@sjcrh/proteinpaint-client 2.213.0 → 2.215.0

package/dist/BoxPlot-6UOLWXPV.js

@@ -0,0 +1,1238 @@
+import {
+  getDefaultBoxplotSettings
+} from "./chunk-BNCNUZ62.js";
+import {
+  CustomDownloadMenu,
+  ListSamples,
+  PlotBase,
+  axisstyle,
+  controlsInit,
+  defaultUiLabels,
+  descrStatsToTSV,
+  drawBoxplot,
+  fillTermWrapper,
+  filterJoin,
+  getChartTitle,
+  getCombinedTermFilter,
+  getFilterItemByTag,
+  getMaxLabelWidth,
+  getSingleCellSpecialCase,
+  getT0T2defaultQ,
+  renderTable,
+  renderTerm1Label,
+  setDescrStatsByTerm,
+  testRowsToTSV
+} from "./chunk-LEVWXJOQ.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-KV4W2ACA.js";
+import "./chunk-PE5N5AC6.js";
+import "./chunk-PZEM6AII.js";
+import {
+  Menu
+} from "./chunk-K2QVSMX7.js";
+import "./chunk-EEB5VE2A.js";
+import "./chunk-3CIL7KH7.js";
+import "./chunk-T4XPCSLP.js";
+import "./chunk-A4BTSAIY.js";
+import "./chunk-J3AJ4C7O.js";
+import {
+  isNumTermCollection,
+  isNumericTerm
+} from "./chunk-VIX2TKWP.js";
+import {
+  isErrorResponse
+} from "./chunk-TZRCFVG7.js";
+import {
+  copyMerge,
+  getCompInit
+} from "./chunk-HBNB5TRH.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-7X6NF7NI.js";
+import "./chunk-W5J3LTYS.js";
+import {
+  axisLeft,
+  axisTop
+} from "./chunk-Z2ZITHT4.js";
+import {
+  format,
+  linear,
+  log
+} from "./chunk-4OLM3KSB.js";
+import "./chunk-6XKAOSQE.js";
+import {
+  decimalPlacesUntilFirstNonZero
+} from "./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 "./chunk-HS5PO5ZQ.js";
+
+// plots/boxplot/model/Model.ts
+var Model = class {
+  constructor(boxplot, config) {
+    this.boxplot = boxplot;
+    this.config = config;
+    this.state = boxplot.state;
+    this.app = boxplot.app;
+    this.settings = config.settings.boxplot;
+  }
+  async getData() {
+    const data = await this.app.vocabApi.getViolinBox(
+      this.setRequestOpts(),
+      {},
+      this.boxplot.api?.getAbortSignal()
+    );
+    return data;
+  }
+  setRequestOpts() {
+    const isNumericTC = this.config.term.term.type == "termCollection" && this.config.term.term.memberType == "numeric";
+    const opts = {
+      plotType: "box",
+      tw: this.getContinousTerm(),
+      filter: this.state.termfilter.filter,
+      filter0: this.state.termfilter.filter0,
+      orderByMedian: this.settings.orderByMedian,
+      isLogScale: this.settings.isLogScale,
+      removeOutliers: this.settings.removeOutliers,
+      showAssocTests: this.settings.showAssocTests
+    };
+    if (!isNumericTC) {
+      if (this.config.term2)
+        opts.overlayTw = this.getContinousTerm() == this.config.term ? this.config.term2 : this.config.term;
+      if (this.config.term0) opts.divideTw = this.config.term0;
+    }
+    return opts;
+  }
+  getContinousTerm() {
+    if (!this.config?.term2) return this.config.term;
+    if (this.config.term.term.type == "termCollection" && this.config.term.term.memberType == "numeric")
+      return this.config.term;
+    return isNumericTerm(this.config.term.term) && this.config.term.q.mode == "continuous" ? this.config.term : this.config.term2;
+  }
+};
+
+// plots/boxplot/viewModel/LegendDataMapper.ts
+var LegendDataMapper = class {
+  constructor(config) {
+    this.legendData = [];
+    this.config = config;
+    const isTerm2 = config?.term2;
+    if (config.term.term.type != "termCollection" && config.term.q?.descrStats) {
+      this.legendData.push({
+        label: `Descriptive Statistics${isTerm2 ? `: ${config.term.term.name}` : ""}`,
+        items: this.setDescrStatItems(config.term.q.descrStats)
+      });
+    }
+    if (isTerm2 && isTerm2.q?.descrStats) {
+      this.legendData.push({
+        label: `Descriptive Statistics: ${config.term2.term.name}`,
+        items: this.setDescrStatItems(isTerm2.q.descrStats)
+      });
+    }
+  }
+  map(charts, uncomputableValues) {
