@sjcrh/proteinpaint-client 2.200.0 → 2.201.0

package/dist/cuminc-WQB6FHVS.js

@@ -1,1148 +0,0 @@
-import {
-  getSeriesTip,
-  renderAtRiskG,
-  renderPvalues
-} from "./chunk-4FQYRDZS.js";
-import {
-  schemeCategory20
-} from "./chunk-V2OJLJSK.js";
-import {
-  PlotBase,
-  controlsInit,
-  defaultUiLabels,
-  fillTermWrapper,
-  getCombinedTermFilter,
-  getT0T2defaultQ,
-  htmlLegend,
-  renderTerm1Label,
-  sayerror
-} from "./chunk-TKW5TW4Z.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-3SHZTAGF.js";
-import {
-  Menu
-} from "./chunk-HYOEWQ5P.js";
-import "./chunk-6QCYT6G2.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-IIT367QZ.js";
-import "./chunk-RZGEKL77.js";
-import {
-  require_partjson_umd
-} from "./chunk-OTTMHVYH.js";
-import "./chunk-GNS6CQMA.js";
-import "./chunk-JVPWIVDT.js";
-import "./chunk-4WF3XDQP.js";
-import "./chunk-7JRDJNLR.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-M3J4MINX.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-MPSLUEI4.js";
-import "./chunk-6PNPHACF.js";
-import "./chunk-WPHUM5S5.js";
-import "./chunk-JNITUVXP.js";
-import {
-  area_default,
-  category10_default,
-  line_default,
-  stepAfter
-} from "./chunk-2KXLYFAO.js";
-import {
-  axisBottom,
-  axisLeft
-} from "./chunk-LOZEKOES.js";
-import "./chunk-VQZ2Z5YU.js";
-import {
-  linear,
-  ordinal
-} from "./chunk-UJELJXJG.js";
-import "./chunk-BZTWTH4Y.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import {
-  select_default
-} from "./chunk-I6Y4O3RR.js";
-import {
-  rgb
-} from "./chunk-Q5RDQNIT.js";
-import "./chunk-DQC5FFGV.js";
-import {
-  __toESM
-} from "./chunk-HFNDKYVF.js";
-
-// plots/cuminc.js
-var import_partjson = __toESM(require_partjson_umd(), 1);
-var Cuminc = class _Cuminc extends PlotBase {
-  static type = "cuminc";
-  constructor(opts) {
-    this.type = _Cuminc.type;
-    this.pj = getPj(this);
-    this.state = {
-      config: copyMerge(
-        {
-          settings: JSON.parse(defaultSettings)
-        },
-        opts.config
-      )
-    };
-    const holder = opts.holder;
-    this.dom = {
-      holder,
-      chartsDiv: holder.append("div").style("margin", "10px"),
-      legendDiv: holder.append("div").style("margin", "5px"),
-      hiddenDiv: holder.append("div").style("margin", "5px 5px 15px 5px")
-    };
-    this.tip = new Menu({ padding: "5px" });
-    this.lineFxn = line_default().curve(stepAfter).x((c) => c.scaledX).y((c) => c.scaledY);
-    this.hidePlotTitle = true;
-    setRenderers(this);
-    this.legendRenderer = htmlLegend(this.dom.legendDiv, {
-      settings: {
-        legendOrientation: "vertical"
-      },
-      handlers: {
-        legend: {
-          click: (e) => this.legendClick(e.target.__data__, e.clientX, e.clientY)
-        }
-      }
-    });
-  }
-  main(results) {
-    this.config = structuredClone(this.state.config);
-    if (this.config.term.term.type != "condition") throw "cuminc term is not a condition term";
-    this.settings = this.config.settings.cuminc;
-    this.settings.xTitleLabel = "Years since entry into the cohort";
-    this.settings.atRiskVisible = false;
-    this.processResults(results);
-    this.pj.refresh({ data: this.currData });
-    this.setTerm2Color(this.pj.tree.charts);
-    this.render();
-  }
-  processResults(results) {
-    const chartIds = Object.keys(results);
-    if (chartIds.length != 1) throw "must be a single chart";
-    const chartId = chartIds[0];
-    const chart = results[chartId];
-    this.currData = [];
-    this.uniqueSeriesIds = /* @__PURE__ */ new Set();
-    for (const seriesId in chart.estimates) {
-      const series = chart.estimates[seriesId];
-      for (const timepoint of series) {
-        const { time, est, low, up, nrisk, nevent, ncensor } = timepoint;
-        const d = {
-          chartId,
-          seriesId,
-          time,
-          cuminc: est * 100,
-          // convert to percentage
-          low: low * 100,
-          high: up * 100,
-          nrisk,
-          nevent,
-          ncensor
-        };
-        this.currData.push(d);
-        this.uniqueSeriesIds.add(d.seriesId);
-      }
-    }
-    this.tests = {};
-    if (chart.tests?.length != 1) throw "must have a single test";
-    const test = chart.tests[0];
-    this.tests[chartId] = [
-      {
-        pvalue: { id: "pvalue", text: test.permutation ? test.pvalue + "*" : test.pvalue },
-        series1: { id: test.series1 },
-        series2: { id: test.series2 },
-        permutation: test.permutation
-      }
-    ];
-    this.refs = {};
-  }
-  setTerm2Color(charts) {
-    if (!charts) return;
-    if (charts.length != 1) throw "should be a single chart";
-    const chart = charts[0];
-    this.term2toColor = {};
-    this.colorScale = this.uniqueSeriesIds.size < 11 ? ordinal(category10_default) : ordinal(schemeCategory20);
-    const legendItems = [];
-    for (const series of chart.serieses) {
-      const color = this.config.term2?.term.values?.[series.seriesId]?.color;
-      const c = {
-        orig: color || (series.seriesId == "" ? this.settings.defaultColor : this.colorScale(series.seriesId))
-      };
-      c.rgb = rgb(c.orig);
-      c.adjusted = c.rgb.toString();
-      this.term2toColor[series.seriesId] = c;
