@sjcrh/proteinpaint-client 2.196.0 → 2.198.0

package/dist/chunk-XPMTUVSS.js

@@ -1,1220 +0,0 @@
-import {
-  getSeriesTip,
-  renderAtRiskG,
-  renderPvalues
-} from "./chunk-KI5KI3ZJ.js";
-import {
-  schemeCategory20
-} from "./chunk-V2OJLJSK.js";
-import {
-  DownloadMenu,
-  PlotBase,
-  controlsInit,
-  defaultUiLabels,
-  downloadChart,
-  fillTermWrapper,
-  getCombinedTermFilter,
-  htmlLegend,
-  rgb2hex,
-  term0_term2_defaultQ
-} from "./chunk-WY2PGUVX.js";
-import {
-  Menu
-} from "./chunk-HYOEWQ5P.js";
-import {
-  require_partjson_umd
-} from "./chunk-OVSKJROY.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-M3J4MINX.js";
-import {
-  isNumericTerm
-} from "./chunk-NNFAUP2I.js";
-import {
-  area_default,
-  category10_default,
-  line_default,
-  stepAfter
-} from "./chunk-TJYRBEBK.js";
-import {
-  axisBottom,
-  axisLeft
-} from "./chunk-LOZEKOES.js";
-import {
-  linear,
-  ordinal
-} from "./chunk-SOTB4FRE.js";
-import {
-  select_default
-} from "./chunk-I6Y4O3RR.js";
-import {
-  rgb
-} from "./chunk-OMR2DT66.js";
-import {
-  __toESM
-} from "./chunk-HFNDKYVF.js";
-
-// plots/survival/survival.ts
-var import_partjson = __toESM(require_partjson_umd(), 1);
-var t0_t2_defaultQ = structuredClone(term0_term2_defaultQ);
-Object.assign(t0_t2_defaultQ, {
-  numeric: {
-    mode: "discrete",
-    type: "custom-bin",
-    preferredBins: "median"
-  },
-  geneExpression: {
-    mode: "discrete",
-    type: "custom-bin",
-    preferredBins: "median"
-  },
-  ssGSEA: {
-    mode: "discrete",
-    type: "custom-bin",
-    preferredBins: "median"
-  },
-  isoformExpression: {
-    mode: "discrete",
-    type: "custom-bin",
-    preferredBins: "median"
-  },
-  dnaMethylation: {
-    mode: "discrete",
-    type: "custom-bin",
-    preferredBins: "median"
-  }
-});
-var TdbSurvival = class _TdbSurvival extends PlotBase {
-  constructor(opts, api) {
-    super(opts, api);
-    this.components = {};
-    // expected class-specific props
-    this.configTermKeys = ["term", "term0", "term2"];
-    this.activeMenu = false;
-    this.legendClick = (_, __, ___) => {
-    };
-    this.download = () => {
-    };
-    this.getChartImages = () => this.getChartImages();
-    this.loadingWait = 0;
-    this.legendOrder = [];
-    this.term2toColor = {};
-    this.uniqueSeriesIds = /* @__PURE__ */ new Set();
-    // TODO: migrate to this.view method
-    this.render = () => {
-    };
-    this.getSymbol = (_) => {
-      return "";
-    };
-    this.type = _TdbSurvival.type;
-    this.settings = Object.assign({}, opts.settings);
-    this.dom = this.getDom();
-    this.pj = getPj(this);
-    this.lineFxn = line_default().curve(stepAfter).x((c) => c.scaledX).y((c) => c.scaledY);
-    this.legendRenderer = htmlLegend(this.dom.legendDiv, {
-      settings: {
-        legendOrientation: "vertical"
-      },
-      handlers: {
-        legend: {
-          click: (e) => this.legendClick(e.target.__data__, e.clientX, e.clientY)
-        }
-      }
-    });
-    this.hiddenRenderer = htmlLegend(this.dom.hiddenDiv, {
-      settings: {
-        legendOrientation: "vertical"
-      },
-      handlers: {
-        legend: {
-          click: (e) => this.legendClick(e.target.__data__, e.clientX, e.clientY)
-        }
-      }
-    });
-  }
-  static {
-    this.type = "survival";
-  }
-  getDom() {
-    const opts = this.opts;
-    const holder = opts.controls ? opts.holder : opts.holder.append("div");
-    const { controls, errdiv, loadingDiv, renderedData, charts, legendDiv } = this.getStandardDomLayout(holder, opts);
-    const dom = {
-      loadingDiv,
-      header: opts.header?.html("Survival Plot"),
-      controls,
-      holder,
-      errdiv,
-      renderedData,
-      chartsDiv: charts.style("margin", "10px").style("display", "flex").style("flex-direction", "row").style("flex-wrap", "wrap").style("max-width", "100vw"),
-      legendDiv: legendDiv.style("margin", "5px 5px 15px 5px"),
-      hiddenDiv: renderedData.append("div").style("margin", "5px 5px 15px 5px"),
-      tip: new Menu({ padding: "5px" }),
-      legendTip: new Menu({ padding: "5px" })
-    };
-    dom.tip.onHide = () => {
-      this.activeMenu = false;
-    };
-    return dom;
-  }
-  async init() {
-    setInteractivity(this);
-    setRenderers(this);
-    await this.setControls();
-  }
-  async setControls() {
-    const state = this.getState(this.app.getState());
-    const controlLabels = state.config.controlLabels;
-    if (!controlLabels) throw "controls labels not found";
-    const stratDisabledMsg = this.app.vocabApi.termdbConfig?.survival?.stratificationDisabledMessage;
-    if (this.opts.controls) {
-      this.opts.controls.on("downloadClick.survival", this.download);
-    } else {
-      this.dom.holder.attr("class", "pp-termdb-plot-viz").style("display", "inline-block").style("min-width", "300px");
-      this.components = {
-        controls: await controlsInit({
-          app: this.app,
-          id: this.id,
-          holder: this.dom.controls.style("display", "inline-block"),
-          inputs: [
-            {
-              type: "term",
-              configKey: "term2",
-              chartType: "survival",
-              usecase: { target: "survival", detail: "term2" },
-              title: controlLabels.term2.title || controlLabels.term2.label,
-              label: controlLabels.term2.label,
-              vocabApi: this.app.vocabApi,
-              numericEditMenuVersion: ["discrete"],
-              defaultQ4fillTW: t0_t2_defaultQ,
-              disabledMessage: stratDisabledMsg
-            },
-            {
-              type: "term",
-              configKey: "term0",
-              chartType: "survival",
-              usecase: { target: "survival", detail: "term0" },
-              title: controlLabels.term0.title || controlLabels.term0.label,
-              label: controlLabels.term0.label,