+    const hiddenPlots = this.getHiddenPlots(charts);
+    if (this.config.term.term?.values) {
+      const term1Label = this.config.term2 ? this.config.term.term.name : "Other categories";
+      const term1Data = this.setHiddenCategoryItems(this.config.term, term1Label, hiddenPlots, uncomputableValues || []);
+      if (term1Data) this.legendData.push(term1Data);
+    }
+    if (this.config.term2?.term?.values) {
+      const term2Data = this.setHiddenCategoryItems(
+        this.config.term2,
+        this.config.term2.term.name,
+        hiddenPlots,
+        uncomputableValues || []
+      );
+      if (term2Data) this.legendData.push(term2Data);
+    }
+    return this.legendData;
+  }
+  getHiddenPlots(charts) {
+    const hiddenPlots = Object.values(charts).reduce((plotMap, chart) => {
+      for (const p of chart.plots ?? []) {
+        if (!p.isHidden || plotMap.has(p.key)) continue;
+        plotMap.set(p.key, {
+          key: p.key,
+          text: p.key,
+          isHidden: true,
+          isPlot: true
+        });
+      }
+      return plotMap;
+    }, /* @__PURE__ */ new Map()).values();
+    return Array.from(hiddenPlots);
+  }
+  setDescrStatItems(stats) {
+    return Object.values(stats).map((s) => ({
+      key: s.key,
+      text: `${s.label}: ${s.value}`,
+      isHidden: false,
+      isPlot: false
+    }));
+  }
+  setHiddenCategoryItems(tw, label, hiddenPlots, uncomputableValues) {
+    const termData = { label, items: [] };
+    if (hiddenPlots.length) {
+      for (const key of Object.keys(tw.q.hiddenValues || {})) {
+        const plot = hiddenPlots.find((p) => p.key === key);
+        if (plot) termData.items.push(plot);
+      }
+    }
+    if (uncomputableValues && uncomputableValues.length) {
+      for (const v of Object.values(tw.term.values || {})) {
+        const uncomputableItem = uncomputableValues.find((u) => u.label === v.label);
+        if (uncomputableItem) {
+          termData.items.push({
+            key: uncomputableItem.label,
+            text: `${uncomputableItem.label}, n=${uncomputableItem.value}`,
+            isHidden: true,
+            isPlot: false
+          });
+        }
+      }
+    }
+    return termData.items.length ? termData : null;
+  }
+};
+
+// plots/boxplot/viewModel/ChartsDataMapper.ts
+var ChartsDataMapper = class {
+  /** Top padding for the svg */
+  #topPad = 20;
+  /** Bottom padding for the svg */
+  #bottomPad = 25;
+  /** Horizontal, or right and left padding */
+  #horizPad = 120;
+  /** For outliers, set a radius rather than using the default. */
+  #outRadius = 5;
+  /** Offset applied when divide by term is present
+   * Creates space for the subtitle*/
+  #divideByOffset = 20;
+  constructor(data, settings, maxLabelLgth, useDefaultSettings) {
+    this.validateInputData(data);
+    this.absMin = data.absMin;
+    this.absMax = data.absMax;
+    this.charts = Object.values(data.charts);
+    this.settings = settings;
+    if (useDefaultSettings) {
+      const { rowHeight, rowSpace } = this.getRowSettings(this.charts);
+      this.rowHeight = rowHeight;
+      this.rowSpace = rowSpace;
+    } else {
+      this.rowHeight = settings.rowHeight;
+      this.rowSpace = settings.rowSpace;
+    }
+    this.totalLabelSize = maxLabelLgth + settings.labelPad;
+    this.totalBoxSize = this.rowHeight + this.rowSpace;
+  }
+  /** Same checks are in the server route */
+  validateInputData(data) {
+    if (!data) throw new Error("No data provided to ChartDataMapper");
+    if (!data.charts) throw new Error("No charts data provided to ChartDataMapper");
+    if (!Array.isArray(data.charts) && typeof data.charts !== "object")
+      throw new Error("Invalid charts data provided to ChartDataMapper");
+    if (data.absMin === void 0 || data.absMax === void 0)
+      throw new Error("Missing absMin or absMax in data provided to ChartDataMapper");