-      if (!legendItems.find((d) => d.seriesId == series.seriesId)) {
-        legendItems.push({
-          seriesId: series.seriesId,
-          text: series.seriesLabel,
-          color: this.term2toColor[series.seriesId].adjusted
-        });
-      }
-    }
-    if (this.config.term2 && legendItems.length) {
-      this.legendData = [
-        {
-          name: this.config.term2.term.name,
-          items: legendItems
-        }
-      ];
-    } else {
-      this.legendData = [];
-    }
-    const chartTests = this.tests[chart.chartId];
-    if (chartTests.length != 1) throw "should have one test";
-    const test = chartTests[0];
-    for (const key in test) {
-      if (key == "pvalue") {
-        test[key].color = "#000";
-      } else if (key.startsWith("series")) {
-        const item = legendItems.find((item2) => item2.seriesId == test[key].id);
-        test[key].color = item.color;
-        test[key].text = item.text;
-      } else {
-        continue;
-      }
-    }
-  }
-};
-var MassCumInc = class _MassCumInc {
-  static type = "cuminc";
-  constructor(opts) {
-    this.type = _MassCumInc.type;
-    this.chartIncrement = 0;
-  }
-  async init(appState) {
-    const opts = this.opts;
-    const controls = this.opts.controls ? null : opts.holder.append("div");
-    const holder = opts.controls ? opts.holder : opts.holder.append("div");
-    this.dom = {
-      errorDiv: holder.append("div"),
-      loadingDiv: holder.append("div").style("position", "absolute").style("display", "none").style("padding", "20px").html("Loading ..."),
-      header: opts.header,
-      controls,
-      holder,
-      chartsDiv: holder.append("div").style("margin", "10px"),
-      legendDiv: holder.append("div").style("margin", "5px"),
-      hiddenDiv: holder.append("div").style("margin", "5px 5px 15px 5px")
-    };
-    this.tip = new Menu({ padding: "5px" });
-    if (this.dom.header) this.dom.header.html("Cumulative Incidence Plot");
-    this.settings = Object.assign({}, this.opts.settings);
-    this.pj = getPj(this);
-    this.lineFxn = line_default().curve(stepAfter).x((c) => c.scaledX).y((c) => c.scaledY);
-    setInteractivity(this);
-    setRenderers(this);
-    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.hideLegendItem(e.target.__data__)
-        }
-      }
-    });
-    await this.setControls(appState);
-  }
-  async setControls(appState) {
-    const config = appState.plots.find((p) => p.id === this.id);
-    const controlLabels = config.controlLabels;
-    if (!controlLabels) throw "controls labels not found";
-    if (this.opts.controls) {
-      this.opts.controls.on("downloadClick.cuminc", this.download);
-    } else {
-      this.dom.holder.attr("class", "pp-termdb-plot-viz").style("display", "inline-block").style("min-width", "300px").style("margin-left", "50px");
-      const options = [];
-      for (const grade in config.term.term.values) {
-        const v = config.term.term.values[grade];
-        if (v.uncomputable) continue;
-        options.push({
-          label: v.label,
-          value: grade
-        });
-      }
-      this.components = {
-        controls: await controlsInit({
-          app: this.app,
-          id: this.id,
-          holder: this.dom.controls.style("display", "inline-block"),
-          inputs: [
-            {
-              type: "term",
-              configKey: "term",
-              chartType: "cuminc",
-              usecase: { target: "cuminc", detail: "term" },
-              label: controlLabels.term1?.label || renderTerm1Label,
-              vocabApi: this.app.vocabApi,
-              menuOptions: "edit"
-            },
-            {
-              type: "term",
-              configKey: "term2",
-              chartType: "cuminc",
-              usecase: { target: "cuminc", detail: "term2" },
-              title: controlLabels.term2.title || controlLabels.term2.label,
-              label: controlLabels.term2.label,
-              vocabApi: this.app.vocabApi,
-              numericEditMenuVersion: ["discrete"],
-              defaultQ4fillTW: getT0T2defaultQ(true)
-            },
-            {
-              type: "term",
-              configKey: "term0",
-              chartType: "cuminc",
-              usecase: { target: "cuminc", detail: "term0" },
-              title: controlLabels.term0.title || controlLabels.term0.label,
-              label: controlLabels.term0.label,
-              vocabApi: this.app.vocabApi,
-              numericEditMenuVersion: ["discrete"],
-              defaultQ4fillTW: getT0T2defaultQ(true)
-            },
-            {
-              label: "Minimum sample size of series",
-              type: "number",
-              chartType: "cuminc",
-              settingsKey: "minSampleSize"
-            },
-            {
-              label: "Minimum at-risk count of event",
-              type: "number",
-              chartType: "cuminc",
-              settingsKey: "minAtRisk"
-            },
-            {
-              label: "Chart width",
-              type: "number",
-              chartType: "cuminc",
-              settingsKey: "svgw",
-              title: "The internal width of the chart plot"
-            },
-            {
