@sjcrh/proteinpaint-client 2.183.0 → 2.183.2-0

package/dist/Volcano-QBYYJYVW.js

@@ -1,1185 +0,0 @@
-import {
-  VolcanoModel
-} from "./chunk-Q7PYFSNU.js";
-import {
-  GeneSetEditUI,
-  MultiTermWrapperEditUI,
-  PlotBase,
-  axisstyle,
-  controlsInit,
-  downloadTable,
-  fillTermWrapper,
-  getCombinedTermFilter,
-  getDefaultVolcanoSettings,
-  getGEunit,
-  getSampleNum,
-  renderTable,
-  sayerror,
-  table2col,
-  to_svg,
-  validateVolcanoSettings
-} from "./chunk-OXJ2TWDO.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-V6DLLX4N.js";
-import "./chunk-7RN3L2BX.js";
-import {
-  Menu
-} from "./chunk-A6TQGNDQ.js";
-import "./chunk-HYZG6OPC.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-5EF5U7MX.js";
-import "./chunk-2K5DSRBJ.js";
-import "./chunk-UCLS2SVB.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-MVTCBVSX.js";
-import "./chunk-SEQLC4AD.js";
-import {
-  roundValueAuto
-} from "./chunk-L4QG7XZE.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-KQMEJUWI.js";
-import "./chunk-UJU3Q7QJ.js";
-import "./chunk-WGL6FIUE.js";
-import {
-  DNA_METHYLATION,
-  GENE_EXPRESSION,
-  SINGLECELL_CELLTYPE
-} from "./chunk-6ITDJ5UR.js";
-import "./chunk-XYFDBYOY.js";
-import "./chunk-TV74I3Y5.js";
-import "./chunk-IH7ILDJS.js";
-import {
-  axisBottom,
-  axisLeft
-} from "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import {
-  linear
-} from "./chunk-OAWQ6LOO.js";
-import "./chunk-SEEYV6P2.js";
-import {
-  selectAll_default,
-  select_default
-} from "./chunk-NDWTN4U5.js";
-import {
-  rgb
-} from "./chunk-OMR2DT66.js";
-import "./chunk-HFNDKYVF.js";
-
-// plots/volcano/viewModel/VolcanoViewModel.ts
-var VolcanoViewModel = class {
-  constructor(config, response, settings) {
-    this.numSignificant = 0;
-    this.numNonSignificant = 0;
-    this.minLogFoldChange = 0;
-    this.maxLogFoldChange = 0;
-    //Used for the y axis domain
-    this.minLogPValue = 0;
-    this.maxLogPValue = 0;
-    //Used in place of 0 p values that cannot be log transformed
-    this.minNonZeroPValue = 1e-9;
-    this.offset = 10;
-    this.bottomPad = 60;
-    this.horizPad = 70;
-    this.topPad = 40;
-    this.config = config;
-    this.response = response;
-    this.pValueCutoff = settings.pValue;
-    this.plotX = this.horizPad + this.offset * 2;
-    const controlColor = this.config?.tw?.term?.values?.[this.config?.samplelst?.groups[0].name]?.color || "red";
-    const caseColor = this.config?.tw?.term?.values?.[this.config?.samplelst?.groups[1].name].color || "blue";
-    const barplot = caseColor && controlColor ? { colorNegative: controlColor, colorPositive: caseColor } : {};
-    this.pValueTable = {
-      columns: [
-        { label: "log\u2082(fold-change)", barplot, sortable: true },
-        { label: "Original p-value", sortable: true },
-        { label: "Adjusted p-value", sortable: true }
-      ],
-      //Arr set in setPointData()
-      rows: [],
-      height: settings.height + this.topPad
-    };
-    this.settings = settings;
-    this.termType = config.termType;
-    this.dataType = this.setDataType();
-    this.setMinMaxValues();
-    const plotDim = this.setPlotDimensions();
-    this.setPTableColumns();
-    const pointData = this.setPointData(plotDim, controlColor, caseColor);
-    const foldChangeIdx = this.pValueTable.columns.findIndex((c) => c.label.includes("log\u2082(fold-change)"));
-    this.pValueTable.rows.sort((a, b) => b[foldChangeIdx].value - a[foldChangeIdx].value);
-    this.viewData = {
-      images: response.images || [],
-      termInfo: this.setTermInfo(plotDim),
-      plotDim,
-      pointData,
-      pValueTableData: this.pValueTable,
-      statsData: this.setStatsData(),
-      userActions: this.setUserActions()
-    };
-  }
-  setDataType() {
-    if (this.termType == GENE_EXPRESSION) return "genes";
-    else if (this.termType == DNA_METHYLATION) return "promoters";
-    else if (this.termType == SINGLECELL_CELLTYPE) return "genes";
-    else throw new Error(`Unknown termType: ${this.termType}`);
-  }
-  setMinMaxValues() {
-    for (const d of this.response.data) {
-      this.minLogFoldChange = Math.min(this.minLogFoldChange, d.fold_change);
-      this.maxLogFoldChange = Math.max(this.maxLogFoldChange, d.fold_change);
-      if (d[`${this.settings.pValueType}_p_value`] != 0) {
-        this.minLogPValue = Math.min(this.minLogPValue, -Math.log10(d[`${this.settings.pValueType}_p_value`]));
-        this.maxLogPValue = Math.max(this.maxLogPValue, -Math.log10(d[`${this.settings.pValueType}_p_value`]));
-        this.minNonZeroPValue = Math.min(this.minNonZeroPValue, d[`${this.settings.pValueType}_p_value`]);
-      }
-    }
-  }
-  setPlotDimensions() {
-    const xScale = linear().domain([this.minLogFoldChange, this.maxLogFoldChange]).range([0, this.settings.width]);
-    const yScale = linear().domain([this.minLogPValue, this.maxLogPValue]).range([this.settings.height, 0]);
-    return {
-      svg: {
-        //20 is for the term info above the plot
-        height: this.settings.height + this.topPad + this.bottomPad * 2 + this.offset * 3,
-        width: this.settings.width + this.horizPad * 2
-      },
-      top: {
-        x: this.plotX,
-        y: 5
-      },
-      xAxisLabel: {
-        x: this.horizPad + this.settings.width / 2 + this.offset,
-        y: this.topPad + this.settings.height + this.bottomPad + this.offset
-      },
-      xScale: {
-        scale: xScale,
-        x: this.plotX,
-        y: this.settings.height + this.topPad + this.offset * 2
-      },
-      yAxisLabel: {
-        text: `-log10(${this.settings.pValueType} P value)`,
-        x: this.horizPad / 3,
-        y: this.topPad + this.settings.height / 2
-      },
-      yScale: {
-        scale: yScale,
-        x: this.horizPad,
-        y: this.topPad
-      },
-      plot: {
-        height: this.settings.height,
-        width: this.settings.width,
-        x: this.plotX,
-        y: this.topPad
-      },
-      logFoldChangeLine: {
-        x: xScale(0) + this.plotX,
-        y1: this.topPad,
-        y2: this.settings.height + this.offset * 4
-      }
-    };
-  }
-  setTermInfo(plotDim) {