+  }
+  /** Set the row settings based on all plots */
+  getRowSettings(charts) {
+    let totalNumPlots = 0;
+    for (const chart of charts) {
+      totalNumPlots = totalNumPlots + chart.plots.filter((p) => !p.isHidden).length;
+    }
+    const isLargePlotCount = totalNumPlots > 20;
+    const rowHeight = totalNumPlots > 10 ? isLargePlotCount ? 20 : 35 : 50;
+    const rowSpace = totalNumPlots > 10 ? isLargePlotCount ? 10 : 12 : 15;
+    return { rowHeight, rowSpace };
+  }
+  map(config) {
+    const chartData = {};
+    for (const chart of this.charts) {
+      let incrPad = 40;
+      const plotDim = this.setPlotDimensions(chart, config, this.settings, incrPad);
+      if (config?.term0) incrPad += this.#divideByOffset;
+      incrPad += 30;
+      chartData[chart.chartId] = {
+        plotDim,
+        plots: this.setPlotData(chart, config, this.settings, incrPad),
+        wilcoxon: chart?.wilcoxon || null
+      };
+    }
+    return chartData;
+  }
+  setPlotDimensions(chart, config, settings, incrPad) {
+    const svg = this.setSvgDimensions(settings, chart, incrPad, config);
+    const plotCenter = this.totalLabelSize + settings.plotLength / 2;
+    const plotDim = {
+      //Add 1 to the max is big enough so the upper line to boxplot isn't cutoff
+      domain: [this.absMin, this.absMax <= 1 ? this.absMax : this.absMax + 1],
+      range: [0, settings.plotLength],
+      svg,
+      subtitle: this.setSubtitleDimensions(
+        config,
+        settings,
+        svg.height,
+        chart.chartId,
+        chart.sampleCount,
+        plotCenter,
+        incrPad
+      ),
+      title: this.setTitleDimensions(config, settings, svg.height, plotCenter, incrPad),
+      axis: {
+        x: settings.isVertical ? this.#horizPad / 2 + incrPad + this.#topPad : this.totalLabelSize,
+        y: this.#topPad + (settings.isVertical ? settings.labelPad : incrPad + 20),
+        values: (ticks) => {
+          if (settings.isLogScale) return this.filterTickValues(ticks);
+          return ticks;
+        },
+        format: (d) => {
+          if (settings.isLogScale) {
+            if (Number.isInteger(d)) return format(".0f")(d);
+            const dec = decimalPlacesUntilFirstNonZero(d);
+            if (dec > 1) return format(`.${dec + 1}f`)(d);
+            return format(".2f")(d);
+          }
+          return d.toString();
+        }
+      }
+    };
+    if (config?.term0) {
+      if (settings.isVertical) plotDim.axis.x += this.#divideByOffset;
+      else plotDim.axis.y += this.#divideByOffset;
+    }
+    return plotDim;
+  }
+  setSvgDimensions(settings, chart, incrPad, config) {
+    let plotsSpace = chart.plots.filter((p) => !p.isHidden).length * this.totalBoxSize + this.#topPad + this.#bottomPad + incrPad;
+    if (config?.term0) plotsSpace += this.#divideByOffset + incrPad;
+    const length = settings.plotLength + this.totalLabelSize + this.#horizPad / 2;
+    return {
+      width: settings.isVertical ? plotsSpace + this.#horizPad : length,
+      height: settings.isVertical ? length : plotsSpace
+    };
+  }
+  setSubtitleDimensions(config, settings, height, chartId, sampleCount, plotCenter, incrPad) {
+    const dim = {
+      x: null,
+      y: null,
+      text: null
+    };
+    if (config.term0) {
+      dim.x = settings.isVertical ? this.#horizPad / 2 : plotCenter;
+      dim.y = settings.isVertical ? height - plotCenter - this.#horizPad / 2 : this.#topPad + incrPad / 2;
+      dim.text = getChartTitle(config, chartId, sampleCount);
+    }
+    return dim;
+  }
+  setTitleDimensions(config, settings, height, plotCenter, incrPad) {
+    const dim = {
+      x: settings.isVertical ? this.#horizPad / 2 : plotCenter,
+      y: settings.isVertical ? height - plotCenter - this.#horizPad / 2 : this.#topPad + incrPad / 2,