-              vocabApi: this.app.vocabApi,
-              numericEditMenuVersion: ["discrete"],
-              defaultQ4fillTW: t0_t2_defaultQ,
-              disabledMessage: stratDisabledMsg
-            },
-            {
-              label: "Chart width",
-              type: "number",
-              chartType: "survival",
-              settingsKey: "svgw",
-              title: "The internal width of the chart plot"
-            },
-            {
-              label: "Chart height",
-              type: "number",
-              chartType: "survival",
-              settingsKey: "svgh",
-              title: "The internal height of the chart plot"
-            },
-            {
-              label: "95% Confidence Interval",
-              boxLabel: "Visible",
-              type: "checkbox",
-              chartType: "survival",
-              settingsKey: "ciVisible",
-              title: "Display the 95% confidence interval"
-            },
-            {
-              label: "Median Survival",
-              boxLabel: "Visible",
-              type: "checkbox",
-              chartType: "survival",
-              settingsKey: "medianSurvivalVisible",
-              title: "Display dashed lines indicating the median survival time (50% probability)"
-            },
-            {
-              label: "Censored Symbol",
-              type: "radio",
-              chartType: "survival",
-              settingsKey: "symbol",
-              options: [
-                { label: "Tick", value: "vtick" },
-                { label: "X", value: "x" }
-              ],
-              title: "Symbol for displaying censored samples"
-            },
-            {
-              label: "Survival Time Visualized",
-              type: "number",
-              chartType: "survival",
-              settingsKey: "maxTimeToEvent",
-              title: "The maximum time-to-event to be displayed in the survival plot, affects only the visual representation and does not impact other analyses. All available data is still used to compute p-values. If this value is left empty or set to 0, no cutoff will be applied."
-            },
-            {
-              label: "Time Unit",
-              type: "radio",
-              chartType: "survival",
-              settingsKey: "timeUnit",
-              options: [
-                { label: "years", value: "years" },
-                { label: "months", value: "months" },
-                { label: "weeks", value: "weeks" },
-                { label: "days", value: "days" }
-              ],
-              title: `The unit to display in the x-axis title, like 'years'`
-            },
-            {
-              label: "X-axis ticks",
-              type: "text",
-              chartType: "survival",
-              settingsKey: "xTickValues",
-              title: `Option to customize the x-axis tick values, enter as comma-separated values. Will be ignored if empty`,
-              processInput: (value) => value ? value.split(",").map(Number) : []
-            },
-            {
-              label: "At-risk counts",
-              boxLabel: "Visible",
-              type: "checkbox",
-              chartType: "survival",
-              settingsKey: "atRiskVisible",
-              title: "Display the at-risk counts"
-            },
-            //{label: 'At-risk label offset', type: 'numeric', chartType: 'survival', settingsKey: 'atRiskLabelOffset'},
-            {
-              label: "Default color",
-              type: "color",
-              chartType: "survival",
-              settingsKey: "defaultColor",
-              title: "Default plot color"
-            }
-          ]
-        })
-      };
-      this.components.controls.on("downloadClick.survival", this.download);
-    }
-  }
-  getState(appState) {
-    const config = appState.plots.find((p) => p.id === this.id);
-    if (!config) {
-      throw `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`;
-    }
-    const parentConfig = appState.plots.find((p) => p.id === this.parentId);
-    const termfilter = getCombinedTermFilter(appState, config.filter || parentConfig?.filter);
-    return {
-      isVisible: config.term.term.type == "survival" || config.term2?.term.type == "survival",
-      genome: this.app.vocabApi.vocab.genome,
-      dslabel: this.app.vocabApi.vocab.dslabel,
-      activeCohort: appState.activeCohort,
-      termfilter,
-      config: {
-        // NOTE: will create mutable copies of tw terms in async main() below
-        term: config.term,
-        term0: config.term0 || null,
-        term2: config.term2 || null,
-        controlLabels: config.controlLabels,
-        settings: config.settings.survival
-      },
-      termdbConfig: appState.termdbConfig
-    };
-  }
-  async main() {
-    if (!this.state.isVisible) {
-      this.dom.holder.style("display", "none");
-      return;
-    }
-    let data;
-    try {
-      this.state.config = await this.getMutableConfig();
-      this.maySetSandboxHeader();
-      this.toggleLoadingDiv();
-      Object.assign(this.settings, this.state.config.settings);
-      this.settings.defaultHidden = this.getDefaultHidden();
-      this.settings.hidden = this.settings.customHidden || this.settings.defaultHidden;
-      this.settings.xTitleLabel = this.getXtitleLabel();
-      const reqOpts = this.getDataRequestOpts();
-      data = await this.app.vocabApi.getNestedChartSeriesData(reqOpts, this.api?.getAbortSignal());
-    } catch (e) {
-      if (this.app.isAbortError(e)) return;
-      this.toggleLoadingDiv("none", "none");
-      throw e;
-    }
-    this.serverData = data;
-    this.toggleLoadingDiv("none");
-    this.app.vocabApi.syncTermData(this.state.config, data);
-    this.currData = this.processData(data);
-    this.refs = data.refs;
-    this.pj.refresh({ data: this.currData });
-    this.setTerm2Color(this.pj.tree.charts);