-              label: "Chart height",
-              type: "number",
-              chartType: "cuminc",
-              settingsKey: "svgh",
-              title: "The internal height of the chart plot"
-            },
-            {
-              label: "X-axis ticks",
-              type: "text",
-              chartType: "cuminc",
-              settingsKey: "xTickValues",
-              placeholder: "tick,tick,...",
-              processInput: (value) => value ? value.split(",").map(Number) : []
-            },
-            {
-              label: "Y-axis ticks",
-              type: "text",
-              chartType: "cuminc",
-              settingsKey: "yTickValues",
-              placeholder: "tick,tick,...",
-              processInput: (value) => value ? value.split(",").map(Number) : []
-            },
-            {
-              label: "At-risk counts",
-              boxLabel: "Visible",
-              type: "checkbox",
-              chartType: "cuminc",
-              settingsKey: "atRiskVisible",
-              title: "Display the at-risk counts"
-            },
-            {
-              label: "95% confidence interval",
-              boxLabel: "Visible",
-              type: "checkbox",
-              chartType: "cuminc",
-              settingsKey: "ciVisible"
-            },
-            {
-              label: "Default color",
-              type: "color",
-              chartType: "cuminc",
-              settingsKey: "defaultColor"
-            }
-          ]
-        })
-      };
-      this.components.controls.on("downloadClick.cuminc", 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 = this.parentId && appState.plots.find((p) => p.id === this.parentId);
-    const termfilter = getCombinedTermFilter(appState, config.filter || parentConfig?.filter);
-    return {
-      genome: this.app.vocabApi.vocab.genome,
-      dslabel: this.app.vocabApi.vocab.dslabel,
-      activeCohort: appState.activeCohort,
-      termfilter,
-      config: {
-        term: JSON.parse(JSON.stringify(config.term)),
-        term0: config.term0 ? JSON.parse(JSON.stringify(config.term0)) : null,
-        term2: config.term2 ? JSON.parse(JSON.stringify(config.term2)) : null,
-        settings: config.settings.cuminc
-      }
-    };
-  }
-  async main() {
-    try {
-      this.config = structuredClone(this.state.config);
-      this.dom.errorDiv.html("");
-      if (this.dom.header)
-        this.dom.header.html(
-          this.state.config.term.term.name + ' <span style="opacity:.6;font-size:.7em;margin-left:10px;">CUMULATIVE INCIDENCE</span>'
-        );
-      if (this.config.term.term.type != "condition") throw "cuminc term is not a condition term";
-      this.toggleLoadingDiv();
-      Object.assign(this.settings, this.config.settings);
-      this.settings.defaultHidden = this.getDefaultHidden();
-      this.settings.hidden = this.settings.customHidden || this.settings.defaultHidden;
-      this.settings.xTitleLabel = "Years since diagnosis";
-      const reqOpts = this.getDataRequestOpts();
-      const results = await this.app.vocabApi.getNestedChartSeriesData(reqOpts);
-      if (results.error) throw results.error;
-      this.toggleLoadingDiv("none");
-      this.app.vocabApi.syncTermData(this.config, results);
-      this.processResults(results);
-      this.pj.refresh({ data: this.currData });
-      this.sortSerieses(this.pj.tree.charts);
-      this.setTerm2Color(this.pj.tree.charts);
-      this.render();
-    } catch (e) {
-      console.error(e);
-    }
-  }
-  // creates an opts object for the vocabApi.getNestedChartsData()
-  getDataRequestOpts() {
-    const c = this.config;
-    const opts = {
-      chartType: "cuminc",
-      term: c.term,
-      filter: this.state.termfilter.filter,
-      minSampleSize: c.settings.minSampleSize
-    };
-    if (c.term2) opts.term2 = c.term2;
-    if (c.term0) opts.term0 = c.term0;
-    return opts;
-  }
-  getDefaultHidden() {
-    const hidden = [];
-    const term2 = this.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;
-  }
-  processResults(results) {
-    const s = this.settings;
-    const c = this.config;
-    const estimates = {};
-    const tests = {};
-    this.currData = [];
-    this.tests = {};
-    this.noData = [];
-    if (Object.keys(results.data).length === 0) {
-      sayerror(this.dom.errorDiv, "No data available");
-    }
-    this.uniqueSeriesIds = /* @__PURE__ */ new Set();
-    const lowSampleSize = results.lowSampleSize;
-    const noEvents = results.noEvents;
-    this.refs = results.refs;
-    for (const chartId in results.data) {
-      const chart = results.data[chartId];
-      if (chart.estimates) {
-        for (const seriesId in chart.estimates) {
-          const series = chart.estimates[seriesId];
-          if (!series.filter((timepoint) => timepoint.nrisk >= s.minAtRisk && timepoint.est > 0).length) {
-            chartId in noEvents ? noEvents[chartId].push(seriesId) : noEvents[chartId] = [seriesId];
-            continue;
-          }
-          chartId in estimates ? estimates[chartId][seriesId] = series : estimates[chartId] = { [seriesId]: series };
-        }
-        if (!(chartId in estimates)) this.noData.push(chartId);
-      } else {