+      text: config.term.q.mode == "continuous" ? config.term.term.name : config.term2.term.name
+    };
+    if (config?.term0) {
+      if (settings.isVertical) dim.x += this.#divideByOffset + 10;
+      else dim.y += this.#divideByOffset + 10;
+    }
+    return dim;
+  }
+  filterTickValues(ticks) {
+    if (!ticks || ticks.length == 0) {
+      throw new Error("No ticks provided to filterTickValues");
+    }
+    const significantLessThanOne = ticks.filter((t) => t < 1).length / ticks.length;
+    const range = ticks[ticks.length - 1] - ticks[0];
+    const spread = range > 1e3 ? 4 : range > 100 ? 3 : 2;
+    const formattedTicks = ticks.filter((t, i) => {
+      if (t === 0 || i == ticks.length - 1 && i % spread !== 0) return t;
+      else if (t <= 1 && significantLessThanOne > 0.5) {
+        if (i % 5 === 0) return t;
+      } else if (i % spread === 0) return t;
+    });
+    return formattedTicks;
+  }
+  setPlotData(chart, config, settings, incrPad) {
+    const plots = structuredClone(chart.plots.filter((p) => !p.isHidden));
+    for (const plot of plots) {
+      let color;
+      const term2 = config.term2;
+      if (term2) {
+        if (term2.q.type == "predefined-groupset" || term2.q.type == "custom-groupset") {
+          const groupset = term2.q.type == "predefined-groupset" ? term2.term.groupsetting.lst[term2.q.predefined_groupset_idx] : term2.q.customset;
+          if (!groupset) throw "groupset is missing";
+          const group = groupset.groups.find((g) => g.name == plot.seriesId);
+          if (group?.color) color = group.color;
+        } else {
+          color = term2.term.values?.[plot.seriesId]?.color;
+        }
+      }
+      if (!color) color = settings.color;
+      if (!plot.color) plot.color = color;
+      if (settings.displayMode == "dark") plot.color = rgb(plot.color).brighter(0.75);
+      if (plot.boxplot.out.length) {
+        const maxOut = plot.boxplot.out.reduce(
+          (a, b) => Math.max(a.value, b.value)
+        );
+        if (maxOut && maxOut.value > chart.absMax) chart.absMax = maxOut.value;
+        plot.boxplot.radius = this.#outRadius;
+      }
+      plot.boxplot.rectFill = settings.displayMode == "dark" ? "black" : settings.displayMode == "filled" ? color : "white";
+      plot.x = settings.isVertical ? this.#horizPad / 2 + incrPad : this.totalLabelSize;
+      plot.y = this.#topPad + (settings.isVertical ? settings.plotLength + settings.labelPad : incrPad);
+      incrPad += this.totalBoxSize;
+      plot.chartId = chart.chartId || " ";
+    }
+    return plots;
+  }
+};
+
+// plots/boxplot/viewModel/ViewModel.ts
+var ViewModel = class {
+  constructor(config, data, settings, maxLabelLgth, useDefaultSettings) {
+    const chartsMapper = new ChartsDataMapper(data, settings, maxLabelLgth, useDefaultSettings);
+    const legendMapper = new LegendDataMapper(config);
+    const charts = chartsMapper.map(config);
+    this.rowHeight = chartsMapper.rowHeight;
+    this.rowSpace = chartsMapper.rowSpace;
+    this.viewData = {
+      backgroundColor: settings.displayMode == "dark" ? "black" : "white",
+      textColor: settings.displayMode == "dark" ? "white" : "black",
+      charts,
+      legend: legendMapper.map(data.charts, data.uncomputableValues || [])
+    };
+  }
+};
+
+// plots/boxplot/interactions/BoxPlotInteractions.ts
+var BoxPlotInteractions = class {
+  constructor(boxplot, getResData) {
+    this.app = boxplot.app;
+    this.boxplot = boxplot;
+    this.dom = boxplot.dom;
+    this.id = boxplot.id;
+    this.getResData = getResData;
+  }
+  help() {
+    window.open("https://github.com/stjude/proteinpaint/wiki/Box-plot");
+  }
+  /** Option to add a global filter from the box plot label menu. */
+  addFilter(plot) {
+    const state = this.app.getState();
+    const sampleList = this.initListSamples(plot);
+    const filterUiRoot = getFilterItemByTag(state.termfilter.filter, "filterUiRoot");
