevel = Math.max(
+    1,
+    s.zoomLevel * d.mainw / Math.max(c.endCell.x - c.startCell.x, 2 * d.colw) * 0.7
+  );
+  const zoomLevel = Math.max(minZoomLevel, Math.min(tentativeZoomLevel, maxZoomLevel));
+  self.app.dispatch({
+    type: "plot_edit",
+    id: self.id,
+    config: {
+      settings: {
+        matrix: {
+          zoomLevel,
+          zoomCenterPct: 0.5,
+          //zoomLevel < 1 && d.mainw >= d.zoomedMainW ? 0.5 : zoomCenter / d.mainw,
+          zoomIndex,
+          zoomGrpIndex: centerCell.grpIndex
+        }
+      }
+    }
+  });
+  self.resetInteractions();
+}
+function showTable4selectedSamples(clickedSampleNames) {
+  const templates = this.state.termdbConfig.urlTemplates;
+  const rows = templates?.sample ? clickedSampleNames.map((c) => [
+    { value: this.hierClusterData.bySampleId[c].label, url: `${templates.sample.base}${c}` }
+  ]) : clickedSampleNames.map((c) => [{ value: this.hierClusterData.bySampleId[c].label }]);
+  const columns = [{ label: this.settings.matrix.controlLabels.Sample }];
+  renderTable({
+    rows,
+    columns,
+    div: this.dom.dendroClickMenu.clear().d.append("div").style("margin", "10px"),
+    showLines: true,
+    maxHeight: "35vh",
+    resize: true
+  });
+}
+function showTable4selectedRows(clickedRowNames, rowType) {
+  const templates = this.state.termdbConfig.urlTemplates;
+  const rows = [];
+  if (templates?.gene && this.config.dataType == "geneExpression" && this.hierClusterData.byTermId) {
+    for (const i of clickedRowNames) {
+      const genesymbol = this.terms.find((t) => t.tw?.$id == i)?.tw?.term?.gene;
+      if (!genesymbol) continue;
+      const gencode = this.hierClusterData.byTermId[i]?.gencodeId;
+      if (gencode) {
+        rows.push([{ value: genesymbol, url: `${templates.gene.base}${gencode}` }]);
+      } else {
+        rows.push([{ value: genesymbol }]);
+      }
+    }
+  } else {
+    for (const i of clickedRowNames) {
+      const tw = this.terms.find((t) => t.tw?.$id == i)?.tw;
+      if (!tw) continue;
+      const n = tw.term?.gene || tw.term?.name;
+      if (!n) continue;
+      rows.push([{ value: n }]);
+    }
+  }
+  const div = this.dom.dendroClickMenu.clear().d.append("div").style("margin", "10px");
+  const buttonDiv = div.append("div").style("padding", "5px");
+  const copyButton = buttonDiv.append("button").html(`Copy ${rowType}`).attr("class", ".sja_menu_div button").style("margin-top", "2px").style("padding", "5px").on("click", () => {
+    const geneNames = rows.map((row) => row[0].value).join("\n");
+    navigator.clipboard.writeText(geneNames).then(() => {
+    }, console.warn);
+    copyButton.html(`Copy ${rowType}&nbsp;&check;`);
+  });
+  renderTable({
+    rows,
+    columns: [{ label: rowType }],
+    div: div.append("div"),
+    showLines: true,
+    maxHeight: "35vh",
+    resize: true
+  });
+}
+function getClusterFromTopDendrogram(event) {
+  if (event.target.tagName == "image") this.imgBox = event.target.getBoundingClientRect();
+  else return;
+  const y = event.clientY - this.imgBox.y - event.target.clientTop;
+  const xMin = this.dimensions.xMin;
+  const x = event.clientX - this.imgBox.x - event.target.clientLeft + xMin;
+  for (const [clusterId, cluster] of this.hierClusterData.clustering.col.mergedClusters) {
+    const { x1, y1, x2, y2, clusterY } = cluster.clusterPosition;
+    if (x1 <= x && x <= x2 && clusterY - 5 < y && y < clusterY + 5 || clusterY <= y && y <= y1 && x1 - 5 < x && x < x1 + 5 || clusterY <= y && y <= y2 && x2 - 5 < x && x < x2 + 5) {
+      return clusterId;
+    }
+  }
+}
+function getClusterFromLeftDendrogram(event) {
+  if (event.target.tagName == "image") this.imgBox = event.target.getBoundingClientRect();