-    if (this.termType != GENE_EXPRESSION && this.termType != DNA_METHYLATION) return;
-    const getLabel = (name) => {
-      if (name.length >= 25) return name.substring(0, 20) + "...";
-      return name;
-    };
-    return {
-      //Set slightly above the plot
-      y: plotDim.top.y + 10,
-      first: {
-        // color: controlColor || this.settings.defaultSignColor,
-        label: getLabel(`${this.config.samplelst.groups[0].name} (${this.response.sample_size1})`),
-        x: 0
-        // rectX: this.settings.width/2 - 10,
-      },
-      second: {
-        // color: caseColor || this.settings.defaultSignColor,
-        label: getLabel(`${this.config.samplelst.groups[1].name} (${this.response.sample_size2})`),
-        x: this.settings.width
-        // rectX: this.settings.width/2 + 10,
-      }
-    };
-  }
-  setPointData(plotDim, controlColor, caseColor) {
-    const radius = Math.max(this.settings.width, this.settings.height) / 80;
-    const dataCopy = structuredClone(this.response.data);
-    for (const d of dataCopy) {
-      const highlightKey = this.termType === DNA_METHYLATION ? d.promoter_id : d.gene_name;
-      d.highlighted = this.config?.highlightedData?.includes(highlightKey);
-      d.significant = this.isSignificant(d);
-      this.getGenesColor(d, d.significant, controlColor, caseColor);
-      if (d.significant) {
-        this.numSignificant++;
-        const row = [
-          { value: roundValueAuto(d.fold_change) },
-          { value: roundValueAuto(d.original_p_value) },
-          { value: roundValueAuto(d.adjusted_p_value) }
-        ];
-        if (this.termType == DNA_METHYLATION) {
-          row.splice(0, 0, { value: d.promoter_id || "" }, { value: d.gene_name || "" });
-        } else {
-          row.splice(0, 0, { value: d.gene_name || "" });
-        }
-        this.pValueTable.rows.push(row);
-      } else {
-        this.numNonSignificant++;
-      }
-      d.x = plotDim.xScale.scale(d.fold_change) + this.plotX;
-      const y = d[`${this.settings.pValueType}_p_value`] == 0 ? this.minNonZeroPValue : d[`${this.settings.pValueType}_p_value`];
-      d.y = plotDim.yScale.scale(-Math.log10(y)) + this.topPad;
-      d.radius = radius;
-    }
-    dataCopy.sort((a, b) => a.highlighted - b.highlighted);
-    return dataCopy;
-  }
-  isSignificant(d) {
-    return -Math.log10(d[`${this.settings.pValueType}_p_value`]) > this.pValueCutoff && Math.abs(d.fold_change) > this.settings.foldChangeCutoff;
-  }
-  getGenesColor(d, significant, controlColor, caseColor) {
-    if (!d.gene_name && this.termType != DNA_METHYLATION)
-      throw new Error(`Missing gene_name in data: ${JSON.stringify(d)}`);
-    if (significant) {
-      if (controlColor && caseColor) d.color = d.fold_change > 0 ? caseColor : controlColor;
-      else d.color = this.settings.defaultSignColor;
-    } else d.color = this.settings.defaultNonSignColor;
-  }
-  setStatsData() {
-    const tableRows = [
-      {
-        label: `Percentage of significant ${this.dataType}`,
-        value: roundValueAuto(this.numSignificant * 100 / (this.numSignificant + this.numNonSignificant))
-      },
-      {
-        label: `Number of significant ${this.dataType}`,
-        value: this.numSignificant
-      },
-      {
-        label: `Number of total ${this.dataType}`,
-        value: this.numSignificant + this.numNonSignificant
-      }
-    ];
-    if (this.termType == GENE_EXPRESSION || this.termType == DNA_METHYLATION) {
-      tableRows.push(
-        {
-          label: this.config.samplelst.groups[0].name + " sample size (control group)",
-          value: this.response.sample_size1
-        },
-        {
-          label: this.config.samplelst.groups[1].name + " sample size (case group)",
-          value: this.response.sample_size2
-        }
-      );
-    }
-    if (this.response.bcv !== void 0 && this.response.bcv !== null) {
-      tableRows.push({
-        label: "Biological coefficient of variation",
-        value: roundValueAuto(this.response.bcv)
-      });
-    }
-    return tableRows;
-  }
-  setPTableColumns() {
-    if (this.termType == DNA_METHYLATION) {
-      this.pValueTable.columns.splice(0, 0, { label: "Promoter", sortable: true }, { label: "Gene(s)", sortable: true });
-    } else {
-      this.pValueTable.columns.splice(0, 0, { label: "Gene Name", sortable: true });
-    }
-  }
-  setUserActions() {
-    const userActions = {
-      noShow: /* @__PURE__ */ new Set()
-    };
-    if (this.termType == GENE_EXPRESSION) {
-      if (this.settings.method == "edgeR" && getSampleNum(this.config) > 100) {
-        userActions.noShow.add("Confounding factors");
-      }
-      if (this.settings.method == "wilcoxon") userActions.noShow.add("Confounding factors");
-    }
-    return userActions;
-  }
-};
-
-// plots/volcano/interactions/VolcanoInteractions.ts
-var VolcanoInteractions = class {
-  constructor(app, id, dom) {
-    this.app = app;
-    this.dom = dom;
-    this.id = id;
-    this.pValueTableData = [];
-    this.data = [];
-  }
-  /** Launches a multi-term select tree
-   * On submit, dispatches a plot_edit action with the new confounders */
-  async confoundersMenu() {
-    const state = this.app.getState();
-    const config = state.plots.find((p) => p.id === this.id);
-    if (config.termType !== GENE_EXPRESSION && config.termType !== DNA_METHYLATION) return;
-    const allowedGroupNames = /* @__PURE__ */ new Set([config.samplelst.groups[0].name, config.samplelst.groups[1].name]);
-    const grpTerms = new Set(
-      (this.app?.vocabApi?.state.groups || []).filter((g) => allowedGroupNames.has(g.name)).flatMap(
-        (g) => g.filter.lst.flatMap((f) => {
-          if (f.tvs?.term) return f.tvs.term;
-          else return f.lst.map((l) => l.tvs.term);
-        })
-      )
-    );
-    const disable_terms = grpTerms.size ? Array.from(grpTerms) : [];
-    const maxNum = config.settings.volcano.method == "edgeR" ? 1 : 2;
-    const ui = new MultiTermWrapperEditUI({
-      app: this.app,
-      callback: async (tws) => {
-        this.dom.actionsTip.hide();
-        await this.app.dispatch({
-          type: "plot_edit",
-          id: this.id,
-          config: { confounderTws: tws }