+    const filter = filterJoin([filterUiRoot, sampleList.tvslst]);
+    filter.tag = "filterUiRoot";
+    this.app.dispatch({
+      type: "filter_replace",
+      filter
+    });
+  }
+  /** Option to hide a plot from the box plot label menu. */
+  hidePlot(plot) {
+    const plotConfig = this.getPlotConfig();
+    const config = structuredClone(plotConfig);
+    const contTerm = config.term.q.mode == "continuous" ? "term2" : "term";
+    if (!config[contTerm].q.hiddenValues) config[contTerm].q.hiddenValues = {};
+    config[contTerm].q.hiddenValues[plot.key] = 1;
+    this.app.dispatch({
+      type: "plot_edit",
+      id: this.id,
+      config
+    });
+  }
+  /** Trigger when clicking on a hidden plot in the legend */
+  unhidePlot(item) {
+    const plotConfig = this.getPlotConfig();
+    const config = structuredClone(plotConfig);
+    const contTerm = config.term.q.mode == "continuous" ? "term2" : "term";
+    delete config[contTerm].q.hiddenValues[item.key];
+    this.app.dispatch({
+      type: "plot_edit",
+      id: this.id,
+      config
+    });
+  }
+  initListSamples(plot) {
+    const state = this.app.getState();
+    const plotConfig = this.getPlotConfig();
+    const config = structuredClone(plotConfig);
+    const bins = this.getResData().bins;
+    const start = this.getResData().absMin;
+    const end = this.getResData().absMax;
+    const contTerm = config.term.q.mode == "continuous" ? config.term : config.term2;
+    const term = config.term != contTerm ? contTerm : config.term;
+    const term2 = config.term != contTerm ? config.term : config.term2;
+    const sampleList = new ListSamples({
+      app: this.app,
+      termfilter: state.termfilter,
+      term,
+      term2,
+      term0: config.term0,
+      plot,
+      bins,
+      start,
+      end
+    });
+    return sampleList;
+  }
+  /** Option from box plot label to show the samples in a table within the tooltip. */
+  async listSamples(plot) {
+    const sampleList = this.initListSamples(plot);
+    const data = await sampleList.getData();
+    const [rows, columns, samples] = sampleList.setTableData(data);
+    return [rows, columns, samples];
+  }
+  /** Callback for color picker in plot(s) label menu */
+  updatePlotColor(plot, color) {
+    if (!plot.seriesId) return;
+    const plotConfig = this.getPlotConfig();
+    const config = structuredClone(plotConfig);
+    config.term2.term.values[plot.seriesId].color = color;
+    this.app.dispatch({
+      type: "plot_edit",
+      id: this.id,
+      config
+    });
+  }
+  getPlotConfig() {
+    return this.boxplot.state.config;
+  }
+  clearDom() {
+    this.dom.error.style("padding", "").text("");
+    this.dom.charts.selectAll("*").remove();
+    this.dom.legend.selectAll("*").remove();
+  }
+};
+
+// plots/boxplot/view/LegendRender.ts
+var LegendRenderer = class {
+  constructor(legendDiv, legendData, interactions, textColor) {
+    this.interactions = interactions;
+    this.textColor = textColor;
+    this.renderLegend(legendDiv, legendData);
+  }
+  renderLegend(legendDiv, legendData) {
+    legendDiv.attr("id", "sjpp-boxplot-legend");
+    for (const section of legendData) {
+      legendDiv.append("div").style("opacity", "0.75").style("color", this.textColor).text(section.label);
+      const sectionDiv = legendDiv.append("div").style("padding-left", "10px");
+      for (const item of section.items) {
+        this.addItem(item, sectionDiv);
+      }
+    }
+  }
+  addItem(item, sectionDiv) {
+    const legendItem = sectionDiv.append("div");
+    if (item.isPlot) {
+      legendItem.append("div").style("display", "inline-block").style("margin-right", "3px").style("position", "relative").style("vertical-align", "middle").html(`<svg xmlns="http://www.w3.org/2000/svg" width="16" height="16" fill="${this.textColor}" class="bi bi-arrow-counterclockwise" viewBox="0 0 16 16" style="vertical-align: middle; display: block; margin: auto;">