+  else return;
+  const y = event.clientY - this.imgBox.y - event.target.clientTop;
+  const xMin = this.dimensions.xMin;
+  const x = event.clientX - this.imgBox.x - event.target.clientLeft + xMin;
+  for (const [clusterId, cluster] of this.hierClusterData.clustering.row.mergedClusters) {
+    const { x1, y1, x2, y2, clusterX } = cluster.clusterPosition;
+    if (y1 <= y && y <= y2 && clusterX - 5 < x && x < clusterX + 5 || clusterX <= x && x <= x1 && y1 - 5 < y && y < y1 + 5 || clusterX <= x && x <= x2 && y2 - 5 < y && y < y2 + 5) {
+      return clusterId;
+    }
+  }
+}
+function setClusteringBtn(holder, callback) {
+  const cl = this.config.settings.matrix.controlLabels;
+  const dataType = this.config.dataType;
+  const clusterRowLabel = cl.Terms;
+  const cluteringButtonLabel = `${termType2label(dataType)} Clustering`;
+  holder.append("button").datum({
+    label: cluteringButtonLabel,
+    getCount: () => this.hcTermGroup?.lst.length || 0,
+    showCount: "hide",
+    rows: [
+      {
+        label: `Cluster ${cl.Samples}`,
+        title: `Option to enable ${cl.samples} clustering, instead of enabling ${cl.samples} sorting.`,
+        type: "checkbox",
+        chartType: "hierCluster",
+        settingsKey: "clusterSamples",
+        boxLabel: `Cluster ${cl.Samples} (Disable ${cl.Samples} Sorting)`,
+        callback: (checked) => {
+          if (!checked) {
+            this.config.settings.hierCluster.yDendrogramHeight = 0;
+            this.config.settings.hierCluster.clusterSamples = false;
+          } else {
+            this.config.divideBy = null;
+            this.config.settings.hierCluster.yDendrogramHeight = 200;
+            this.config.settings.hierCluster.clusterSamples = true;
+          }
+          this.app.dispatch({
+            type: "plot_edit",
+            id: this.id,
+            config: this.config
+          });
+        }
+      },
+      {
+        label: `Cluster ${clusterRowLabel}`,
+        title: `Option to enable ${clusterRowLabel} clustering, instead of enabling ${clusterRowLabel} sorting.`,
+        type: "checkbox",
+        chartType: "hierCluster",
+        settingsKey: "clusterRows",
+        boxLabel: `Cluster ${clusterRowLabel} (Disable ${clusterRowLabel} Sorting)`,
+        callback: (checked) => {
+          if (!checked) {
+            this.config.settings.hierCluster.clusterRows = false;
+            this.config.settings.hierCluster.sortClusterRows = "asListed";
+          } else {
+            this.config.settings.hierCluster.clusterRows = true;
+            this.config.settings.hierCluster.sortClusterRows = void 0;
+          }
+          this.app.dispatch({
+            type: "plot_edit",
+            id: this.id,
+            config: this.config
+          });
+        }
+      },
+      {
+        label: `Sort ${clusterRowLabel}`,
+        title: `Set how to order the ${clusterRowLabel} as rows`,
+        type: "radio",
+        chartType: "hierCluster",
+        settingsKey: "sortClusterRows",
+        options: [
+          { label: `By input ${clusterRowLabel} order`, value: "asListed" },
+          { label: `By ${clusterRowLabel} name`, value: "byName" }
+        ],
+        styles: { padding: 0, "padding-right": "10px", margin: 0, display: "inline-block" },
+        getDisplayStyle(plot) {
+          return plot.settings.hierCluster.clusterRows ? "none" : "table-row";
+        }
+      },
+      {
+        label: "Z-score Transformation",
+        title: `Option to do Z-score transformation`,
+        type: "checkbox",
+        chartType: "hierCluster",
+        settingsKey: "zScoreTransformation",
+        boxLabel: `Perform Z-score Transformation`,