-        this.noData.push(chartId);
-      }
-      if (chart.tests && Object.keys(estimates).length > 0) {
-        tests[chartId] = chart.tests.filter(
-          (test) => test.series1 in estimates[chartId] && test.series2 in estimates[chartId] && !s.hidden.includes(test.series1) && !s.hidden.includes(test.series2)
-        );
-      }
-    }
-    for (const chartId in estimates) {
-      const chart = estimates[chartId];
-      for (const seriesId in chart) {
-        const series = chart[seriesId];
-        for (const timepoint of series) {
-          const { time, est, low, up, nrisk, nevent, ncensor } = timepoint;
-          const d = {
-            chartId,
-            seriesId,
-            time,
-            cuminc: est * 100,
-            // convert to percentage
-            low: low * 100,
-            high: up * 100,
-            nrisk,
-            nevent,
-            ncensor
-          };
-          if (d.nrisk < s.minAtRisk) {
-            this.currData.push(d);
-            break;
-          }
-          this.currData.push(d);
-          this.uniqueSeriesIds.add(d.seriesId);
-        }
-      }
-    }
-    for (const chartId in tests) {
-      for (const test of tests[chartId]) {
-        const d = {
-          pvalue: { id: "pvalue", text: test.permutation ? test.pvalue + "*" : test.pvalue },
-          series1: { id: test.series1 },
-          series2: { id: test.series2 },
-          permutation: test.permutation
-        };
-        chartId in this.tests ? this.tests[chartId].push(d) : this.tests[chartId] = [d];
-      }
-    }
-    this.lowSampleSize = {};
-    for (const chartId in lowSampleSize) {
-      this.lowSampleSize[chartId] = lowSampleSize[chartId].map(
-        (seriesId) => c.term2?.term.values?.[seriesId]?.label || seriesId
-      );
-    }
-    this.noEvents = {};
-    for (const chartId in noEvents) {
-      this.noEvents[chartId] = noEvents[chartId].map((seriesId) => c.term2?.term.values?.[seriesId]?.label || seriesId);
-    }
-  }
-  sortSerieses(charts) {
-    if (!charts) return;
-    for (const chart of charts) {
-      const seriesIDs = chart.serieses.map((series) => series.seriesId);
-      const seriesOrder = [
-        ...seriesIDs.filter((seriesId) => !this.settings.defaultHidden.includes(seriesId)),
-        ...seriesIDs.filter((seriesId) => this.settings.defaultHidden.includes(seriesId))
-      ];
-      chart.serieses.sort((a, b) => seriesOrder.indexOf(a.seriesId) - seriesOrder.indexOf(b.seriesId));
-    }
-  }
-  setTerm2Color(charts) {
-    if (!charts) {
-      this.legendData = [];
-      return;
-    }
-    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) {
-        const color = this.config.term2?.term.values?.[series.seriesId]?.color;
-        const c = {
-          orig: color || (series.seriesId == "" ? this.settings.defaultColor : this.colorScale(series.seriesId))
-        };
-        c.rgb = rgb(c.orig);
-        c.adjusted = c.rgb.toString();
-        this.term2toColor[series.seriesId] = c;
-        if (!legendItems.find((d) => d.seriesId == series.seriesId)) {
-          legendItems.push({
-            seriesId: series.seriesId,
-            text: series.seriesLabel,
-            color: this.term2toColor[series.seriesId].adjusted,
-            isHidden: this.settings.hidden.includes(series.seriesId)
-          });
-        }
-      }
-    }
-    if (this.config.term2 && legendItems.length) {
-      this.legendData = [
-        {
-          name: this.config.term2.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 if (key.startsWith("series")) {
-            const item = legendItems.find((item2) => item2.seriesId == test[key].id);
-            test[key].color = item.color;
-            test[key].text = item.text;
-          } else {
-            continue;
-          }
-        }
-      }
-    }
-  }
-  // 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 cumincInit = getCompInit(MassCumInc);
-var componentInit = cumincInit;
-function setRenderers(self) {
-  self.render = function() {
-    const data = self.pj.tree.charts || [];
-    if (self.noData?.length) {
-      data.push(
-        ...self.noData.map((chartId) => {
-          let chartTitle = chartId;
-          const t0 = self.config.term0;
-          if (t0) {
-            if (t0.q?.type == "predefined-groupset" || t0.q?.type == "custom-groupset") return { chartId, chartTitle };
-            if (t0.term.values) {
-              const value = t0.term.values[chartId];
-              if (value && value.label) chartTitle = value.label;
-            }
-          }
-          return { chartId, chartTitle };
-        })
-      );
-    }
-    const chartDivs = self.dom.chartsDiv.selectAll(".pp-cuminc-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.config.term2) self.dom.hiddenDiv.style("display", "none");
-    else {
-      self.dom.hiddenDiv.style("display", "");
-      self.hiddenRenderer(self.hiddenData);
-    }
-  };
-  self.addCharts = function(chart) {
-    const s = self.settings;
-    const div = select_default(this).append("div").attr("class", "pp-cuminc-chart").attr("data-testid", "sjpp-cuminc-plotDiv").style("opacity", chart.serieses ? 0 : 1).style("display", "inline-block").style("margin", s.chartMargin + "px").style("padding", "10px").style("top", 0).style("left", 0).style("text-align", "center").style("vertical-align", "top").style("background", 1 ? chart.color : "");