-    this.symbol = this.getSymbol(7);
-    this.render();
-  }
-  maySetSandboxHeader() {
-    if (!this.dom.header) return;
-    const { term, term2 } = this.state.config;
-    const mainTerm = term.term.name;
-    if (term2?.type) {
-      this.dom.header.html(`${term2.getTitleText?.() || term2.term.name}  vs ${mainTerm}`);
-    } else {
-      this.dom.header.html(`${mainTerm} plot`);
-    }
-  }
-  // creates an opts object for the vocabApi.getNestedChartsData()
-  getDataRequestOpts() {
-    const c = this.state.config;
-    const opts = {
-      chartType: "survival",
-      term: c.term,
-      filter: this.state.termfilter.filter,
-      filter0: this.state.termfilter.filter0
-    };
-    if (c.term2) {
-      opts.term2 = c.term2;
-    }
-    if (c.term0) opts.term0 = c.term0;
-    return opts;
-  }
-  getDefaultHidden() {
-    const hidden = [];
-    const term2 = this.state.config.term2;
-    if (!term2) return hidden;
-    const hiddenValues = term2.q.hiddenValues;
-    if (hiddenValues && Object.keys(hiddenValues).length) {
-      for (const k in hiddenValues) {
-        hidden.push(term2.term.values[k].label);
-      }
-    }
-    return hidden;
-  }
-  getXtitleLabel() {
-    const termNum = this.state.config.term.term.type == "survival" ? "term" : "term2";
-    const xUnit = this.settings.timeUnit ? this.settings.timeUnit : this.state.config[termNum].term.unit;
-    const xTitleLabel = `Time to Event (${xUnit})`;
-    return xTitleLabel;
-  }
-  processData(data) {
-    this.uniqueSeriesIds = /* @__PURE__ */ new Set();
-    this.msg = "";
-    const rows = [];
-    const estKeys = ["survival", "lower", "upper"];
-    for (const d of data.case) {
-      const obj = {};
-      data.keys.forEach((k, i) => {
-        obj[k] = estKeys.includes(k) ? Number(d[i]) : d[i];
-      });
-      obj.time = obj.time * this.getTimeFactor();
-      rows.push(obj);
-      this.uniqueSeriesIds.add(obj.seriesId);
-    }
-    this.tests = {};
-    if (data.tests) {
-      for (const chartId in data.tests) {
-        const chartTests = data.tests[chartId];
-        this.tests[chartId] = [];
-        for (const test of chartTests) {
-          if (this.settings.hidden.includes(test.series1) || this.settings.hidden.includes(test.series2)) continue;
-          this.tests[chartId].push({
-            pvalue: { id: "pvalue", text: test.pvalue },
-            series1: { id: test.series1 },
-            series2: { id: test.series2 }
-          });
-        }
-        if (!this.tests[chartId].length) delete this.tests[chartId];
-      }
-    }
-    if (data.refs.byTermId) {
-      const byTermId = data.refs.byTermId;
-      const msg = byTermId[this.state.config.term.term.id]?.survMsg;
-      if (msg) {
-        this.msg = msg;
-      }
-    }
-    return rows;
-  }
-  // time factor that converts survival data from default time unit to the current time unit.
-  getTimeFactor() {
-    const numUnitInOneYear = this.settings.numUnitInOneYear || 1;
-    const timeUnit = this.settings.timeUnit || "years";
-    switch (timeUnit) {
-      case "years":
-        return 1 / numUnitInOneYear * 1;
-      case "months":
-        return 1 / numUnitInOneYear * 12;
-      case "weeks":
-        return 1 / numUnitInOneYear * 52;
-      case "days":
-        return 1 / numUnitInOneYear * 365.25;
-      default:
-        throw "unknown time Unit for survival data";
-    }
-  }
-  setTerm2Color(charts) {
-    if (!charts) return;
-    const config = this.state.config;
-    const t2values = copyMerge({}, config.term2?.term?.values || {}, config.term2?.values || {});
-    const values = this.refs.bins[2] && [this.refs.bins[2]] || Object.values(t2values);
-    let t2groups;
-    if (config.term2?.q.type == "predefined-groupset" || config.term2?.q.type == "custom-groupset") {
-      const groupset = config.term2.q.type == "predefined-groupset" ? config.term2.term.groupsetting.lst[config.term2.q.predefined_groupset_idx] : config.term2.q.customset;
-      if (!groupset) throw "groupset is missing";
-      t2groups = groupset.groups;
-    }
-    this.term2toColor = {};
-    this.colorScale = this.uniqueSeriesIds.size < 11 ? ordinal(category10_default) : ordinal(schemeCategory20);
-    const legendItems = [];
-    for (const chart of charts) {
-      for (const series of chart.serieses) {
-        let color;
-        const v = values.find(
-          (v2) => v2.seriesId === series.seriesId || v2.key === series.seriesId || v2.name === series.seriesId || v2.label === series.seriesId
-        );
-        color = v?.color;
-        if (!color && t2groups?.length) {
-          const group = t2groups.find((g) => g.name == series.seriesId);
-          color = group?.color;
-          if (color === "#D3D3D3" && group?.filter?.lst?.find((f) => f?.type === "tvs" && f.tvs.genotype == "wt"))
-            color = "rgb(105,105,105)";
-        }
-        const orig = color || (series.seriesId == "" ? this.settings.defaultColor : this.colorScale(series.seriesId));
-        const _rgb = rgb(orig);
-        const adjusted = _rgb.toString();
-        const c = { orig, rgb: _rgb, adjusted, hex: rgb2hex(adjusted) };
-        this.term2toColor[series.seriesId] = c;
-        if (!legendItems.find((d) => d.seriesId == series.seriesId)) {
-          legendItems.push({
-            key: series.seriesId,
-            seriesId: series.seriesId,
-            text: series.seriesLabel,
-            color: this.term2toColor[series.seriesId].adjusted,
-            isHidden: this.settings.hidden.includes(series.seriesId)
-          });
-        }
-      }
-    }
-    if (this.refs.orderedKeys) {
-      const s = this.refs.orderedKeys.series;
-      legendItems.sort((a, b) => s.indexOf(a.seriesId) - s.indexOf(b.seriesId));
-    }
-    if (!this.legendOrder.length) {
-      this.legendOrder = legendItems.map((item) => item.seriesId);
-    } else {