-        });
-      },
-      holder: this.dom.actionsTip.d,
-      headerText: "Select confounders",
-      maxNum,
-      state,
-      twList: config.confounderTws,
-      disable_terms
-    });
-    await ui.renderUI();
-  }
-  clearDom() {
-    this.dom.holder.selectAll('div[id="sjpp-volcano-actions"]').remove();
-    this.dom.holder.selectAll('svg[id="sjpp-volcano-svg"]').remove();
-    this.dom.holder.selectAll('div[id="sjpp-volcano-stats"]').remove();
-    this.dom.holder.selectAll('div[id="sjpp-volcano-pValueTable"]').remove();
-    this.dom.holder.selectAll('div[id="sjpp-volcano-images"]').remove();
-    this.dom.error.selectAll("*").remove();
-  }
-  download(termType) {
-    this.dom.actionsTip.clear().showunder(this.dom.controls.select("div").node());
-    const opts = [
-      {
-        text: "Download plot",
-        callback: () => {
-          const svg = this.dom.holder.select("svg").node();
-          to_svg(svg, `Differential ${termType} analysis volcano`, { apply_dom_styles: true });
-        }
-      },
-      {
-        text: "Download p value table",
-        callback: () => {
-          downloadTable(this.pValueTableData.rows, this.pValueTableData.columns);
-        }
-      }
-    ];
-    for (const opt of opts) {
-      this.dom.actionsTip.d.append("div").attr("class", "sja_menuoption").text(opt.text).on("click", opt.callback);
-    }
-  }
-  async highlightDataPoint(value) {
-    const config = this.app.getState().plots.find((p) => p.id === this.id);
-    const highlightedData = config.highlightedData.includes(value) ? config.highlightedData.filter((d) => d !== value) : [...config.highlightedData, value];
-    await this.app.dispatch({
-      type: "plot_edit",
-      id: this.id,
-      config: { highlightedData }
-    });
-  }
-  /** When clicking on a data point, launches the box plot in a separate sandbox
-   * For geneExpression, value == gene symbol */
-  async launchBoxPlot(value) {
-    const config = this.app.getState().plots.find((p) => p.id === this.id);
-    if (config.termType != GENE_EXPRESSION) return;
-    const values = {};
-    for (const group of config.samplelst.groups) {
-      values[group.name] = {
-        key: group.name,
-        label: group.name,
-        list: group.values
-      };
-    }
-    const setTerm = () => {
-      if (config.termType == GENE_EXPRESSION) {
-        return {
-          q: { mode: "continuous" },
-          term: {
-            gene: value,
-            name: value,
-            type: config.termType
-          }
-        };
-      } else return config.term;
-    };
-    this.app.dispatch({
-      type: "plot_create",
-      config: {
-        chartType: "summary",
-        childType: "boxplot",
-        term: setTerm(),
-        term2: {
-          q: { groups: config.tw.q.groups, type: "custom-samplelst" },
-          term: config.tw.term
-        }
-      }
-    });
-  }
-  /** Launch a violin plot for a gene expression data point. */
-  async launchViolinGeneExp(value) {
-    const config = this.app.getState().plots.find((p) => p.id === this.id);
-    if (config.termType != GENE_EXPRESSION) return;
-    this.app.dispatch({
-      type: "plot_create",
-      config: {
-        chartType: "summary",
-        childType: "violin",
-        term: {
-          q: { mode: "continuous" },
-          term: {
-            gene: value,
-            name: value,
-            type: config.termType
-          }
-        },
-        term2: {
-          q: { groups: config.tw.q.groups, type: "custom-samplelst" },
-          term: config.tw.term
-        }
-      }
-    });
-  }
-  launchGeneSetEdit() {
-    const plotConfig = this.app.getState().plots.find((p) => p.id === this.id);
-    const holder = this.dom.actionsTip.d.append("div").style("padding", "5px");
-    const limitedGenesList = plotConfig.termType === DNA_METHYLATION ? this.data.map((d) => d.promoter_id) : this.data.map((d) => d.gene_name);
-    new GeneSetEditUI({
-      holder,
-      genome: this.app.opts.genome,
-      vocabApi: this.app.vocabApi,
-      limitedGenesList,
-      geneList: plotConfig.highlightedData.map((d) => {
-        return { gene: d };
-      }),
-      customInputs: [
-        {
-          label: "Cancel highlight",
-          getDisplayStyle: () => plotConfig.highlightedData.length > 0 ? "" : "none",
-          showInput: async () => {
-            await this.app.dispatch({
-              type: "plot_edit",
-              id: this.id,
-              config: { highlightedData: [] }
-            });
-            this.dom.actionsTip.hide();
-          }
-        }
-      ],
-      callback: async (result) => {
-        const highlightedData = result.geneList.map((d) => d.gene);
-        await this.app.dispatch({
-          type: "plot_edit",
-          id: this.id,
-          config: { highlightedData }
-        });
-        this.dom.actionsTip.hide();
-      }
-    });
-  }
-  /** When clicking on a DM data point, dispatches a DMR plot that runs DMRCate
-   * analysis and renders a genome browser Block with DMR regions on their own
-   * track. */
-  async launchDmr(d) {
-    const config = this.app.getState().plots.find((p) => p.id === this.id);
-    if (config.termType !== DNA_METHYLATION) return;
-    const controlColor = config?.tw?.term?.values?.[config?.samplelst?.groups[0].name]?.color || "#ff0000";
-    const caseColor = config?.tw?.term?.values?.[config?.samplelst?.groups[1].name]?.color || "#0000ff";
-    const label = d.promoterId || `${d.chr}:${d.start}-${d.stop}`;
-    const dmrConfig = {
-      chartType: "dmr",
-      headerText: `DMR: ${label}`,
-      coordinateOverride: { chr: d.chr, start: d.start, stop: d.stop },
-      group1: config.samplelst.groups[0].values || [],
-      group2: config.samplelst.groups[1].values || [],
-      group1Name: config.samplelst.groups[0].name,
-      group2Name: config.samplelst.groups[1].name,
-      settings: {
-        colors: { group1: controlColor, group2: caseColor }
-      }
-    };
-    this.app.dispatch({
-      type: "plot_create",
-      config: dmrConfig
-    });
-  }
-  /** Launch a violin/box plot for a DNA methylation promoter.