-    div.append("div").attr("class", "sjpcb-cuminc-title").attr("data-testid", "sjpp-cuminc-plotTitle").style("text-align", "center").style("width", `${s.svgw + 50}px`).style("height", s.chartTitleDivHt + "px").style("font-weight", "600").style("margin", "5px").datum(chart.chartId).html(chart.chartTitle);
-    if (self.hidePlotTitle) div.select(".sjpcb-cuminc-title").style("display", "none");
-    div.append("div").attr("class", "pp-cuminc-chart-noData").attr("data-testid", "sjpp-cuminc-noData").style("display", "none").style("width", `${s.svgw + 50}px`).style("margin", "40px 5px").text("No cumulative incidence data");
-    if (chart.serieses) {
-      setVisibleSerieses(chart, s);
-      const svg = div.append("svg").attr("class", "pp-cuminc-svg");
-      renderSVG(svg, chart, s);
-      div.style("opacity", 1);
-    } else {
-      div.select(".pp-cuminc-chart-noData").style("display", "block");
-    }
-    div.append("div").attr("class", "pp-cuminc-chartLegends").style("vertical-align", "top").style("text-align", chart.serieses ? "left" : "center").style("margin", chart.serieses ? "10px 30px 0px 20px" : "0px").style("display", "none");
-    if (self.tests && chart.chartId in self.tests) {
-      const holder = div.select(".pp-cuminc-chartLegends").style("display", "inline-block").append("div").style("margin-bottom", "30px");
-      renderPvalues({
-        title: "Group comparisons (Gray's test)",
-        holder,
-        plot: "cuminc",
-        tests: self.tests[chart.chartId],
-        s,
-        bins: self.refs.bins
-      });
-    }
-    if (self.noEvents && chart.chartId in self.noEvents) {
-      const skipdiv = div.select(".pp-cuminc-chartLegends").style("display", "inline-block").append("div").style("margin-bottom", "30px");
-      const title = "Skipped series (no events)";
-      renderSkippedSeries(skipdiv, title, self.noEvents[chart.chartId], s);
-    }
-    if (self.lowSampleSize && chart.chartId in self.lowSampleSize) {
-      const skipdiv = div.select(".pp-cuminc-chartLegends").style("display", "inline-block").append("div").style("margin-bottom", "30px");
-      const title = "Skipped series (low sample size)";
-      renderSkippedSeries(skipdiv, title, self.lowSampleSize[chart.chartId], s);
-    }
-  };
-  function setVisibleSerieses(chart, s) {
-    chart.visibleSerieses = s.hidden ? chart.serieses.filter((series) => !s.hidden.includes(series.seriesId)) : chart.serieses;
-  }
-  self.updateCharts = function(chart) {
-    const s = self.settings;
-    const div = select_default(this);
-    div.style("background", 1 ? chart.color : "");
-    div.select(".sjpcb-cuminc-title").style("width", `${s.svgw + 50}px`).style("height", s.chartTitleDivHt + "px").datum(chart.chartId).html(chart.chartTitle);
-    if (self.hidePlotTitle) div.select(".sjpcb-cuminc-title").style("display", "none");
-    div.selectAll(".sjpcb-lock-icon").style("display", s.scale == "byChart" ? "block" : "none");
-    div.selectAll(".sjpcb-unlock-icon").style("display", s.scale == "byChart" ? "none" : "block");
-    if (chart.serieses) {
-      div.select(".pp-cuminc-chart-noData").style("display", "none");
-      setVisibleSerieses(chart, s);
-      renderSVG(div.select("svg"), chart, s);
-    } else {
-      div.select(".pp-cuminc-chart-noData").style("display", "block").style("width", `${s.svgw + 50}px`);
-      div.select("svg").remove();
-      div.select(".pp-cuminc-chartLegends").style("text-align", "center").style("margin", "0px");
-    }
-    div.select(".pp-cuminc-chartLegends").selectAll("*").remove();
-    if (self.tests && chart.chartId in self.tests) {
-      const holder = div.select(".pp-cuminc-chartLegends").style("display", "inline-block").append("div").style("margin-bottom", "30px");
-      renderPvalues({
-        title: "Group comparisons (Gray's test)",
-        holder,
-        plot: "cuminc",
-        tests: self.tests[chart.chartId],
-        s,
-        bins: self.refs.bins
-      });
-    }
-    if (self.noEvents && chart.chartId in self.noEvents) {
-      const skipdiv = div.select(".pp-cuminc-chartLegends").style("display", "inline-block").append("div").style("margin-bottom", "30px");
-      const title = "Skipped series (no events)";
-      renderSkippedSeries(skipdiv, title, self.noEvents[chart.chartId], s);
-    }
-    if (self.lowSampleSize && chart.chartId in self.lowSampleSize) {
-      const skipdiv = div.select(".pp-cuminc-chartLegends").style("display", "inline-block").append("div").style("margin-bottom", "30px");
-      const title = "Skipped series (low sample size)";
-      renderSkippedSeries(skipdiv, title, self.lowSampleSize[chart.chartId], s);
-    }
-  };
-  function renderSVG(svg, chart, s) {
-    const extraHeight = s.atRiskVisible ? s.axisTitleFontSize + 4 + chart.visibleSerieses.length * 2 * s.axisTitleFontSize : 0;
-    svg.attr("width", s.svgw).attr("height", s.svgh + extraHeight).style("overflow", "visible").style("padding-left", "20px");
-    const [clipRect, clipG, mainG, seriesesG, axisG, xAxis, yAxis, xTitle, yTitle, atRiskG, plotRect] = getSvgSubElems(