+                <path stroke="#000" stroke-width="0.25" fill-rule="evenodd" d="M8 3a5 5 0 1 1-4.546 2.914.5.5 0 0 0-.908-.417A6 6 0 1 0 8 2v1z"/>
+                <path d="M8 4.466V.534a.25.25 0 0 0-.41-.192L5.23 2.308a.25.25 0 0 0 0 .384l2.36 1.966A.25.25 0 0 0 8 4.466z"/>
+                </svg>`);
+    }
+    legendItem.append("div").style("display", "inline-block").style("color", this.textColor).style("text-decoration", item.isHidden ? "line-through" : "").text(item.text);
+    if (item.isPlot) {
+      legendItem.attr("aria-label", `Click to unhide plot`).on("click", () => {
+        this.interactions.unhidePlot(item);
+      });
+    }
+  }
+};
+
+// plots/boxplot/view/BoxPlotToolTips.ts
+var BoxPlotToolTips = class {
+  constructor(plot, g, tip, isVertical) {
+    this.tablePadding = "3px";
+    this.plot = plot;
+    this.g = g;
+    this.boxplot = plot.boxplot;
+    this.isVertical = isVertical;
+    this.tip = tip;
+    this.addLabelTooltip();
+    this.addOutliersTooltip();
+  }
+  //Add rendering preferences here to maintain styles
+  //across all tooltip instances
+  addText(text) {
+    this.tip.d.append("div").text(text);
+  }
+  addLabelTooltip() {
+    if (Object.keys(this.plot.descrStats).length < 2) return;
+    this.boxplot.labelG.on("mouseover", (event) => {
+      this.tip.clear();
+      if (this.isVertical) this.tip.show(event.clientX, event.clientY);
+      else this.tip.showunder(this.boxplot.labelG.node());
+      const table = this.tip.d.append("table").attr("class", "sja_simpletable");
+      table.append("tr").style("text-align", "center").append("td").attr("colspan", 2).style("padding", this.tablePadding).text(this.plot.key);
+      for (const stat of Object.values(this.plot.descrStats)) {
+        const row = table.append("tr");
+        row.append("td").style("padding", this.tablePadding).style("opacity", 0.5).text(stat.label);
+        row.append("td").style("padding", this.tablePadding).style("text-align", "center").style("opacity", stat.value === null || stat.value === void 0 ? 0.5 : 1).text(stat.value ?? "N/A");
+      }
+    });
+    this.boxplot.labelG.on("mouseout", () => {
+      this.tip.hide();
+    });
+  }
+  // addLineToolTips() {
+  // 	const addToolTips = (elem, text: string) => {
+  // 		const elemBBox = elem.node().getBBox()
+  // 		//Add an expanded area for the tooltip
+  // 		//Easier for user to hover over
+  // 		this.g
+  // 			.append('rect')
+  // 			.attr('x', elemBBox.x - 10)
+  // 			.attr('y', elemBBox.y - 10)
+  // 			.attr('width', elemBBox.width + 20)
+  // 			.attr('height', elemBBox.height + 20)
+  // 			.attr('fill', 'transparent')
+  // 			.style('pointer-events', 'all')
+  // 			.on('mouseover', () => {
+  // 				this.tip.clear().showunder(elem.node())
+  // 				this.addText(text)
+  // 			})
+  // 			.on('mouseout', () => {
+  // 				this.tip.hide()
+  // 			})
+  // 	}
+  // 	if (this.boxplot.linep50) {
+  // 		const median = this.plot.descrStats.find((d: any) => d.id == 'median')
+  // 		if (!median) throw `Missing median value for ${this.plot.key}`
+  // 		addToolTips(this.boxplot.linep50, `Median: ${median.value}`)
+  // 	}
+  // 	if (this.boxplot.linew1) {
+  // 		addToolTips(this.boxplot.linew1, `${this.boxplot.w1}`)
+  // 	}
+  // 	if (this.boxplot.linew2) {
+  // 		addToolTips(this.boxplot.linew2, `${this.boxplot.w2}`)
+  // 	}
+  // }
+  addOutliersTooltip() {
+    this.g.selectAll("circle").data(this.boxplot.out).each((d, i, nodes) => {
+      const circle = select_default(nodes[i]);
+      circle.on("mouseover", () => {
+        this.tip.clear().showunder(circle.node());
+        this.addText(d.value);
+      });
+      circle.on("mouseout", () => {
+        this.tip.hide();
+      });
+    });
+  }
+};