-   * Creates a methylation term using the promoter's chr/start/stop coordinates.
-   * The tw handler fills in id and unit from termdbConfig. */
-  launchViolin(d) {
-    const config = this.app.getState().plots.find((p) => p.id === this.id);
-    const genomicFeatureType = d.promoter_id ? "promoter" : "gene";
-    const featureName = genomicFeatureType === "gene" ? d.gene_name?.split(",")[0]?.trim() || "" : "";
-    this.app.dispatch({
-      type: "plot_create",
-      config: {
-        chartType: "summary",
-        childType: "violin",
-        term: {
-          q: { mode: "continuous" },
-          term: {
-            genomicFeatureType,
-            featureName,
-            type: DNA_METHYLATION,
-            chr: d.chr,
-            start: d.start,
-            stop: d.stop
-          }
-        },
-        term2: {
-          q: { groups: config.tw.q.groups, type: "custom-samplelst" },
-          term: config.tw.term
-        }
-      }
-    });
-  }
-  async launchDEGClustering() {
-    const geneIndex = this.pValueTableData.columns.findIndex((col) => col.label === "Gene Name");
-    const adjustedPValIndex = this.pValueTableData.columns.findIndex((col) => col.label === "Adjusted p-value");
-    const rowsSorted = [...this.pValueTableData.rows].sort((a, b) => {
-      const aQVal = Number(a[adjustedPValIndex].value);
-      const bQVal = Number(b[adjustedPValIndex].value);
-      return aQVal - bQVal;
-    });
-    const geneList = rowsSorted.slice(0, 100).map((r) => ({ gene: r[geneIndex].value }));
-    const tws = geneList.map((d) => {
-      const gene = d.gene;
-      const unit = getGEunit(this.app.vocabApi);
-      const name = `${gene} ${unit}`;
-      const term = { gene, name, type: GENE_EXPRESSION };
-      const tw = { term, q: {} };
-      return tw;
-    });
-    const group = { lst: tws, type: "hierCluster" };
-    const customVariable = this.app.getState().plots.find((p) => p.id === this.id).tw;
-    const annotationGroup = { lst: [customVariable] };
-    const config = {
-      chartType: "hierCluster",
-      termgroups: [group, annotationGroup],
-      dataType: GENE_EXPRESSION,
-      filter: {
-        in: true,
-        join: "",
-        type: "tvslst",
-        lst: [{ type: "tvs", tvs: { term: customVariable.term } }]
-      }
-    };
-    await this.app.dispatch({
-      type: "plot_create",
-      config: structuredClone(config)
-    });
-  }
-};
-
-// plots/volcano/view/DataPointMouseEvents.ts
-var DataPointMouseEvents = class {
-  constructor(d, circle, hoverTip, clickTip, interactions, termType) {
-    this.termType = termType;
-    circle.on("mouseover", () => {
-      circle.attr("fill-opacity", 0.9);
-      hoverTip.clear().showunder(circle.node());
-      const table = table2col({ holder: hoverTip.d.append("table") });
-      this.addTooltipRows(d, table);
-    });
-    circle.on("mouseout", () => {
-      hoverTip.hide();
-      if (d.highlighted) return;
-      circle.attr("fill-opacity", 0);
-    });
-    circle.on("click", () => {
-      hoverTip.hide();
-      clickTip.onHide = () => {
-        if (!d.highlighted) circle.attr("fill-opacity", 0);
-      };
-      clickTip.clear().showunder(circle.node());
-      const table = table2col({ holder: clickTip.d.append("table") });
-      this.addTooltipRows(d, table);
-      const menuDiv = clickTip.d.append("div").style("padding", "5px");
-      if (termType === DNA_METHYLATION) {
-        const dm = d;
-        menuDiv.append("div").attr("class", "sja_menuoption").text("Violin plot").on("click", () => {
-          clickTip.hide();
-          interactions.launchViolin(dm);
-        });
-        menuDiv.append("div").attr("class", "sja_menuoption").text("DMR analysis").on("click", async () => {
-          clickTip.hide();
-          await interactions.launchDmr({
-            chr: dm.chr,
-            start: dm.start,
-            stop: dm.stop,
-            promoterId: dm.promoter_id
-          });
-        });
-      } else {
-        menuDiv.append("div").attr("class", "sja_menuoption").text("Violin plot").on("click", async () => {
-          clickTip.hide();
-          await interactions.launchViolinGeneExp(d.gene_name);
-        });
-        menuDiv.append("div").attr("class", "sja_menuoption").text("Box plot").on("click", async () => {
-          clickTip.hide();
-          await interactions.launchBoxPlot(d.gene_name);
-        });
-      }
-    });
-  }
-  addTooltipRow(table, text, value) {
-    const [td1, td2] = table.addRow();
-    td1.html(text);
-    td2.text(value);
-  }
-  addTooltipRows(d, table) {
-    if (this.termType === DNA_METHYLATION) {
-      if ("promoter_id" in d) this.addTooltipRow(table, "Promoter", d.promoter_id);
-      if (d.gene_name) this.addTooltipRow(table, "Gene(s)", d.gene_name);
-    } else {
-      this.addTooltipRow(table, "Gene name", d.gene_name);
-    }
-    this.addTooltipRow(table, "log<sub>2</sub>(fold-change)", roundValueAuto(d.fold_change));
-    this.addTooltipRow(table, "Original p-value", roundValueAuto(d.original_p_value));
-    this.addTooltipRow(table, "Adjusted p-value", roundValueAuto(d.adjusted_p_value));
-  }
-};
-
-// plots/volcano/view/VolcanoPlotView.ts
-var VolcanoPlotView = class {
-  constructor(dom, settings, viewData, interactions, termType) {
-    this.dom = dom;
-    this.interactions = interactions;
-    this.settings = settings;
-    this.viewData = viewData;