-      legendItems.sort((a, b) => this.legendOrder.indexOf(a.seriesId) - this.legendOrder.indexOf(b.seriesId));
-    }
-    if ((config.term.term.type == "survival" || config.term2) && legendItems.length) {
-      const termNum = config.term.term.type == "survival" && config.term2 ? "term2" : "term";
-      this.legendData = [
-        {
-          name: config[termNum].term.name,
-          items: legendItems.filter((s) => !s.isHidden)
-        }
-      ];
-      this.hiddenData = [
-        {
-          name: `<span style='color:#aaa; font-weight:400'><span>Hidden categories</span><span style='font-size:0.8rem'> CLICK TO SHOW</span></span>`,
-          items: legendItems.filter((s) => s.isHidden).map((item) => Object.assign({}, item, { isHidden: false }))
-        }
-      ];
-    } else {
-      this.legendData = [];
-    }
-    for (const chartId in this.tests) {
-      const chartTests = this.tests[chartId];
-      for (const test of chartTests) {
-        for (const key in test) {
-          if (key == "pvalue") {
-            test[key].color = "#000";
-          } else {
-            const item = legendItems.find((item2) => item2.seriesId == test[key].id);
-            test[key].color = item.color;
-            test[key].text = item.text;
-          }
-        }
-      }
-    }
-  }
-};
-var survivalInit = getCompInit(TdbSurvival);
-var componentInit = survivalInit;
-function setRenderers(self) {
-  self.render = function() {
-    const data = self.pj.tree.charts || [{ chartId: "No survival data" }];
-    const chartDivs = self.dom.chartsDiv.selectAll(".pp-survival-chart").data(data, (d) => d.chartId);
-    chartDivs.exit().remove();
-    chartDivs.each(self.updateCharts);
-    chartDivs.enter().each(self.addCharts);
-    self.dom.holder.style("display", "inline-block");
-    self.dom.chartsDiv.on("mouseover", self.mouseover).on("mouseout", self.mouseout);
-    self.legendRenderer(self.settings.atRiskVisible ? [] : self.legendData);
-    if (!self.hiddenData?.[0]?.items.length) self.dom.hiddenDiv.style("display", "none");
-    else {
-      self.dom.hiddenDiv.style("display", "");
-      self.hiddenRenderer(self.hiddenData);
-    }
-  };
-  const updateHiddenPvalues = (hiddenPvalues) => {
-    self.app.dispatch({
-      type: "plot_edit",
-      id: self.id,
-      config: {
-        settings: {
-          survival: {
-            hiddenPvalues
-          }
-        }
-      }
-    });
-  };
-  const setActiveMenu = (bool) => self.activeMenu = bool;
-  self.addCharts = function(chart) {
-    const s = self.settings;
-    setVisibleSerieses(chart, s);
-    const div = select_default(this).append("div").attr("class", "pp-survival-chart").style("opacity", chart.serieses ? 0 : 1).style("width", "fit-content").style("display", "inline-block").style("margin", s.chartMargin + "px").style("padding", "10px").style("top", 0).style("left", 0).style("text-align", "left").style("vertical-align", "top");
-    div.append("div").style("width", s.svgw + 50 + "px").style("height", s.chartTitleDivHt + "px").style("text-align", "center").style("font-weight", "600").style("margin", "5px").append("div").attr("class", "sjpp-survival-title").attr("data-testid", "sjpp-survival-plotTitle").style("display", "inline-block").style("width", "fit-content").datum(chart).html((chart2) => chart2.chartId);
-    if (chart.serieses) {
-      const svg = div.append("svg").attr("class", "pp-survival-svg");
-      renderSVG(svg, chart, s, 0);
-      div.transition().duration(s.duration).style("opacity", 1);
-      div.append("div").attr("class", "pp-survival-chartLegends").style("vertical-align", "top").style("margin", "10px 10px 10px 10px").style("display", "none");
-      if (self.tests && chart.rawChartId in self.tests) {
-        const holder = div.select(".pp-survival-chartLegends").style("display", "inline-block").append("div").style("margin-bottom", "30px");
-        renderPvalues({
-          title: "Group comparisons (log-rank test)",
-          holder,
-          plot: "survival",
-          tests: self.tests[chart.rawChartId],
-          s,
-          bins: self.refs.bins,
-          tip: self.app.tip,
-          setActiveMenu,
-          updateHiddenPvalues
-        });
-      }
-      if (self.msg) {
-        const fontSize = s.axisTitleFontSize ? s.axisTitleFontSize - 2 : 15;
-        const holder = div.select(".pp-survival-chartLegends").style("display", "inline-block").append("div");
-        holder.style("font-size", fontSize + "px").style("font-style", "italic").text(self.msg);
-      }
-    }
-  };
-  function setVisibleSerieses(chart, s) {
-    chart.visibleSerieses = chart.serieses?.filter((series) => !s.hidden.includes(series.seriesId)) || [];
-    const maxSeriesLabelLen = chart.visibleSerieses.reduce(
-      (maxlen, a) => a.seriesLabel && a.seriesLabel.length > maxlen ? a.seriesLabel.length : maxlen,
-      0
-    );
-    const extraPaddingForNoOverlay = maxSeriesLabelLen === 0 ? s.atRiskNoOverlayExtraPadding : 0;
-    chart.atRiskLabelWidth = s.atRiskVisible ? maxSeriesLabelLen * (s.axisTitleFontSize - 2) * 0.4 + s.atRiskLabelOffset + extraPaddingForNoOverlay : 0;
-  }
-  self.updateCharts = function(chart) {
-    if (!chart.serieses) return;
-    const s = self.settings;
-    setVisibleSerieses(chart, s);
-    const div = select_default(this);
-    div.transition().duration(s.duration).style("width", "fit-content");
-    div.select(".sjpp-survival-title").style("width", s.svgw + 50).style("height", s.chartTitleDivHt + "px").datum(chart.chartId).html(chart.chartId);
-    div.selectAll(".sjpp-lock-icon").style("display", s.scale == "byChart" ? "block" : "none");
-    div.selectAll(".sjpp-unlock-icon").style("display", s.scale == "byChart" ? "none" : "block");
-    renderSVG(div.select("svg"), chart, s, s.duration);
-    div.select(".pp-survival-chartLegends").style("display", "none").selectAll("*").remove();