+        callback: (checked) => {
+          if (!checked) {
+            this.config.settings.hierCluster.zScoreTransformation = false;
+            this.config.settings.hierCluster.colorScale = "whiteRed";
+          } else {
+            this.config.settings.hierCluster.zScoreTransformation = true;
+            this.config.settings.hierCluster.colorScale = "blueWhiteRed";
+          }
+          this.app.dispatch({
+            type: "plot_edit",
+            id: this.id,
+            config: this.config
+          });
+        }
+      },
+      {
+        label: `Clustering Method`,
+        title: `Sets which clustering method to use`,
+        type: "radio",
+        chartType: "hierCluster",
+        settingsKey: "clusterMethod",
+        options: clusterMethodLst
+      },
+      {
+        label: `Distance Method`,
+        title: `Sets which distance method to use for clustering`,
+        type: "radio",
+        chartType: "hierCluster",
+        settingsKey: "distanceMethod",
+        options: distanceMethodLst
+      },
+      {
+        label: `Column Dendrogram Height`,
+        title: `The maximum height to render the column dendrogram`,
+        type: "number",
+        chartType: "hierCluster",
+        settingsKey: "yDendrogramHeight",
+        getDisplayStyle(plot) {
+          return plot.settings.hierCluster.clusterSamples ? "table-row" : "none";
+        }
+      },
+      {
+        label: `Row Dendrogram Width`,
+        title: `The maximum width to render the row dendrogram`,
+        type: "number",
+        chartType: "hierCluster",
+        settingsKey: "xDendrogramHeight",
+        getDisplayStyle(plot) {
+          return plot.settings.hierCluster.clusterRows ? "table-row" : "none";
+        }
+      },
+      {
+        label: `Z-score Cap`,
+        title: `Cap the Z-score scale to not exceed this absolute value`,
+        type: "number",
+        chartType: "hierCluster",
+        settingsKey: "zScoreCap"
+      },
+      {
+        label: `Color Scheme`,
+        title: `Sets which color scheme to use`,
+        type: "radio",
+        chartType: "hierCluster",
+        settingsKey: "colorScale",
+        options: [
+          {
+            label: "Blue-White-Red",
+            value: "blueWhiteRed",
+            title: `color scheme Blue-White-Red`
+          },
+          {
+            label: "Green-Black-Red",
+            value: "greenBlackRed",
+            title: `color scheme Green-Black-Red`
+          },
+          {
+            label: "Blue-Yellow-Red",
+            value: "blueYellowRed",
+            title: `color scheme Blue-Yellow-Red`
+          },
+          {
+            label: "Green-White-Red",
+            value: "greenWhiteRed",
+            title: `color scheme Green-White-Red`
+          },
+          {
+            label: "Blue-Black-Yellow",
+            value: "blueBlackYellow",
+            title: `color scheme Blue-Black-Yellow`
+          }
+        ]
+      }
+    ],
+    customInputs: updateClusteringControls
+  }).html((d) => d.label).style("margin", "2px 0").on("click", callback);
+}
+function updateClusteringControls(self, app, parent, table) {
+  if (parent.chartType == "hierCluster" && !parent.config.settings.hierCluster.zScoreTransformation) {
+    const zScoreCapControl = select_default(
+      table.selectAll("td").filter(function() {
+        return select_default(this).text() == "Z-score Cap";
+      }).node().closest("tr")
+    );
+    zScoreCapControl.style("display", "none");
+    const colorSchemeControl = select_default(
+      table.selectAll("td").filter(function() {
+        return select_default(this).text() == "Color Scheme";
+      }).node().closest("tr")