-    const actions = this.dom.holder.append("div").attr("id", "sjpp-volcano-actions").style("display", "block").style("z-index", 1).style("position", "relative");
-    const svg = this.dom.holder.append("svg").style("display", "inline-block").attr("id", "sjpp-volcano-svg").style("vertical-align", "top");
-    this.volcanoDom = {
-      actions,
-      svg,
-      top: svg.append("g").attr("id", "sjpp-volcano-top"),
-      xAxis: svg.append("g").attr("id", "sjpp-volcano-xAxis"),
-      yAxis: svg.append("g").attr("id", "sjpp-volcano-yAxis"),
-      xAxisLabel: svg.append("text").attr("id", "sjpp-volcano-xAxisLabel").attr("text-anchor", "middle"),
-      yAxisLabel: svg.append("text").attr("id", "sjpp-volcano-yAxisLabel").attr("text-anchor", "middle"),
-      plot: svg.append("g").attr("id", "sjpp-volcano-plot"),
-      pValueTable: this.dom.holder.append("div").attr("id", "sjpp-volcano-pValueTable").style("display", "none")
-    };
-    this.termType = termType;
-    const plotDim = this.viewData.plotDim;
-    this.renderUserActions();
-    this.renderPlot(plotDim);
-    renderDataPoints(this);
-    this.renderFoldChangeLine(plotDim);
-    this.renderStatsMenu();
-    this.renderPValueTable();
-  }
-  renderUserActions() {
-    this.dom.actionsTip.d.style("overflow", "hidden");
-    this.volcanoDom.actions.style("margin-left", "20px").style("padding", "5px");
-    this.addActionButton(
-      "Confounding factors",
-      [GENE_EXPRESSION, DNA_METHYLATION],
-      () => this.interactions.confoundersMenu()
-    );
-    this.addActionButton(
-      "Highlight genes",
-      [GENE_EXPRESSION, SINGLECELL_CELLTYPE, DNA_METHYLATION],
-      () => this.interactions.launchGeneSetEdit()
-    );
-    this.addActionButton("Statistics", [GENE_EXPRESSION, SINGLECELL_CELLTYPE, DNA_METHYLATION], () => {
-      this.renderStatsMenu();
-    });
-    const sigLabel = this.termType == DNA_METHYLATION ? "Number of significant promoters" : "Number of significant genes";
-    const numSigGenes = this.viewData.statsData.find((d) => d.label == sigLabel)?.value;
-    if (numSigGenes) {
-      const sigText = this.termType == DNA_METHYLATION ? `${numSigGenes} DM promoters:` : `${numSigGenes} DE genes:`;
-      this.volcanoDom.actions.append("span").text(sigText).style("margin-left", "10px").style("font-weight", "bold");
-      this.addActionButton("Show p-value table", [GENE_EXPRESSION, SINGLECELL_CELLTYPE, DNA_METHYLATION], () => {
-        this.volcanoDom.pValueTable.style(
-          "display",
-          this.volcanoDom.pValueTable.style("display") == "none" ? "inline-block" : "none"
-        );
-      });
-    }
-    if (numSigGenes && numSigGenes >= 3) {
-      this.addActionButton(
-        `Hierarchical clustering of ${numSigGenes > 100 ? "top 100" : numSigGenes} DE genes`,
-        [GENE_EXPRESSION],
-        async () => {
-          await this.interactions.launchDEGClustering();
-        }
-      );
-    }
-  }
-  /** Use the termTypes arr to render the buttons in a consistent order */
-  addActionButton(text, termTypes, callback) {
-    if (this.viewData.userActions.noShow.has(text)) return;
-    if (!termTypes.includes(this.termType)) return;
-    const button = this.volcanoDom.actions.append("button").attr("class", "sja_menuoption").style("margin", "3px").style("padding", "3px").text(text).on("click", () => {
-      this.dom.actionsTip.clear().showunder(button.node());
-      callback();
-    });
-  }
-  renderPlot(plotDim) {
-    this.volcanoDom.svg.attr("width", plotDim.svg.width).attr("height", plotDim.svg.height);
-    this.renderTermInfo(plotDim);
-    this.volcanoDom.yAxisLabel.attr(
-      "transform",
-      `translate(${plotDim.yAxisLabel.x}, ${plotDim.yAxisLabel.y}) rotate(-90)`
-    );
-    this.setSvgSubscriptLabel(this.volcanoDom.yAxisLabel, "-log", "10", `(${this.settings.pValueType} p-value)`);
-    this.volcanoDom.xAxisLabel.attr("transform", `translate(${plotDim.xAxisLabel.x}, ${plotDim.xAxisLabel.y})`);
-    this.setSvgSubscriptLabel(this.volcanoDom.xAxisLabel, "log", "2", "(fold-change)");
-    this.renderScale(plotDim.xScale);
-    this.renderScale(plotDim.yScale, true);
-    this.volcanoDom.plot.append("rect").attr("width", plotDim.plot.width).attr("height", plotDim.plot.height).attr("stroke", "#ededed").attr("fill", "transparent").attr("shape-rendering", "crispEdges").attr("transform", `translate(${plotDim.plot.x}, ${plotDim.plot.y})`);
-  }
-  renderTermInfo(plotDim) {
-    if (this.viewData.termInfo == void 0) return;
-    this.volcanoDom.top.attr("transform", `translate(${plotDim.top.x}, ${plotDim.top.y})`);
-    const y = this.viewData.termInfo.y;
-    const addLabel = (term) => {
-      return this.volcanoDom.top.append("text").attr("font-size", "0.9em").attr("transform", `translate(${term.x}, ${y + 10})`).text(term.label);
-    };
-    const firstTerm = this.viewData.termInfo.first;
-    addLabel(firstTerm);
-    const secondTerm = this.viewData.termInfo.second;
-    const secondLabel = addLabel(secondTerm);
-    secondLabel.attr("text-anchor", "end");
-  }
-  renderScale(scale, isLeft = false) {
-    const scaleG = this.volcanoDom[isLeft ? "yAxis" : "xAxis"].append("g").attr("transform", `translate(${scale.x}, ${scale.y})`).call(isLeft ? axisLeft(scale.scale) : axisBottom(scale.scale));
-    axisstyle({
-      axis: scaleG,
-      color: "black",
-      showline: true
-    });
-  }
-  renderFoldChangeLine(plotDim) {