-      svg,
-      chart
-    );
-    clipRect.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);
-    const xOffset = s.svgPadding.left;
-    mainG.attr("transform", "translate(" + xOffset + "," + s.svgPadding.top + ")");
-    const serieses = seriesesG.selectAll(".sjpcb-cuminc-series").data(chart.visibleSerieses, (d) => d && d[0] ? d[0].seriesId : "");
-    serieses.exit().remove();
-    serieses.each(function(series, i) {
-      select_default(this).attr("data-testid", `sjpp-cuminc-series-${series.seriesId || ""}`);
-      renderSeries(select_default(this), series, s);
-    });
-    serieses.enter().append("g").attr("class", "sjpcb-cuminc-series").attr("data-testid", (d) => `sjpp-cuminc-series-${d.seriesId || ""}`).each(function(series, i) {
-      renderSeries(select_default(this), series, s);
-    });
-    renderAxes(xAxis, xTitle, yAxis, yTitle, s, chart);
-    renderAtRiskG({
-      g: atRiskG,
-      s,
-      chart,
-      term2toColor: self.term2toColor,
-      onSerieClick: self.legendClick
-    });
-    plotRect.attr("x", 0).attr("width", s.svgw - s.svgPadding.left - s.svgPadding.right).attr("y", 0).attr("height", s.svgh - s.svgPadding.top - s.svgPadding.bottom + s.xAxisOffset);
-    svg.seriesTip.update({
-      xScale: chart.xScale,
-      xTitleLabel: s.xTitleLabel,
-      decimals: s.seriesTipDecimals,
-      serieses: chart.visibleSerieses.map((s2) => {
-        const seriesLabel = s2.seriesLabel ? `${s2.seriesLabel}:` : "Cumulative Incidence:";
-        const color = self.term2toColor[s2.seriesId].adjusted;
-        return {
-          data: s2.data.map((d) => {
-            return {
-              x: d.x,
-              html: `<span style='color: ${color}'>${seriesLabel} ${d.y.toFixed(2)} (${d.low.toFixed(2)} - ${d.high.toFixed(2)})</span>`
-            };
-          })
-        };
-      })
-    });
-  }
-  function renderSkippedSeries(div, title, serieses, s) {
-    const fontSize = s.axisTitleFontSize - 2;
-    div.selectAll("*").remove();
-    if (!serieses.some((v) => v)) {
-      return;
-    }
-    div.append("div").style("padding-bottom", "5px").style("font-size", fontSize + "px").style("font-weight", "bold").text(title);
-    const seriesesDiv = div.append("div").style("padding-bottom", "5px").style("font-size", fontSize + "px");
-    seriesesDiv.selectAll("div").data(serieses).enter().append("div").attr("class", "pp-cuminc-chartLegends-skipped").text((d) => d);
-  }
-  function getSvgSubElems(svg, chart) {
-    let clipRect, clipG, mainG, seriesesG, axisG, xAxis, yAxis, xTitle, yTitle, atRiskG, plotRect, line;
-    if (!svg.select(".sjpcb-cuminc-mainG").size()) {
-      const clipId = `${self.id}-${self.chartIncrement++}`;
-      clipRect = svg.append("defs").append("clipPath").attr("id", clipId).append("rect");
-      clipG = svg.append("g").attr("class", "sjpcb-cuminc-clipG");
-      mainG = svg.append("g").attr("class", "sjpcb-cuminc-mainG").attr("data-testid", "sjpp-cuminc-main-g");
-      seriesesG = mainG.append("g").attr("class", "sjpcb-cuminc-seriesesG").attr("clip-path", `url(#${clipId})`);
-      axisG = mainG.append("g").attr("class", "sjpcb-cuminc-axis");
-      xAxis = axisG.append("g").attr("class", "sjpcb-cuminc-x-axis");
-      yAxis = axisG.append("g").attr("class", "sjpcb-cuminc-y-axis");
-      xTitle = axisG.append("g").attr("class", "sjpcb-cuminc-x-title").attr("data-testid", "sjpp-cuminc-x-title");
-      yTitle = axisG.append("g").attr("class", "sjpcb-cuminc-y-title").attr("data-testid", "sjpp-cuminc-y-title");
-      atRiskG = mainG.append("g").attr("class", "sjpp-cuminc-atrisk");
-      line = mainG.append("line").attr("class", "sjpcb-plot-tip-line").attr("stroke", "#000").attr("stroke-width", "2px");
-      plotRect = mainG.append("rect").attr("class", "sjpcb-plot-tip-rect").style("fill", "transparent");
-    } else {
-      clipRect = svg.select("defs clipPath rect");
-      clipG = svg.select(".sjpcb-cuminc-clipG");
-      mainG = svg.select(".sjpcb-cuminc-mainG");
-      seriesesG = mainG.select(".sjpcb-cuminc-seriesesG");
-      axisG = mainG.select(".sjpcb-cuminc-axis");
-      xAxis = axisG.select(".sjpcb-cuminc-x-axis");
-      yAxis = axisG.select(".sjpcb-cuminc-y-axis");
-      xTitle = axisG.select(".sjpcb-cuminc-x-title");
-      yTitle = axisG.select(".sjpcb-cuminc-y-title");
-      atRiskG = mainG.select(".sjpp-cuminc-atrisk");
-      plotRect = mainG.select(".sjpcb-plot-tip-rect");
-      line = mainG.select(".sjpcb-plot-tip-line");
-    }
-    if (!svg.seriesTip) {
-      svg.seriesTip = getSeriesTip(line, plotRect, self.app?.tip);
-    }
-    return [clipRect, clipG, mainG, seriesesG, axisG, xAxis, yAxis, xTitle, yTitle, atRiskG, plotRect];
-  }
-  function renderSeries(g, series, s) {
-    g.selectAll("path").remove();
-    g.append("path").attr("data-testid", `sjpp-cuminc-curve-${series.seriesId || ""}`).attr("d", self.lineFxn(series.data.map((d) => ({ scaledX: d.scaledX, scaledY: d.scaledY[0] })))).style("fill", "none").style("stroke", self.term2toColor[series.seriesId].adjusted).style("stroke-width", 2).style("stroke-linecap", "square").style("opacity", 1).style("stroke-opacity", 1);
-    g.append("path").attr("data-testid", `sjpp-cuminc-ci-${series.seriesId || ""}`).attr(