+
+// plots/boxplot/view/BoxPlotLabelMenu.ts
+var BoxPlotLabelMenu = class {
+  constructor(plot, app, interactions, tip, isVertical) {
+    const options = [];
+    if (app.getState().nav.header_mode === "with_tabs")
+      options.push({
+        text: `Add filter: ${plot.key}`,
+        isVisible: () => true,
+        callback: () => interactions.addFilter(plot)
+      });
+    options.push({
+      text: `Hide ${plot.key}`,
+      isVisible: () => true,
+      callback: () => interactions.hidePlot(plot)
+    });
+    const { samples } = interactions.getPlotConfig().controlLabels;
+    if (app.getState().nav.header_mode === "with_tabs")
+      options.push({
+        text: `List ${samples}`,
+        isVisible: (state) => state.termdbConfig.displaySampleIds && app.vocabApi.hasVerifiedToken(),
+        callback: async (event) => {
+          if (isVertical) tip.clear().show(event.clientX, event.clientY);
+          else tip.clear().showunder(plot.boxplot.labelG.node());
+          const [rows, columns] = await interactions.listSamples(plot);
+          const tableDiv = tip.d.append("div");
+          renderTable({
+            rows,
+            columns,
+            div: tableDiv,
+            maxHeight: "35vh",
+            resize: true,
+            showLines: true,
+            dataTestId: "sjpp-listsampletable"
+          });
+        }
+      });
+    if (app.opts?.boxplot?.allow2selectSamples) {
+      const ss = app.opts.boxplot.allow2selectSamples;
+      options.push({
+        text: ss.buttonText,
+        isVisible: (state) => state.termdbConfig.displaySampleIds && app.vocabApi.hasVerifiedToken(),
+        callback: async () => {
+          const table = await interactions.listSamples(plot);
+          const samples2 = table[2];
+          ss.callback({
+            samples: await app.vocabApi.convertSampleId(samples2, ss.attributes),
+            source: ss.defaultSelectionLabel || `Selected from boxplot`
+          });
+        }
+      });
+    }
+    plot.boxplot.labelG.on("click", (event) => {
+      tip.clear();
+      if (isVertical) tip.show(event.clientX, event.clientY);
+      else tip.showunder(plot.boxplot.labelG.node());
+      const state = app.getState();
+      for (const opt of options) {
+        if (!opt.isVisible(state)) continue;
+        tip.d.append("div").classed("sja_menuoption", true).text(opt.text).on("click", (event2) => {
+          tip.hide();
+          opt.callback(event2);
+        });
+      }
+      if (plot.color) {
+        tip.d.append("div").style("padding", "5px 10px").style("display", "inline-block").text("Color:").append("input").attr("type", "color").property("value", rgb(plot.color).formatHex()).on("change", (event2) => {
+          interactions.updatePlotColor(plot, event2.target.value);
+          tip.hide();
+        });
+      }
+    });
+  }
+};
+
+// plots/boxplot/view/AssociationTableRender.ts
+var AssociationTableRender = class {
+  constructor(div, data) {
+    const wrapper = div.style("vertical-align", "top").style("margin-top", "30px");
+    wrapper.append("div").text("Group comparisons (Wilcoxon's rank sum test)").style("font-weight", "600").style("text-align", "center");
+    const tableDiv = wrapper.append("div").style("margin-top", "5px");
+    renderTable({
+      div: tableDiv,
+      columns: [{ label: "Group 1" }, { label: "Group 2" }, { label: "P-Value" }],
+      rows: data
+    });
+  }
+};
+
+// plots/boxplot/view/ChartRender.ts
+var ChartRender = class {
+  constructor(dom, settings, app, interactions, chart, backgroundColor, textColor) {
+    this.app = app;
+    this.interactions = interactions;
+    this.textColor = textColor;
+    const plotDim = chart.plotDim;
+    dom.svg.transition().attr("width", plotDim.svg.width).attr("height", plotDim.svg.height).style("fill", backgroundColor);