-    if (self.tests && chart.rawChartId in self.tests) {
-      const holder = div.select(".pp-survival-chartLegends").style("display", "inline-block").append("div").style("margin-bottom", "30px");
-      renderPvalues({
-        title: "Group comparisons (log-rank test)",
-        holder,
-        plot: "survival",
-        tests: self.tests[chart.rawChartId],
-        s,
-        bins: self.refs.bins,
-        tip: self.app.tip,
-        setActiveMenu,
-        updateHiddenPvalues
-      });
-    }
-    if (self.msg) {
-      const fontSize = s.axisTitleFontSize ? s.axisTitleFontSize - 2 : 15;
-      const holder = div.select(".pp-survival-chartLegends").style("display", "inline-block").append("div");
-      holder.style("font-size", fontSize + "px").style("font-style", "italic").text(self.msg);
-    }
-  };
-  function renderSVG(svg, chart, s, duration) {
-    chart.svg = svg;
-    const extraHeight = s.atRiskVisible ? s.axisTitleFontSize + 4 + chart.visibleSerieses.length * 2 * (s.axisTitleFontSize + 4) : 0;
-    svg.transition().duration(duration).attr("width", s.svgw + chart.atRiskLabelWidth).attr("height", s.svgh + extraHeight).style("overflow", "visible").style("padding-left", "5px");
-    const [mainG, seriesesG, axisG, xAxis, yAxis, xTitle, yTitle, atRiskG, plotRect, medianSurvivalG] = getSvgSubElems(svg);
-    const xOffset = chart.atRiskLabelWidth + s.svgPadding.left + 10;
-    mainG.attr("transform", "translate(" + xOffset + "," + s.svgPadding.top + ")");
-    const serieses = seriesesG.selectAll(".sjpp-survival-series").data(chart.visibleSerieses, (d) => d && d[0] ? d[0].seriesId : "");
-    serieses.exit().remove();
-    serieses.each(function(series, i) {
-      renderSeries(select_default(this), chart, series, i, s);
-    });
-    serieses.enter().append("g").attr("class", "sjpp-survival-series").each(function(series, i) {
-      renderSeries(select_default(this), chart, series, i, s);
-    });
-    renderAxes(xAxis, xTitle, yAxis, yTitle, s, chart);
-    renderMedianSurvival(medianSurvivalG, chart, s);
-    renderAtRiskG({
-      g: atRiskG,
-      s,
-      chart,
-      order: self.legendOrder,
-      term2toColor: self.term2toColor,
-      onSerieClick: self.legendClick
-    });
-    plotRect.attr("x", 0).attr("width", s.svgw - s.svgPadding.left - s.svgPadding.right).attr("y", 0).attr("height", s.svgh - s.svgPadding.top - s.svgPadding.bottom + s.xAxisOffset);
-    svg.seriesTip.update({
-      xScale: chart.xScale,
-      xTitleLabel: s.xTitleLabel,
-      decimals: s.seriesTipDecimals,
-      serieses: chart.visibleSerieses.map((s2) => {
-        const seriesLabel = `${s2.seriesLabel || "Probability"}:`;
-        const color = self.term2toColor[s2.seriesId].adjusted || "#000";
-        return {
-          data: s2.data.map((d) => {
-            return {
-              x: d.x,
-              html: `<span style='color: ${color}'>${seriesLabel} ${(100 * d.y).toFixed(2)}% (${(100 * d.lower).toFixed(2)} - ${(100 * d.upper).toFixed(
-                2
-              )})</span>`
-            };
-          })
-        };
-      })
-    });
-  }
-  function getSvgSubElems(svg) {
-    let mainG, seriesesG, axisG, xAxis, yAxis, xTitle, yTitle, atRiskG, plotRect, line, medianSurvivalG;
-    if (!svg.select(".sjpp-survival-mainG").size()) {
-      mainG = svg.append("g").attr("class", "sjpp-survival-mainG");
-      seriesesG = mainG.append("g").attr("class", "sjpcb-survival-seriesesG");
-      medianSurvivalG = mainG.append("g").attr("class", "sjpp-survival-median");
-      axisG = mainG.append("g").attr("class", "sjpp-survival-axis");
-      xAxis = axisG.append("g").attr("class", "sjpp-survival-x-axis");
-      yAxis = axisG.append("g").attr("class", "sjpp-survival-y-axis");
-      xTitle = axisG.append("g").attr("class", "sjpp-survival-x-title");
-      yTitle = axisG.append("g").attr("class", "sjpp-survival-y-title");
-      atRiskG = mainG.append("g").attr("class", "sjpp-survival-atrisk");
-      line = mainG.append("line").attr("class", "sjpcb-plot-tip-line").attr("stroke", "#000").attr("stroke-width", "1px");
-      plotRect = mainG.append("rect").attr("class", "sjpcb-plot-tip-rect").style("fill", "transparent");
-    } else {
-      mainG = svg.select(".sjpp-survival-mainG");
-      seriesesG = mainG.select(".sjpcb-survival-seriesesG");
-      medianSurvivalG = mainG.select(".sjpp-survival-median");
-      axisG = mainG.select(".sjpp-survival-axis");
-      xAxis = axisG.select(".sjpp-survival-x-axis");
-      yAxis = axisG.select(".sjpp-survival-y-axis");
-      xTitle = axisG.select(".sjpp-survival-x-title");
-      yTitle = axisG.select(".sjpp-survival-y-title");
-      atRiskG = mainG.select(".sjpp-survival-atrisk");
-      plotRect = mainG.select(".sjpcb-plot-tip-rect");
-      line = mainG.select(".sjpcb-plot-tip-line");
-    }
-    if (!svg.seriesTip) {
-      svg.seriesTip = getSeriesTip(line, plotRect, self.dom.tip);
-    }
-    return [mainG, seriesesG, axisG, xAxis, yAxis, xTitle, yTitle, atRiskG, plotRect, medianSurvivalG];
-  }
-  function renderSeries(g, chart, series, i, s) {
-    let processedData = series.data;
-    if (s.maxTimeToEvent) {
-      processedData = series.data.filter((d) => d.x <= s.maxTimeToEvent);
-    }
-    g.selectAll("path").remove();
-    g.append("path").attr(
-      "d",
-      area_default().curve(stepAfter).x((c) => c.scaledX).y0((c) => c.scaledY[1]).y1((c) => c.scaledY[2])(processedData)
-    ).style("display", s.ciVisible ? "" : "none").style("fill", self.term2toColor[series.seriesId].adjusted).style("opacity", "0.15").style("stroke", "none");
-    renderSubseries(
-      s,
-      g,
-      processedData.map((d) => {
-        return {
-          seriesId: d.seriesId,
-          x: d.x,
-          y: d.y,
-          scaledX: d.scaledX,
-          scaledY: d.scaledY[0],
-          seriesName: "survival",
-          seriesLabel: series.seriesLabel,
-          nevent: d.nevent,