-      "d",
-      area_default().curve(stepAfter).x((c) => c.scaledX).y0((c) => c.scaledY[1]).y1((c) => c.scaledY[2])(series.data)
-    ).style("display", s.ciVisible ? "" : "none").style("fill", self.term2toColor[series.seriesId].adjusted).style("opacity", "0.15").style("stroke", "none");
-  }
-  function renderAxes(xAxis, xTitle, yAxis, yTitle, s, chart) {
-    const xTicks = axisBottom(chart.xScale).tickValues(chart.xTickValues);
-    const yTicks = axisLeft(chart.yScale).tickValues(chart.yTickValues);
-    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(yTicks);
-    xTitle.select("text, title").remove();
-    const xText = xTitle.attr(
-      "transform",
-      "translate(" + (s.svgw - s.svgPadding.left - s.svgPadding.right) / 2 + "," + (s.svgh - s.axisTitleFontSize - 4) + ")"
-    ).append("text").attr("data-testid", "sjpp-cuminc-x-title-text").style("text-anchor", "middle").style("font-size", s.axisTitleFontSize + "px").text(s.xTitleLabel);
-    const yTitleLabel = "Cumulative Incidence (%)";
-    yTitle.select("text, title").remove();
-    const yText = yTitle.attr(
-      "transform",
-      "translate(" + (-s.svgPadding.left / 2 - s.axisTitleFontSize) + "," + (s.svgh - s.svgPadding.top - s.svgPadding.bottom) / 2 + ")rotate(-90)"
-    ).append("text").attr("data-testid", "sjpp-cuminc-y-title-text").style("text-anchor", "middle").style("font-size", s.axisTitleFontSize + "px").text(yTitleLabel);
-  }
-}
-function setInteractivity(self) {
-  const labels = {
-    cuminc: "Cumulative incidence",
-    low: "Lower 95% CI",
-    high: "Upper 95% CI"
-  };
-  self.mouseover = function(event2) {
-    const d = event2.target.__data__;
-  };
-  self.mouseout = function() {
-    self.app.tip.hide();
-  };
-  self.legendClick = function(d, x, y) {
-    if (d === void 0) return;
-    const menu = self.tip.clear();
-    if (self.config.term2 == null) {
-      const color2 = rgb(self.settings.defaultColor).formatHex();
-      const colorDiv = menu.d.append("div").attr("class", "sja_sharp_border").style("padding", "0px 10px").text("Edit color:");
-      const input = colorDiv.append("input").attr("type", "color").attr("value", color2).on("change", () => {
-        const color3 = input.node().value;
-        self.app.dispatch({
-          type: "plot_edit",
-          id: self.id,
-          config: { settings: { cuminc: { defaultColor: color3 } } }
-        });
-        menu.hide();
-      });
-      menu.show(x, y);
-      return;
-    }
-    if (!d.seriesId) return;
-    menu.d.append("div").attr("class", "sja_menuoption sja_sharp_border").text(`Hide`).on("click", async (e) => {
-      menu.hide();
-      self.hideLegendItem(d);
-    });
-    let color = self.term2toColor[d.seriesId]?.adjusted;
-    if (color) {
-      color = rgb(color).formatHex();
-      const colorDiv = menu.d.append("div").attr("class", "sja_sharp_border").style("padding", "0px 10px").text("Edit color:");
-      const input = colorDiv.append("input").attr("type", "color").attr("value", color).on("change", () => {
-        const t2 = self.config.term2;
-        const term2 = structuredClone(t2);
-        if (!term2.term.values) term2.term.values = { [d.seriesId]: {} };
-        else if (!term2.term.values[d.seriesId]) term2.term.values[d.seriesId] = {};
-        term2.term.values[d.seriesId].color = input.node().value;
-        self.app.dispatch({
-          type: "plot_edit",
-          id: self.id,
-          config: {
-            term2
-          }
-        });
-        menu.hide();
-      });
-    }
-    menu.show(event.clientX, event.clientY);
-  };
-  self.hideLegendItem = function(d) {
-    const hidden = self.settings.hidden.slice();
-    const i = hidden.indexOf(d.seriesId);
-    i == -1 ? hidden.push(d.seriesId) : hidden.splice(i, 1);
-    self.app.dispatch({
-      type: "plot_edit",
-      id: self.id,
-      config: {
-        settings: {
-          cuminc: {
-            customHidden: hidden
-          }
-        }
-      }
-    });
-  };
-}
-var defaultSettings = JSON.stringify({
-  controls: {
-    term2: null,
-    // the previous overlay value may be displayed as a convenience for toggling
-    term0: null
-  },
-  cuminc: {
-    minSampleSize: 10,
-    // sent to server-side
-    minAtRisk: 10,
-    atRiskVisible: true,
-    atRiskLabelOffset: -10,
-    seriesTipDecimals: 0,
-    ciVisible: true,
-    radius: 5,
-    fill: "#fff",
-    stroke: "#000",
-    fillOpacity: 0,
-    chartMargin: 10,
-    svgw: 400,
-    svgh: 300,
-    svgPadding: {
-      top: 20,
-      left: 55,
-      right: 20,
-      bottom: 50
-    },
-    axisTitleFontSize: 16,
-    xAxisOffset: 5,
-    yAxisOffset: -5,
-    defaultColor: "#2077b4"
-  }
-});
-async function getPlotConfig(opts, app) {
-  if (!opts.term) throw "cuminc: opts.term{} missing";
-  try {
-    await fillTermWrapper(opts.term, app.vocabApi, {
-      condition: { mode: "cuminc" }
-    });
-    if (opts.term2)
-      await fillTermWrapper(opts.term2, app.vocabApi, opts.term2.bins || opts.term2.q ? null : getT0T2defaultQ(true));
-    if (opts.term0)
-      await fillTermWrapper(opts.term0, app.vocabApi, opts.term0.bins || opts.term0.q ? null : getT0T2defaultQ(true));
-  } catch (e) {
-    throw `${e} [cuminc getPlotConfig()]`;