-    this.volcanoDom.plot.append("line").attr("stroke", "#ccc").attr("shape-rendering", "crispEdges").attr("x1", plotDim.logFoldChangeLine.x).attr("x2", plotDim.logFoldChangeLine.x).attr("y1", plotDim.logFoldChangeLine.y1).attr("y2", plotDim.logFoldChangeLine.y2);
-  }
-  renderStatsMenu() {
-    for (const img of this.viewData.images || []) {
-      this.dom.actionsTip.d.append("img").style("display", "inline-block").style("margin-left", "10px").style("margin-top", "-30px").attr("width", 450).attr("height", 450).attr("src", img.src);
-    }
-    const tableHolder = this.dom.actionsTip.d.append("div").style("display", this.viewData.images.length == 1 ? "inline-block" : "block").style("margin", `${this.viewData.images.length == 1 ? `40px 10px` : `0px 0px`} 0px 5px`).style("vertical-align", "top");
-    const table = table2col({ holder: tableHolder });
-    for (const d of this.viewData.statsData) {
-      const [td1, td2] = table.addRow();
-      td1.text(d.label);
-      td2.style("text-align", "end").text(d.value);
-    }
-  }
-  renderPValueTable() {
-    const maxTableRows = 5e3;
-    const allRows = this.viewData.pValueTableData.rows;
-    const rows = allRows.length > maxTableRows ? allRows.slice(0, maxTableRows) : allRows;
-    if (allRows.length > maxTableRows) {
-      this.volcanoDom.pValueTable.append("div").style("padding", "5px 10px").style("font-size", ".8em").style("color", "#666").text(
-        `Showing top ${maxTableRows.toLocaleString()} of ${allRows.length.toLocaleString()} significant results (sorted by fold-change)`
-      );
-    }
-    renderTable({
-      columns: this.viewData.pValueTableData.columns,
-      rows,
-      div: this.volcanoDom.pValueTable,
-      showLines: true,
-      maxHeight: `${this.viewData.pValueTableData.height}px`,
-      resize: true,
-      header: { allowSort: true },
-      noRadioBtn: true,
-      noButtonCallback: (i) => {
-        const gene = this.viewData.pValueTableData.rows[i][0].value;
-        if (!gene) return;
-        this.interactions.highlightDataPoint(gene);
-      },
-      hoverEffects: (tr, row) => {
-        const circles = this.volcanoDom.plot.selectAll("circle").nodes();
-        const dataKey = this.termType === DNA_METHYLATION ? "promoter_id" : "gene_name";
-        const circle = circles.find((d) => d.__data__[dataKey] == row[0].value);
-        if (!circle || circle.__data__.highlighted) return;
-        let clone;
-        tr.on("mouseover", () => {
-          if (circle.__data__.highlighted || clone) return;
-          clone = this.volcanoDom.plot.node()?.appendChild(circle.cloneNode(true));
-          clone.setAttribute("fill-opacity", 0.9);
-        });
-        tr.on("mouseleave", () => {
-          if (!clone) return;
-          clone.remove();
-          clone = null;
-        });
-        this.volcanoDom.pValueTable.on("mouseover", () => {
-          selectAll_default(circles).attr("stroke-opacity", 0.075);
-        });
-        this.volcanoDom.pValueTable.on("mouseleave", () => {
-          selectAll_default(circles).attr("stroke-opacity", (d) => d.significant ? 0.35 : 0.2);
-        });
-      }
-    });
-  }
-  setSvgSubscriptLabel(textElem, prefix, subscript, suffix) {
-    textElem.text(null);
-    textElem.append("tspan").text(prefix);
-    textElem.append("tspan").attr("baseline-shift", "sub").attr("font-size", "0.7em").text(subscript);
-    textElem.append("tspan").text(suffix);
-  }
-};
-function renderDataPoints(self) {
-  self.volcanoDom.plot.selectAll("circle").data(self.viewData.pointData).enter().append("circle").attr("stroke", (d) => rgb(d.color).formatHex()).attr("stroke-opacity", (d) => d.significant ? 0.35 : 0.2).attr("stroke-width", (d) => d.significant ? 1.5 : 1).attr("fill", self.settings.defaultHighlightColor).attr("fill-opacity", (d) => d.highlighted ? 0.9 : 0).attr("cx", (d) => d.x).attr("cy", (d) => d.y).attr("r", (d) => d.radius).each(function(d) {
-    const circle = select_default(this);
-    new DataPointMouseEvents(d, circle, self.dom.hoverTip, self.dom.clickTip, self.interactions, self.termType);
-  });
-}
-
-// plots/volcano/VolcanoControlInputs.ts
-var VolcanoControlInputs = class {
-  constructor(config, termType) {
-    this.config = config;
-    if (this.config.termType == GENE_EXPRESSION) this.sampleNum = getSampleNum(config);
-    this.termType = termType;
-    this.inputs = [
-      {
-        label: "P value significance (-log\u2081\u2080)",
-        type: "number",
-        chartType: "volcano",
-        settingsKey: "pValue",
-        title: "The p-value threshold to determine statistical significance",
-        min: 0,
-        // 5e-324 is the smallest positive number greater than 0 representable
-        // in IEEE 64-bit floating point (i.e. javascripts native Number.MIN_VALUE)
-        // -Math.log10(5e-324) = 323.3
-        max: 323.3,
-        step: 1
-      },
-      {
-        label: "P value",
-        type: "radio",
-        chartType: "volcano",
-        settingsKey: "pValueType",
-        title: "Toggle between original and adjusted pvalues for volcano plot",
-        options: [
-          { label: "Adjusted", value: "adjusted" },
-          { label: "Original", value: "original" }
-        ]
-      },
-      {
-        label: "Fold change (log\u2082)",
-        type: "number",
-        chartType: "volcano",
-        settingsKey: "foldChangeCutoff",
-        title: "The fold change threshold to determine biological significance",
-        min: -10,
-        max: 10
-      },