-          ncensor: d.ncensor,
-          nrisk: d.nrisk
-        };
-      })
-    );
-    renderSubseries(
-      s,
-      g.append("g"),
-      processedData.map((d) => {
-        return {
-          seriesId: d.seriesId,
-          x: d.x,
-          y: d.lower,
-          scaledX: d.scaledX,
-          scaledY: d.scaledY[1],
-          seriesName: "lower",
-          seriesLabel: series.seriesLabel,
-          nevent: d.nevent,
-          ncensor: 0,
-          // no censor marks for lower CI
-          nrisk: d.nrisk
-        };
-      })
-    );
-    renderSubseries(
-      s,
-      g.append("g"),
-      processedData.map((d) => {
-        return {
-          seriesId: d.seriesId,
-          x: d.x,
-          y: d.upper,
-          scaledX: d.scaledX,
-          scaledY: d.scaledY[2],
-          seriesName: "upper",
-          // no censor marks for upper CI
-          seriesLabel: series.seriesLabel,
-          nevent: d.nevent,
-          ncensor: 0,
-          nrisk: d.nrisk
-        };
-      })
-    );
-  }
-  function renderSubseries(s, g, data) {
-    g.selectAll("g").remove();
-    const lineData = data.filter((d, i) => i === 0 || d.nevent || i === data.length - 1);
-    const censoredData = data.filter((d) => d.ncensor);
-    const seriesName = data[0].seriesName;
-    const color = self.term2toColor[data[0].seriesId].adjusted;
-    if (seriesName == "survival") {
-      g.append("path").attr("d", self.lineFxn(lineData)).style("fill", "none").style("stroke", color).style("opacity", 1).style("stroke-opacity", 1);
-    }
-    const subg1 = g.append("g").attr("class", "sjpp-survival-censored");
-    const censored = subg1.selectAll(".sjpp-survival-censored-x").data(censoredData, (d) => d.x);
-    censored.exit().remove();
-    censored.attr("transform", (c) => `translate(${c.scaledX},${c.scaledY})`).style("stroke", color).style("display", "");
-    censored.enter().append("path").attr("class", "sjpp-survival-censored-x").attr("transform", (c) => `translate(${c.scaledX},${c.scaledY})`).attr("d", self.symbol).style("fill", "transparent").style("fill-opacity", s.fillOpacity).style("stroke", color).style("display", "");
-  }
-  function renderAxes(xAxis, xTitle, yAxis, yTitle, s, chart) {
-    let xTicks;
-    if (s.xTickValues?.length) {
-      chart.xTickValues = s.xTickValues.filter(
-        (v) => v === 0 || v >= chart.xMin && v <= Math.min(s.maxTimeToEvent || chart.xMax, chart.xMax)
-      );
-      xTicks = axisBottom(chart.xScale).tickValues(chart.xTickValues);
-    } else {
-      chart.xTickValues = [];
-      xTicks = axisBottom(chart.xScale).ticks(4).tickFormat((xval) => {
-        chart.xTickValues.push(xval);
-        return xval;
-      });
-    }
-    const pixelOffset = -0.5;
-    xAxis.attr(
-      "transform",
-      `translate(${pixelOffset}, ${s.svgh - s.svgPadding.top - s.svgPadding.bottom + s.xAxisOffset + pixelOffset})`
-    ).call(xTicks);
-    yAxis.attr("transform", `translate(${s.yAxisOffset + pixelOffset}, ${pixelOffset})`).call(axisLeft(linear().domain(chart.yScale.domain()).range(chart.yScale.range())).ticks(5));
-    xTitle.select("text, title").remove();
-    xTitle.attr(
-      "transform",
-      "translate(" + (s.svgw - s.svgPadding.left - s.svgPadding.right) / 2 + "," + (s.svgh - s.axisTitleFontSize - 4) + ")"
-    ).append("text").style("text-anchor", "middle").style("font-size", s.axisTitleFontSize + "px").text(s.xTitleLabel);
-    const yTitleLabel = "Probability of Survival";
-    yTitle.select("text, title").remove();
-    yTitle.attr(
-      "transform",
-      "translate(" + (-s.svgPadding.left / 2 - s.axisTitleFontSize) + "," + (s.svgh - s.svgPadding.top - s.svgPadding.bottom) / 2 + ")rotate(-90)"
-    ).append("text").style("text-anchor", "middle").style("font-size", s.axisTitleFontSize + "px").text(yTitleLabel);
-  }
-  function renderMedianSurvival(g, chart, s) {
-    g.selectAll("*").remove();
-    if (!s.medianSurvivalVisible) return;
-    const yMid = chart.yScale(0.5);
-    const yBottom = chart.yScale(0);
-    const getMedianPoint = (series) => {
-      const data = s.maxTimeToEvent ? series.data.filter((d) => d.x <= s.maxTimeToEvent) : series.data;
-      return data.find((d) => d.y <= 0.5);
-    };
-    const medianScaledXs = [];
-    for (const series of chart.visibleSerieses) {
-      const medianPoint = getMedianPoint(series);
-      if (medianPoint) medianScaledXs.push(chart.xScale(medianPoint.x));
-    }
-    if (!medianScaledXs.length) return;
-    g.append("line").attr("x1", 0).attr("y1", yMid).attr("x2", Math.max(...medianScaledXs)).attr("y2", yMid).attr("stroke", "#000").attr("stroke-width", 1).attr("stroke-dasharray", "4,4");
-    for (const scaledX of medianScaledXs) {
-      g.append("line").attr("x1", scaledX).attr("y1", yMid).attr("x2", scaledX).attr("y2", yBottom).attr("stroke", "#000").attr("stroke-width", 1).attr("stroke-dasharray", "4,4");
-    }
-  }
-  self.getSymbol = function(size) {
-    const s = size, h = s / 2;
-    switch (self.settings.symbol) {
-      case "x":
-        return `M -${h},-${h} l ${s},${s} M ${h},-${h} l -${s},${s}`;
-      case "vtick":
-        return `M 0,-${h} L 0,${h}`;
-      default:
-        throw `Unrecognized survival plot symbol='${self.settings.symbol}'`;
-    }
-  };
-}
-function setInteractivity(self) {
-  self.download = function(event) {
-    const charts = self.getChartImages();
-    const menu = new DownloadMenu(charts, self.state.config.term.term.name);
-    menu.show(event.clientX, event.clientY, event.target);
-  };
-  self.getChartImages = function() {
-    const charts = [];
-    if (!self.pj.tree.charts) return charts;
-    for (const chart of self.pj.tree.charts) {
-      charts.push({ name: chart.chartId, svg: chart.svg });
-    }
-    return charts;
-  };
-  self.mouseover = function() {
-  };
-  self.mouseout = function() {
-    if (self.activeMenu) return;