+    );
+    colorSchemeControl.style("display", "none");
+  }
+  if (parent.chartType == "hierCluster" && parent.config.dataType !== "geneExpression") {
+    const geneInputTr = table.insert("tr", () => table.select("tr").node());
+    geneInputTr.append("td").attr("class", "sja-termdb-config-row-label").html("Hierarchical Clustering Term Set");
+    const td1 = geneInputTr.append("td").style("display", "block").style("padding", "5px 0px");
+    const editGrpDiv = td1.append("div").append("label");
+    const clusteringBtn = self.btns.node();
+    editGrpDiv.append("button").html("Edit Set").on("click", () => {
+      app.tip.clear();
+      const backDiv = app.tip.d.append("div").style("padding", "5px");
+      backDiv.attr("tabindex", 0).style("padding", "5px").style("text-decoration", "underline").style("cursor", "pointer").style("margin-bottom", "12px").html(`&#171; Back`).on("click", () => clusteringBtn.click()).on("keyup", (event) => {
+        if (event.key == "Enter") event.target.click();
+      });
+      const setEdiUiHolder = app.tip.d.append("div");
+      parent.showDictTermSelection(setEdiUiHolder);
+    });
+  }
+}
+
+export {
+  getAllChildrenClusterIds,
+  addSelectedSamplesOptions,
+  addSelectedRowsOptions,
+  triggerZoomBranch,
+  showTable4selectedSamples,
+  showTable4selectedRows,
+  getClusterFromTopDendrogram,
+  getClusterFromLeftDendrogram,
+  setClusteringBtn,
+  hierCluster_interactivity_exports
+};
+//# sourceMappingURL=chunk-FNW6BKOA.js.map

package/dist/chunk-FR5USNAT.js

@@ -0,0 +1,54 @@
+import {
+  addGeneSearchbox
+} from "./chunk-C3HEDQPT.js";
+import {
+  Menu
+} from "./chunk-ELJX3QIQ.js";
+
+// termdb/handlers/snp.ts
+var SearchHandler = class {
+  init(opts) {
+    this.callback = opts.callback;
+    const geneSearch = addGeneSearchbox({
+      tip: new Menu({ padding: "0px" }),
+      genome: opts.genomeObj,
+      row: opts.holder,
+      searchOnly: "snp",
+      allowVariant: true,
+      callback: () => this.selectSnp(geneSearch)
+    });
+  }
+  async selectSnp(geneSearch) {
+    const { chr, ref, alt, fromWhat } = geneSearch;
+    if (!chr || !ref || !alt || !fromWhat) throw "missing chr, ref, alt, or fromWhat of snp";
+    let start, stop;
+    if (!geneSearch.start && !geneSearch.stop) {
+      if (geneSearch.pos) {
+        start = geneSearch.pos - 1;
+        stop = geneSearch.pos;
+      } else {
+        throw "missing coordinate of snp";
+      }
+    } else {
+      start = geneSearch.start;
+      stop = geneSearch.stop;
+    }
+    const term = {
+      id: fromWhat,
+      chr,
+      start,
+      stop,
+      name: fromWhat,
+      ref,
+      alt: typeof alt == "string" ? [alt] : alt,
+      // is string if input to geneSearch was in variant or hgvs format // TODO: update genesearch.ts to parse alternative alleles from any input format into arrays
+      type: "snp"
+    };
+    this.callback(term);
+  }
+};
+
+export {
+  SearchHandler
+};
+//# sourceMappingURL=chunk-FR5USNAT.js.map

package/dist/chunk-FSLOUTTK.js

@@ -0,0 +1,37 @@
+import {
+  DMR_SCAN_ELEMENT_TYPE
+} from "./chunk-SB36AUG7.js";
+
+// plots/gsea/settings/defaults.ts
+function isDmrScanRanking(opts) {
+  return opts?.elementType === DMR_SCAN_ELEMENT_TYPE || opts?.gsea_params?.daRequest?.element_type === DMR_SCAN_ELEMENT_TYPE;
+}
+function getDefaultGseaSettings(overrides = {}, opts = {}) {
+  const defaults = {
+    fdr_cutoff: 0.05,
+    num_permutations: 1e3,
+    top_genesets: 40,
+    pathway: opts?.gsea_params?.pathway ?? void 0,
+    geneset_name: null,
+    min_gene_set_size_cutoff: 0,
+    /* 500 only for a DMR scan's gene-body ranking, where blitzgsea's null fit is unstable above it.