-      //Preferably, keep all the display (e.g. colors, sizes, etc.) controls
-      //at the bottom of the list or at least together
-      {
-        label: "Plot height",
-        type: "number",
-        chartType: "volcano",
-        settingsKey: "height",
-        title: "Height of the plot in pixels",
-        min: 300,
-        max: 1e3
-      },
-      {
-        label: "Plot width",
-        type: "number",
-        chartType: "volcano",
-        settingsKey: "width",
-        title: "Width of the plot in pixels",
-        min: 300,
-        max: 1e3
-      },
-      {
-        label: "Significant value color",
-        type: "color",
-        chartType: "volcano",
-        title: "Default color for significant data points.",
-        settingsKey: "defaultSignColor",
-        getDisplayStyle: () => {
-          if (this.config.termType == SINGLECELL_CELLTYPE) return "none";
-          const controlColor = this.config.tw?.term?.values?.[this.config.samplelst.groups[0].name]?.color;
-          const caseColor = this.config.tw?.term?.values?.[this.config.samplelst.groups[1].name].color;
-          if (controlColor && caseColor) return "none";
-          else return "";
-        }
-      },
-      {
-        label: "Non-significant value color",
-        type: "color",
-        chartType: "volcano",
-        title: "Default color for non-significant data points.",
-        settingsKey: "defaultNonSignColor"
-      },
-      {
-        label: "Highlight color",
-        type: "color",
-        chartType: "volcano",
-        title: "Default color for highlighted data points.",
-        settingsKey: "defaultHighlightColor"
-      }
-    ];
-    this.setVolcanoControlInputs();
-  }
-  /** Add more term type specific controls here. */
-  setVolcanoControlInputs() {
-    this.addGeneExpControlInputs();
-    this.addDNAMethControlInputs();
-    this.addSingleCellCTControlInputs();
-  }
-  addGeneExpControlInputs() {
-    if (this.termType !== GENE_EXPRESSION) return;
-    const geInputs = [
-      {
-        label: "Minimum read count",
-        type: "number",
-        chartType: "volcano",
-        settingsKey: "minCount",
-        title: "The smallest number of reads required for a gene to be considered in the analysis",
-        min: 0,
-        max: 1e4
-      },
-      {
-        label: "Minimum total read count",
-        type: "number",
-        chartType: "volcano",
-        settingsKey: "minTotalCount",
-        title: "The smallest total number of reads required for a gene to be considered in the analysis",
-        min: 0,
-        max: 1e4
-      },
-      {
-        label: "CPM cutoff",
-        type: "number",
-        chartType: "volcano",
-        settingsKey: "cpmCutoff",
-        title: "The minimum normalized expression threshold to retain only genes with sufficient expression",
-        min: 0
-      },
-      {
-        label: "Method",
-        type: "radio",
-        chartType: "volcano",
-        settingsKey: "method",
-        title: "Toggle between analysis methods",
-        options: this.getMethodOptions()
-      }
-      // {
-      // 	label: 'Rank Genes by',
-      // 	type: 'radio',
-      // 	chartType: 'volcano',
-      // 	settingsKey: 'rankBy',
-      // 	title: 'Rank genes by either the absolute value of the fold change or the variance',
-      // 	options: [
-      // 		{ label: 'abs(Fold Change)', value: 'abs(foldChange)' },
-      // 		{ label: 'Variance', value: 'variance' }
-      // 	],
-      // 	//TODO: will enable this feature when there is backhand support
-      // 	getDisplayStyle: () => 'none'
-      // }
-    ];
-    this.inputs.splice(0, 0, ...geInputs);
-  }
-  addDNAMethControlInputs() {
-    if (this.termType !== DNA_METHYLATION) return;
-    const dmInputs = [
-      {
-        label: "Min samples per group",
-        type: "number",
-        chartType: "volcano",
-        settingsKey: "minSamplesPerGroup",
-        title: "Minimum non-NA samples required per group for a promoter to be tested",
-        min: 1,
-        max: 100
-      }
-    ];
-    this.inputs.splice(0, 0, ...dmInputs);
-  }
-  addSingleCellCTControlInputs() {
-    if (this.termType !== SINGLECELL_CELLTYPE) return;
-    const scctInputs = [];
-    this.inputs.splice(0, 0, ...scctInputs);
-  }
-  getMethodOptions() {
-    if (this.termType !== GENE_EXPRESSION) return;
-    const settings = this.config.settings.volcano;
-    const features = JSON.parse(sessionStorage.getItem("optionalFeatures"));
-    if (features?.runDE_methods?.length) {
-      const opts = [];
-      for (const m of features.runDE_methods) {
-        opts.push({ label: m, value: m.toLowerCase() });
-      }
-      return opts;
-    }
-    if (this.sampleNum < settings.sampleNumCutoff) {
-      return [
-        { label: "edgeR", value: "edgeR" },
-        { label: "Wilcoxon", value: "wilcoxon" },
-        { label: "Limma", value: "limma" }
-      ];
-    } else return [{ label: "Wilcoxon", value: "wilcoxon" }];
-  }
-};
-
-// plots/volcano/Volcano.ts
-var Volcano = class _Volcano extends PlotBase {
-  static {
-    this.type = "volcano";
-  }
-  constructor(opts, api) {
-    super(opts, api);
-    if (this.opts.parentId) this.parentId = this.opts.parentId;
-    this.type = _Volcano.type;
-    this.components = {
-      controls: {}
-    };
-    this.termType = opts.termType;
-    const holder = opts.holder.classed("sjpp-diff-analysis-main", true);