-  }
-  const config = {
-    id: opts.term.term.id,
-    controlLabels: Object.assign({}, defaultUiLabels, app.vocabApi.termdbConfig.uiLabels || {}),
-    settings: JSON.parse(defaultSettings)
-  };
-  return copyMerge(config, opts);
-}
-function getPj(self) {
-  const pj = new import_partjson.default({
-    template: {
-      xMin: ">=x()",
-      xMax: "<=x()",
-      yMin: ">=yMin()",
-      yMax: "<=yMax()",
-      charts: [
-        {
-          chartId: "@key",
-          chartTitle: "=chartTitle()",
-          xMin: ">=x()",
-          xMax: "<=x()",
-          "__:xTickValues": "=xTickValues()",
-          "__:yTickValues": "=yTickValues()",
-          "__: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: "$cuminc",
-                  low: "$low",
-                  high: "$high",
-                  "_1:scaledX": "=scaledX()",
-                  "_1:scaledY": "=scaledY()",
-                  nrisk: "$nrisk",
-                  nevent: "$nevent",
-                  ncensor: "$ncensor"
-                },
-                "$time"
-              ]
-            },
-            "$seriesId"
-          ],
-          "@done()": "=sortSerieses()"
-        },
-        "$chartId"
-      ]
-    },
-    "=": {
-      chartTitle(row) {
-        if (!self.state?.config?.term) return row.chartId;
-        const s = self.settings;
-        const cutoff = self.config.term.q.breaks[0];
-        if (!row.chartId || row.chartId == "-") {
-          return cutoff == 5 ? "CTCAE grade 5" : `CTCAE grade ${cutoff}-5`;
-        }
-        const t0 = self.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.config.term0.term.values[row.chartId];
-        return value && value.label ? value.label : row.chartId;
-      },
-      seriesLabel(row, context) {
-        const t2 = self.config?.term2;
-        if (!t2) return context.self.seriesId;
-        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;
-        return seriesId;
-      },
-      x(row) {
-        if (self.settings.hidden?.includes(row.seriesId)) return;
-        return row.time;
-      },
-      yMin(row) {
-        if (self.settings.hidden?.includes(row.seriesId)) return;
-        return self.settings.ciVisible ? row.low : row.cuminc;
-      },
-      yMax(row) {
-        if (self.settings.hidden?.includes(row.seriesId)) return;
-        return self.settings.ciVisible ? row.high : row.cuminc;
-      },
-      xTickValues(row, context) {
-        const s = self.settings;
-        if (s.xTickValues?.length) {
-          return s.xTickValues;
-        } else {
-          const xMin = (
-            /*s.scale == 'byChart' ? context.self.xMin : */
-            context.root.xMin
-          );
-          const xMax = (
-            /*s.scale == 'byChart' ? context.self.xMax : */
-            context.root.xMax
-          );
-          return computeTickValues(xMin, xMax);
-        }
-      },
-      xScale(row, context) {
-        const s = self.settings;
-        const min = Math.min(...context.self.xTickValues);
-        const max = Math.max(...context.self.xTickValues);
-        return linear().domain([min, max]).range([0, s.svgw - s.svgPadding.left - s.svgPadding.right]);
-      },
-      scaledX(row, context) {
-        const xScale = context.context.context.context.parent.xScale.clamp(false);
-        return xScale(context.self.x);
-      },
-      yTickValues(row, context) {
-        const s = self.settings;
-        if (s.yTickValues?.length) {
-          return s.yTickValues;
-        } else {
-          const yMin = (
-            /*s.scale == 'byChart' ? context.self.yMin : */
-            context.root.yMin
-          );
-          const yMax = (
-            /*s.scale == 'byChart' ? context.self.yMax : */
-            context.root.yMax
-          );
-          return computeTickValues(yMin, yMax);
-        }
-      },
-      yScale(row, context) {
-        const s = self.settings;
-        const min = Math.min(...context.self.yTickValues);
-        const max = Math.max(...context.self.yTickValues);
-        return linear().domain([max, min]).range([0, s.svgh - s.svgPadding.top - s.svgPadding.bottom]);
-      },
-      scaledY(row, context) {
-        const yScale = context.context.context.context.parent.yScale.clamp(false);
-        const s = context.self;
-        return [yScale(s.y), yScale(s.low), yScale(s.high)];
-      },
-      sortSerieses(result) {
-        if (!self.refs.bins) return;
-        const labelOrder = self.refs.bins.map((b) => b.label);
-        result.serieses.sort((a, b) => labelOrder.indexOf(a.seriesId) - labelOrder.indexOf(b.seriesId));
-      }
-    }
-  });
-  return pj;
-}
-function computeTickValues(min, max) {
-  const tickWidth = (max - min) / 5;
-  const log = Math.floor(Math.log10(tickWidth));
-  const tickWidth_rnd = Math.round(tickWidth / (5 * 10 ** log)) * (5 * 10 ** log) || 1 * 10 ** log;
-  const tickValues = [];
-  let tick = min;
-  while (tick <= Math.min(100, max + tickWidth_rnd)) {
-    tickValues.push(tick);
-    tick = tick + tickWidth_rnd;
-  }
-  if (!tickValues.includes(0)) tickValues.unshift(0);
-  return tickValues;
-}
-export {
-  Cuminc,
-  componentInit,
-  cumincInit,
-  getPlotConfig
-};
-//# sourceMappingURL=cuminc-WQB6FHVS.js.map