-    self.app.tip.hide();
-  };
-  self.legendClick = function(d, x, y) {
-    if (d === void 0) return;
-    const hidden = self.settings.hidden.slice();
-    const i = hidden.indexOf(d.seriesId);
-    if (i == -1) {
-      hidden.push(d.seriesId);
-      self.showLegendItemMenu(d, hidden, x, y);
-    } else {
-      hidden.splice(i, 1);
-      self.app.dispatch({
-        type: "plot_edit",
-        id: self.id,
-        config: {
-          settings: {
-            survival: {
-              customHidden: hidden
-            }
-          }
-        }
-      });
-    }
-  };
-  self.showLegendItemMenu = function(d, hidden, x, y) {
-    const term2 = self.state.config.term2?.term || null;
-    const seriesLabel = term2?.values?.[d.seriesId]?.label || d.seriesId;
-    const header = `<div style='padding-bottom:8px'><b>${seriesLabel}</b></div>`;
-    const data = d.seriesId || d.seriesId === 0 ? d : { seriesId: d.id, dataId: d.dataId };
-    if (!data.seriesId && !data.dataId) {
-      if (!term2) {
-        const label = self.dom.legendTip.clear().d.append("div").html("Edit color: ");
-        const input = label.append("input").attr("type", "color").attr("value", self.settings.defaultColor).on("change", () => self.adjustColor(input.property("value"), d));
-        self.dom.legendTip.show(x, y);
-      }
-      return;
-    }
-    const options = [];
-    options.push({
-      label: "Hide",
-      callback: () => {
-        menu.hide();
-        self.app.dispatch({
-          type: "plot_edit",
-          id: self.id,
-          config: {
-            settings: {
-              survival: {
-                customHidden: hidden
-              }
-            }
-          }
-        });
-      }
-    });
-    if (self.legendData[0]?.items.length > 1) {
-      options.push({
-        label: "Move&nbsp;",
-        setInput: (holder) => {
-          const legendIndex = self.legendOrder.indexOf(d.seriesId);
-          if (legendIndex != 0)
-            holder.append("button").html("up").on("click", () => {
-              menu.hide();
-              self.adjustLegendOrder(d, -1);
-            });
-          if (legendIndex < self.legendData[0]?.items.length - 1)
-            holder.append("button").html("down").on("click", () => {
-              menu.hide();
-              self.adjustLegendOrder(d, 1);
-            });
-        }
-      });
-    }
-    options.push({
-      //label: 'Color',
-      //callback: d => {}
-      setInput: (holder) => {
-        const label = holder.append("div");
-        label.html("Edit color: ");
-        const input = label.append("input").attr("type", "color").attr("value", self.term2toColor[d.seriesId].hex).on("change", () => self.adjustColor(input.property("value"), d));
-      }
-    });
-    if (!options.length) return;
-    const menu = self.dom.legendTip.clear();
-    menu.d.append("div").html(header);
-    menu.d.append("div").selectAll("div").data(options).enter().append("div").attr("class", (d2) => d2.label == "Hide" ? "sja_menuoption" : "sja_menuoption_not_interactive").on("click", (event, c) => {
-      if (c.setInput) return;
-      self.app.tip.hide();
-      c.callback(d);
-    }).each(function(d2) {
-      const div = select_default(this);
-      if (d2.label) div.append("div").style("display", "inline-block").html(d2.label);
-      if (d2.setInput)
-        d2.setInput(
-          div.append("div").style("display", "inline-block")
-          //.style('margin-left', '10px')
-        );
-    });
-    menu.show(x, y);
-  };
-  self.adjustLegendOrder = (d, increment) => {
-    const oldIndex = self.legendOrder.indexOf(d.seriesId);
-    if (oldIndex == -1) return;
-    let newIndex = oldIndex + increment;
-    newIndex = Math.max(0, Math.min(self.legendOrder.length - 1, newIndex));
-    self.legendOrder.splice(oldIndex, 1);
-    self.legendOrder.splice(newIndex, 0, d.seriesId);
-    self.app.dispatch({
-      type: "app_refresh"
-    });
-    self.app.tip.hide();
-  };
-  self.adjustColor = (value, d) => {
-    const color = rgb(value).formatHex();
-    const t2 = self.state.config.term2;
-    if (!t2) {
-      self.app.dispatch({
-        type: "plot_edit",
-        id: self.id,
-        config: { settings: { survival: { defaultColor: color } } }
-      });
-    } else {
-      const term2 = structuredClone(t2);
-      if (!term2.values) term2.values = {};
-      const values = term2.values;
-      if (!values[d.seriesId]) values[d.seriesId] = {};
-      if (!("key" in values[d.seriesId])) values[d.seriesId].key = d.seriesId;
-      values[d.seriesId].color = color;
-      self.app.dispatch({
-        type: "plot_edit",
-        id: self.id,
-        config: {
-          term2
-        }
-      });
-    }
-    self.app.tip.hide();
-  };
-  self.showMenuForSelectedChart = function() {
-    self.dom.tip.clear();
-    self.activeMenu = true;
-    self.dom.tip.showunder(this).d.append("button").html("Download SVG").on("click", () => {
-      if (!self.state) return;
-      const chartDiv = select_default(this.closest(".pp-survival-chart"));
-      downloadChart(
-        chartDiv.select(".sjpp-survival-mainG"),
-        "Survival_Plot",
-        chartDiv.node()
-        // use to get computed styles
-      );
-    });
-  };
-}
-async function getPlotConfig(opts, app) {
-  if (!opts.term) throw "survival getPlotConfig: opts.term{} missing";
-  try {
-    await fillTermWrapper(opts.term, app.vocabApi);
-    if (opts.term2)
-      await fillTermWrapper(opts.term2, app.vocabApi, opts.term2.bins || opts.term2.q ? void 0 : t0_t2_defaultQ);
-    if (opts.term0)
-      await fillTermWrapper(opts.term0, app.vocabApi, opts.term0.bins || opts.term0.q ? void 0 : t0_t2_defaultQ);
-  } catch (e) {
-    throw `${e} [survival getPlotConfig()]`;
-  }
-  const config = {
-    controlLabels: Object.assign({}, defaultUiLabels, app.vocabApi.termdbConfig.uiLabels || {}),