-    const controls = typeof opts.controls == "object" ? opts.controls : holder || holder.append("div");
-    const error = opts.holder.append("div").attr("id", "sjpp-diff-analysis-error").style("opacity", 0.75);
-    this.dom = {
-      holder,
-      controls,
-      error,
-      wait: holder.append("div").attr("id", "sjpp-diff-analysis-wait").style("opacity", 0.75).style("padding", "20px").text("Loading..."),
-      hoverTip: new Menu({ padding: "" }),
-      clickTip: new Menu({ padding: "" }),
-      actionsTip: new Menu({ padding: "" })
-    };
-  }
-  reactsTo(action) {
-    if (action.type.includes("cache_termq")) return true;
-    if (action.type.startsWith("filter")) return true;
-    if (action.type.startsWith("cohort")) return true;
-    if (action.type == "app_refresh") return true;
-    if (action.type.startsWith("plot_")) {
-      return (action.id === this.id || action.id == this.parentId) && (!action.config?.childType || action.config?.childType == this.type);
-    }
-  }
-  getState(appState) {
-    const config = appState.plots.find((p) => p.id === this.id);
-    if (!config) {
-      throw new Error(
-        `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`
-      );
-    }
-    const parentConfig = this.parentId && appState.plots.find((p) => p.id === this.parentId);
-    const termfilter = getCombinedTermFilter(appState, config.filter || parentConfig?.filter);
-    return {
-      config: Object.assign({}, config, {
-        settings: {
-          volcano: config.settings.volcano
-        }
-      }),
-      termfilter
-    };
-  }
-  async setControls() {
-    const plotConfig = this.app.getState().plots.find((p) => p.id === this.id);
-    const controls = new VolcanoControlInputs(plotConfig, this.termType);
-    this.components.controls = await controlsInit({
-      app: this.app,
-      id: this.id,
-      holder: this.dom.controls.style("display", "inline-block"),
-      inputs: controls.inputs
-    });
-    this.components.controls.on("downloadClick.volcano", () => this.interactions.download(this.termType));
-    if (plotConfig.chartType == "differentialAnalysis")
-      this.components.controls.on(
-        "helpClick.differentialAnalysis",
-        () => (
-          //Opens the page for the differential analysis wiki
-          //Can't put in parent as DA does not have a controls component
-          window.open("https://github.com/stjude/proteinpaint/wiki/Differential-analysis")
-        )
-      );
-  }
-  async init() {
-    this.interactions = new VolcanoInteractions(this.app, this.id, this.dom);
-    await this.setControls();
-  }
-  async main() {
-    const config = structuredClone(this.state.config);
-    if (config.chartType != this.type && config.childType != this.type) return;
-    const settings = config.settings.volcano;
-    try {
-      if (!this.interactions) throw new Error("Interactions not initialized");
-      const showWait = setTimeout(() => {
-        this.dom.wait.style("display", "block");
-      }, 500);
-      const model = new VolcanoModel(this.app, config, settings);
-      const response = await model.getData();
-      if (!response || response.error || !response.data || !response.data.length) {
-        sayerror(this.dom.error, response?.error || "No data returned from server");
-        clearTimeout(showWait);
-        this.dom.wait.style("display", "none");
-        return;
-      }
-      this.interactions.clearDom();
-      const viewModel = new VolcanoViewModel(config, response, settings);
-      this.interactions.pValueTableData = viewModel.viewData.pValueTableData;
-      this.interactions.data = response.data;
-      clearTimeout(showWait);
-      this.dom.wait.style("display", "none");
-      new VolcanoPlotView(this.dom, settings, viewModel.viewData, this.interactions, config.termType);
-    } catch (e) {
-      if (e instanceof Error) console.error(e.message || e);
-      else if (e.stack) console.log(e.stack);
-      throw e;
-    }
-  }
-};
-var volcanoInit = getCompInit(Volcano);
-var componentInit = volcanoInit;
-async function getPlotConfig(opts, app) {
-  if (!opts.termType) throw new Error(".termType is required");
-  const config = {
-    settings: {
-      volcano: getDefaultVolcanoSettings(opts.overrides, opts)
-    },
-    highlightedData: opts.highlightedData || [],
-    termType: opts.termType
-  };
-  if (opts.termType == GENE_EXPRESSION) {
-    if (opts.confounderTws) {
-      try {
-        for (const tw of opts.confounderTws) {
-          await fillTermWrapper(tw, app.vocabApi);
-        }
-      } catch (e) {
-        console.error(e.message || e);
-        throw new Error(`Volcano getPlotConfig() failed to fill confounder term wrappers: ${e}`);
-      }
-    }
-    Object.assign(config, {
-      confounderTws: opts.confounderTws || [],
-      samplelst: opts.samplelst
-    });
-  }
-  if (opts.termType == SINGLECELL_CELLTYPE) {
-    Object.assign(config, {
-      //TODO: Fix this logic
-      sample: opts.experimentID || opts.sample || opts.samples?.[0]?.experiments[0]?.experimentID,
-      termId: app.vocabApi.termdbConfig.queries.singleCell.DEgenes.termId,
-      //TODO: 'Cluster' is a fallback for development
-      //Should require opts.categoryName in the future
-      categoryName: opts.categoryName || "Cluster"
-    });
-  }
-  validateVolcanoSettings(config, opts);
-  return copyMerge(config, opts);
-}
-export {
-  componentInit,
-  getPlotConfig,
-  volcanoInit
-};
-//# sourceMappingURL=Volcano-QBYYJYVW.js.map