@sjcrh/proteinpaint-client 2.181.0 → 2.182.0

package/dist/chunk-SPAIFVM2.js

@@ -0,0 +1,1155 @@
+import {
+  getSeriesTip,
+  renderAtRiskG,
+  renderPvalues
+} from "./chunk-KISFQDQE.js";
+import {
+  schemeCategory20
+} from "./chunk-V2OJLJSK.js";
+import {
+  DownloadMenu,
+  PlotBase,
+  controlsInit,
+  defaultUiLabels,
+  downloadChart,
+  fillTermWrapper,
+  getCombinedTermFilter,
+  htmlLegend,
+  rgb2hex,
+  term0_term2_defaultQ
+} from "./chunk-7FEHI46K.js";
+import {
+  Menu
+} from "./chunk-2SRMRC6L.js";
+import {
+  copyMerge,
+  getCompInit
+} from "./chunk-MVTCBVSX.js";
+import {
+  require_partjson_umd
+} from "./chunk-DVDDXOWT.js";
+import {
+  isNumericTerm
+} from "./chunk-MDL2HG3N.js";
+import {
+  area_default,
+  category10_default,
+  line_default,
+  stepAfter
+} from "./chunk-IH7ILDJS.js";
+import {
+  axisBottom,
+  axisLeft
+} from "./chunk-LOZEKOES.js";
+import {
+  linear,
+  ordinal
+} from "./chunk-OAWQ6LOO.js";
+import {
+  select_default
+} from "./chunk-NDWTN4U5.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"
+  }
+});
+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 controls = this.opts.controls ? null : opts.holder.append("div");
+    const holder = opts.controls ? opts.holder : opts.holder.append("div");
+    const loadingDiv = holder.append("div").style("position", "absolute").style("display", "none").style("padding", "20px").html("Loading ...");
+    const chartsDiv = holder.append("div").style("margin", "10px").style("display", "flex").style("flex-direction", "row").style("flex-wrap", "wrap").style("max-width", "100vw");
+    const dom = {
+      loadingDiv,
+      header: opts.header,
+      controls,
+      holder,
+      chartsDiv,
+      legendDiv: holder.append("div").style("margin", "5px 5px 15px 5px"),
+      hiddenDiv: holder.append("div").style("margin", "5px 5px 15px 5px"),
+      tip: new Menu({ padding: "5px" }),
+      legendTip: new Menu({ padding: "5px" })
+    };
+    dom.tip.onHide = () => {
+      this.activeMenu = false;
+    };
+    if (dom.header) dom.header.html("Survival Plot");
+    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";
+    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
+            },
+            {
+              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
+            },
+            {
+              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: "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;
+    }
+    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();
+    let data;
+    try {
+      data = await this.app.vocabApi.getNestedChartSeriesData(reqOpts, this.api?.getAbortSignal());
+    } catch (e) {
+      if (this.app.isAbortError(e)) return;
+      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();
+    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];
+      }
+    }
+    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;
+        }
+        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;
+          }
+        }
+      }
+    }
+  }
+  // helper so that 'Loading...' does not flash when not needed
+  toggleLoadingDiv(display = "") {
+    if (display != "none") {
+      this.dom.loadingDiv.style("opacity", 0).style("display", display).transition().duration("loadingWait" in this ? this.loadingWait : 0).style("opacity", 1);
+    } else {
+      this.dom.loadingDiv.style("display", display);
+    }
+    this.loadingWait = 1e3;
+  }
+};
+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").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 80px").style("display", "none");
+      if (self.tests && chart.rawChartId in self.tests) {
+        const holder = div.select(".pp-survival-chartLegends").style("display", "inline-block").append("div");
+        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
+        });
+      }
+    }
+  };
+  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
+    );
+    chart.atRiskLabelWidth = s.atRiskVisible ? maxSeriesLabelLen * (s.axisTitleFontSize - 2) * 0.4 + s.atRiskLabelOffset : 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").selectAll("*").remove();
+    if (self.tests && chart.rawChartId in self.tests) {
+      const holder = div.select(".pp-survival-chartLegends").style("display", "inline-block").append("div");
+      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
+      });
+    }
+  };
+  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", "20px");
+    const [mainG, seriesesG, axisG, xAxis, yAxis, xTitle, yTitle, atRiskG, plotRect] = getSvgSubElems(svg);
+    const xOffset = chart.atRiskLabelWidth + s.svgPadding.left + 70;
+    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);
+    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;
+    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");
+      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");
+      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];
+  }
+  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}, ${pixelOffset})`).call(axisLeft(linear().domain(chart.yScale.domain()).range(chart.yScale.range())).ticks(5));
+    xTitle.select("text, title").remove();
+    xTitle.attr(
+      "transform",
+      "translate(" + (s.svgw - s.svgPadding.left - s.svgPadding.right) / 2 + "," + (s.svgh - s.axisTitleFontSize - 4) + ")"
+    ).append("text").style("text-anchor", "middle").style("font-size", s.axisTitleFontSize + "px").text(s.xTitleLabel);
+    const yTitleLabel = "Probability of Survival";
+    yTitle.select("text, title").remove();
+    yTitle.attr(
+      "transform",
+      "translate(" + (-s.svgPadding.left / 2 - s.axisTitleFontSize) + "," + (s.svgh - s.svgPadding.top - s.svgPadding.bottom) / 2 + ")rotate(-90)"
+    ).append("text").style("text-anchor", "middle").style("font-size", s.axisTitleFontSize + "px").text(yTitleLabel);
+  }
+  self.getSymbol = function(size) {
+    const s = size, h = s / 2;
+    switch (self.settings.symbol) {
+      case "x":
+        return `M -${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);
+    console.log("self.legendOrder:", self.legendOrder);
+    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 values = structuredClone(t2?.term.values || self.legendValues);
+      const term2 = structuredClone(t2);
+      term2.term.values = values;
+      if (!values) term2.term.values = { [d.seriesId]: {} };
+      term2.term.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 `${e} [survival getPlotConfig()]`;
+  }
+  const config = {
+    id: opts.term.term.id,
+    controlLabels: Object.assign({}, defaultUiLabels, app.vocabApi.termdbConfig.uiLabels || {}),
+    settings: {
+      controls: {
+        term2: null,
+        // the previous overlay value may be displayed as a convenience for toggling
+        term0: null
+      },
+      survival: {
+        radius: 5,
+        ciVisible: true,
+        fill: "#fff",
+        stroke: "#000",
+        symbol: "vtick",
+        // 'x', 'vtick'
+        fillOpacity: 0,
+        chartMargin: 10,
+        svgw: 400,
+        svgh: 300,
+        numUnitInOneYear: 1,
+        timeUnit: "years",
+        atRiskVisible: true,
+        atRiskLabelOffset: -20,
+        xTickValues: [],
+        // if undefined or empty, will be ignored
+        seriesTipDecimals: 1,
+        svgPadding: {
+          top: 20,
+          left: 55,
+          right: 20,
+          bottom: 50
+        },
+        axisTitleFontSize: 16,
+        xAxisOffset: 5,
+        yAxisOffset: -5,
+        hiddenPvalues: [],
+        defaultColor: "#2077b4"
+      }
+    }
+  };
+  const overrides = app.vocabApi.termdbConfig.survival || {};
+  copyMerge(config.settings.survival, overrides.settings);
+  return copyMerge(config, opts);
+}
+function getPj(self) {
+  const pj = new import_partjson.default({
+    template: {
+      yMin: ">=yMin()",
+      yMax: "<=yMax()",
+      charts: [
+        {
+          chartId: "@key",
+          rawChartId: "$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-SPAIFVM2.js.map