+    The server enforces that ceiling on the library before the fit (genesetEnrichment.ts); this
+    default only keeps the table's own size filter consistent with it, and daRequest may not be
+    known yet when defaults are first built. Every other caller keeps 20,000, because lowering it
+    for them would silently drop large GO and Reactome sets from analyses that have always shown
+    them. */
+    max_gene_set_size_cutoff: isDmrScanRanking(opts) ? 500 : 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);
+}
+
+export {
+  getDefaultGseaSettings
+};
+//# sourceMappingURL=chunk-FSLOUTTK.js.map

package/dist/chunk-FSLOUTTK.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/gsea/settings/defaults.ts"],
+  "sourcesContent": ["import type { GseaSettings } from './Settings'\nimport { DMR_SCAN_ELEMENT_TYPE } from '#types'\n\n/** Whether this GSEA ranks genes by gene-body delta-beta from a DMR scan rather than by a\n * gene-level fold change. The scan has no gene rows, so the server substitutes that ranking\n * (genesetEnrichment.ts) and it needs a tighter gene-set ceiling than the rest. */\nfunction isDmrScanRanking(opts: any): boolean {\n\t/* daRequest arrives only once GSEA has fetched from the volcano's cache, after these defaults are\n\tbuilt, so a differential analysis also passes the volcano's element class directly. */\n\treturn (\n\t\topts?.elementType === DMR_SCAN_ELEMENT_TYPE || opts?.gsea_params?.daRequest?.element_type === DMR_SCAN_ELEMENT_TYPE\n\t)\n}\n\nexport function getDefaultGseaSettings(overrides = {}, opts: any = {}): GseaSettings {\n\tconst defaults: GseaSettings = {\n\t\tfdr_cutoff: 0.05,\n\t\tnum_permutations: 1000,\n\t\ttop_genesets: 40,\n\t\tpathway: opts?.gsea_params?.pathway ?? undefined,\n\t\tgeneset_name: null,\n\t\tmin_gene_set_size_cutoff: 0,\n\t\t/* 500 only for a DMR scan's gene-body ranking, where blitzgsea's null fit is unstable above it.\n\t\tThe server enforces that ceiling on the library before the fit (genesetEnrichment.ts); this\n\t\tdefault only keeps the table's own size filter consistent with it, and daRequest may not be\n\t\tknown yet when defaults are first built. Every other caller keeps 20,000, because lowering it\n\t\tfor them would silently drop large GO and Reactome sets from analyses that have always shown\n\t\tthem. */\n\t\tmax_gene_set_size_cutoff: isDmrScanRanking(opts) ? 500 : 20000,\n\t\tfilter_non_coding_genes: true,\n\t\tfdr_or_top: 'top',\n\t\tgsea_method: 'blitzgsea'\n\t}\n\tif (JSON.parse(sessionStorage.getItem('optionalFeatures') || '{}')?.gsea_test) {\n\t\t// set default method to CERNO when serverconfig flag gsea_test is defined\n\t\tdefaults.gsea_method = 'cerno'\n\t}\n\treturn Object.assign(defaults, overrides)\n}\n"],
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