@sjcrh/proteinpaint-client 2.187.0 → 2.188.0

package/dist/cuminc-G2UGJUUA.js

@@ -0,0 +1,1148 @@
+import {
+  getSeriesTip,
+  renderAtRiskG,
+  renderPvalues
+} from "./chunk-WQ3U6X4Q.js";
+import {
+  schemeCategory20
+} from "./chunk-V2OJLJSK.js";
+import {
+  PlotBase,
+  controlsInit,
+  defaultUiLabels,
+  fillTermWrapper,
+  getCombinedTermFilter,
+  htmlLegend,
+  renderTerm1Label,
+  term0_term2_defaultQ
+} from "./chunk-2XPDA6NL.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-GHWHLSUX.js";
+import {
+  Menu
+} from "./chunk-HYOEWQ5P.js";
+import "./chunk-HBW42TDT.js";
+import "./chunk-G6O3URDN.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-KWM6B3NL.js";
+import "./chunk-UCLS2SVB.js";
+import {
+  require_partjson_umd
+} from "./chunk-AY4UBGLC.js";
+import "./chunk-2P6Z7JFC.js";
+import "./chunk-MYWJQRTD.js";
+import {
+  copyMerge,
+  getCompInit
+} from "./chunk-MVTCBVSX.js";
+import "./chunk-B43MTEYB.js";
+import "./chunk-2T7VYQLY.js";
+import "./chunk-FDK4UJMN.js";
+import "./chunk-X7GDCYND.js";
+import "./chunk-SJC2C77V.js";
+import "./chunk-C3SYSMNE.js";
+import {
+  area_default,
+  category10_default,
+  line_default,
+  stepAfter
+} from "./chunk-KSGA62R2.js";
+import {
+  axisBottom,
+  axisLeft
+} from "./chunk-LOZEKOES.js";
+import "./chunk-TOU7EVFQ.js";
+import {
+  linear,
+  ordinal
+} from "./chunk-OAWQ6LOO.js";
+import "./chunk-NMBIT4IK.js";
+import "./chunk-KYBIQBXE.js";
+import {
+  select_default
+} from "./chunk-I6Y4O3RR.js";
+import {
+  rgb
+} from "./chunk-OMR2DT66.js";
+import "./chunk-DQC5FFGV.js";
+import {
+  __toESM
+} from "./chunk-HFNDKYVF.js";
+
+// plots/cuminc.js
+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"
+  }
+});
+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 = {
+      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: t0_t2_defaultQ
+            },
+            {
+              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: t0_t2_defaultQ
+            },
+            {
+              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);
+      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 = {};
+    const lowSampleSize = results.lowSampleSize;
+    const noEvents = results.noEvents;
+    this.currData = [];
+    this.uniqueSeriesIds = /* @__PURE__ */ new Set();
+    this.tests = {};
+    this.noData = [];
+    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) {
+        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").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").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").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) {
+      renderSeries(select_default(this), series, s);
+    });
+    serieses.enter().append("g").attr("class", "sjpcb-cuminc-series").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}-${self.chartIncrement++}`;
+      clipRect = svg.append("defs").append("clipPath").attr("id", clipId).append("rect");
+      clipG = svg.append("g").attr("class", "sjpcb-cuminc-clipG");
+      mainG = svg.append("g").attr("class", "sjpcb-cuminc-mainG").attr("data-testid", "sja-cuminc-main-g");
+      seriesesG = mainG.append("g").attr("class", "sjpcb-cuminc-seriesesG").attr("clip-path", `url(#${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");
+      yTitle = axisG.append("g").attr("class", "sjpcb-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("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(
+      "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").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").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 : t0_t2_defaultQ);
+    if (opts.term0)
+      await fillTermWrapper(opts.term0, app.vocabApi, opts.term0.bins || opts.term0.q ? null : t0_t2_defaultQ);
+  } 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-G2UGJUUA.js.map