-    settings: {
-      controls: {
-        term2: null,
-        // the previous overlay value may be displayed as a convenience for toggling
-        term0: null
-      },
-      survival: {
-        radius: 5,
-        ciVisible: true,
-        medianSurvivalVisible: false,
-        fill: "#fff",
-        stroke: "#000",
-        symbol: "vtick",
-        // 'x', 'vtick'
-        fillOpacity: 0,
-        chartMargin: 10,
-        svgw: 400,
-        svgh: 300,
-        numUnitInOneYear: 1,
-        timeUnit: "years",
-        atRiskVisible: true,
-        atRiskLabelOffset: -20,
-        atRiskNoOverlayExtraPadding: 30,
-        // Extra padding when there's no overlay term to prevent "Number at risk" text overlap
-        xTickValues: [],
-        // if undefined or empty, will be ignored
-        seriesTipDecimals: 1,
-        svgPadding: {
-          top: 20,
-          left: 55,
-          right: 20,
-          bottom: 50
-        },
-        axisTitleFontSize: 16,
-        xAxisOffset: 5,
-        yAxisOffset: -5,
-        hiddenPvalues: [],
-        defaultColor: "#2077b4"
-      }
-    }
-  };
-  const overrides = app.vocabApi.termdbConfig.survival || {};
-  copyMerge(config.settings.survival, overrides.settings);
-  return copyMerge(config, opts);
-}
-function getPj(self) {
-  const pj = new import_partjson.default({
-    template: {
-      yMin: ">=yMin()",
-      yMax: "<=yMax()",
-      charts: [
-        {
-          chartId: "@key",
-          rawChartId: "$chartId",
-          xMin: ">$time",
-          xMax: "<$time",
-          "__:xScale": "=xScale()",
-          "__:yScale": "=yScale()",
-          yMin: ">=yMin()",
-          yMax: "<=yMax()",
-          serieses: [
-            {
-              chartId: "@parent.@parent.@key",
-              seriesId: "@key",
-              "__:seriesLabel": "=seriesLabel()",
-              data: [
-                {
-                  "__:seriesId": "@parent.@parent.seriesId",
-                  //color: "$color",
-                  x: "$time",
-                  y: "$survival",
-                  lower: "$lower",
-                  upper: "$upper",
-                  "_1:scaledX": "=scaledX()",
-                  "_1:scaledY": "=scaledY()",
-                  nevent: "$nevent",
-                  ncensor: "$ncensor",
-                  nrisk: "$nrisk"
-                },
-                "=timeCensored()"
-              ]
-            },
-            "$seriesId"
-          ],
-          "@done()": "=sortSerieses()"
-        },
-        "=chartTitle()"
-      ],
-      "@done()": "=sortCharts()"
-    },
-    "=": {
-      chartTitle(row) {
-        if (!row.chartId || row.chartId == "-") {
-          const termNum = self.state.config.term.term.type == "survival" ? "term" : "term2";
-          return self.state.config[termNum].term.name;
-        }
-        const t0 = self.state.config.term0;
-        if (!t0 || !t0.term.values) return row.chartId;
-        if (t0.q?.type == "predefined-groupset" || t0.q?.type == "custom-groupset") return row.chartId;
-        const value = self.state.config.term0.term.values[row.chartId];
-        return value && value.label ? value.label : row.chartId;
-      },
-      seriesLabel(row, context) {
-        const t2 = self.state.config.term2;
-        if (!t2) return;
-        const seriesId = context.self.seriesId;
-        if (t2?.q?.type == "predefined-groupset" || t2?.q?.type == "custom-groupset") return seriesId;
-        if (t2 && t2.term.values && seriesId in t2.term.values) return t2.term.values[seriesId].label;
-        if (isNumericTerm(t2.term)) {
-          return t2.term.name + " " + seriesId;
-        }
-        return seriesId;
-      },
-      timeCensored(row) {
-        return row.time + "-" + row.ncensor;
-      },
-      y(row, context) {
-        const seriesId = context.context.parent.seriesId;
-        return seriesId == "CI" ? [row.lower, row.upper] : row[seriesId];
-      },
-      yMin(row) {
-        return row.lower;
-      },
-      yMax(row) {
-        return row.upper;
-      },
-      xScale(_, context) {
-        const s = self.settings;
-        return linear().domain([0, Math.min(s.maxTimeToEvent || context.self.xMax, context.self.xMax)]).range([0, s.svgw - s.svgPadding.left - s.svgPadding.right]);
-      },
-      scaledX(_, context) {
-        return context.context.context.context.parent.xScale(context.self.x);
-      },
-      scaledY(_, context) {
-        const yScale = context.context.context.context.parent.yScale;
-        const s = context.self;
-        return [yScale(s.y), yScale(s.lower), yScale(s.upper)];
-      },
-      yScale() {
-        const s = self.settings;
-        const domain = [1.05, 0];
-        return linear().domain(domain).range([0, s.svgh - s.svgPadding.top - s.svgPadding.bottom]);
-      },
-      sortSerieses(result) {
-        for (const series of result.serieses) {
-          series.data.sort((a, b) => a.x < b.x ? -1 : 1);
-        }
-        if (self.refs.orderedKeys) {
-          const s = self.refs.orderedKeys.series;
-          result.serieses.sort((a, b) => s.indexOf(a.seriesId) - s.indexOf(b.seriesId));
-        }
-        if (self.refs.bins) {
-          const labelOrder = self.refs.bins.map((b) => b.label);
-          result.serieses.sort((a, b) => labelOrder.indexOf(a.seriesId) - labelOrder.indexOf(b.seriesId));
-        }
-      },
-      sortCharts(result) {
-        if (!self.refs.orderedKeys) return;
-        const c = self.refs.orderedKeys.chart;
-        result.charts.sort(
-          (a, b) => (c.indexOf(a.chartId) == -1 ? c.indexOf(a.rawChartId) : c.indexOf(a.chartId)) - (c.indexOf(b.chartId) == -1 ? c.indexOf(b.rawChartId) : c.indexOf(b.chartId))
-        );
-      }
-    }
-  });
-  return pj;
-}
-
-export {
-  t0_t2_defaultQ,
-  survivalInit,
-  componentInit,
-  getPlotConfig
-};
-//# sourceMappingURL=chunk-XPMTUVSS.js.map