+    const setScaleFunc = settings.isLogScale ? log().base(10) : linear();
+    const scale = setScaleFunc.domain(plotDim.domain).range(plotDim.range);
+    this.renderTitles(plotDim, dom, settings);
+    this.renderBoxPlots(dom, chart, scale, settings);
+    this.renderAxis(plotDim, dom, scale, settings);
+    if (chart.wilcoxon && dom.assocTableDiv) {
+      new AssociationTableRender(dom.assocTableDiv, chart.wilcoxon);
+    }
+  }
+  renderTitles(plotDim, dom, settings) {
+    const transformStr = `translate(${plotDim.title.x}, ${plotDim.title.y})${settings.isVertical ? `,rotate(-90)` : ""}`;
+    dom.title.attr("class", "sjpp-boxplot-title").style("font-weight", 600).attr("text-anchor", "middle").attr("transform", transformStr).attr("fill", this.textColor).text(plotDim.title.text.length > 80 ? plotDim.title.text.slice(0, 80) + "..." : plotDim.title.text);
+    if (plotDim.subtitle.text) {
+      const subTransformStr = `translate(${plotDim.subtitle.x}, ${plotDim.subtitle.y})${settings.isVertical ? `,rotate(-90)` : ""}`;
+      dom.subtitle.attr("class", "sjpp-boxplot-subtitle").style("font-size", "1.1em").attr("text-anchor", "middle").attr("transform", subTransformStr).attr("fill", this.textColor).text(plotDim.subtitle.text.length > 80 ? plotDim.subtitle.text.slice(0, 80) + "..." : plotDim.subtitle.text);
+    }
+  }
+  renderAxis(plotDim, dom, scale, settings) {
+    if (settings.isVertical) scale.range([scale.range()[1], scale.range()[0]]);
+    const ticks = scale.ticks();
+    const tickValues = plotDim.axis.values(ticks);
+    dom.axis.attr("class", "sjpp-boxplot-axis").attr("transform", `translate(${plotDim.axis.x}, ${plotDim.axis.y})`).transition().call(
+      settings.isVertical ? axisLeft(scale).tickValues(tickValues).tickFormat((d) => plotDim.axis.format(d)).tickPadding(8) : axisTop(scale).tickValues(tickValues).tickFormat((d) => plotDim.axis.format(d))
+    );
+    axisstyle({
+      axis: dom.axis,
+      showline: true,
+      fontsize: 12,
+      color: this.textColor
+    });
+  }
+  renderBoxPlots(dom, chart, scale, settings) {
+    for (const plot of chart.plots) {
+      const g = dom.boxplots.append("g").attr("class", "sjpp-boxplot-plot").attr("padding", "5px");
+      drawBoxplot({
+        bp: plot.boxplot,
+        g,
+        color: settings.displayMode == "filled" ? "black" : plot.color,
+        scale,
+        rowheight: settings.rowHeight,
+        labpad: settings.labelPad,
+        labColor: this.textColor
+      });
+      const transformStr = `translate(${plot.x}, ${plot.y})${settings.isVertical ? `, rotate(-90)` : ""}`;
+      g.attr("transform", transformStr);
+      if (settings.isVertical) {
+        g.select("text").attr("transform", "rotate(45)");
+      }
+      new BoxPlotToolTips(plot, g, dom.tip, settings.isVertical);
+      const numCollection = isNumTermCollection(this.interactions.getPlotConfig().term.term);
+      if (!numCollection && chart.plots.length > 1) {
+        const labelMenuTip = new Menu({ padding: "" });
+        new BoxPlotLabelMenu(
+          plot,
+          this.app,
+          this.interactions,
+          labelMenuTip,
+          settings.isVertical
+          /*chart*/
+        );
+      }
+    }
+  }
+};
+
+// plots/boxplot/view/View.ts
+var View = class {
+  constructor(viewData, settings, dom, app, interactions) {
+    this.app = app;
+    this.dom = dom;
+    this.interactions = interactions;
+    this.settings = settings;
+    if (!viewData || !viewData.charts) return;
+    dom.div.style("background-color", viewData.backgroundColor);
+    for (const chart of Object.values(viewData.charts)) {
+      const chartWrapper = dom.charts.append("div").attr("class", "sjpp-boxplot-chart-wrapper");
+      const svg = chartWrapper.append("svg").attr("class", "sjpp-boxplot-svg");
+      chart["svg"] = svg;
+      const chartDom = {
+        svg,
+        tip: dom.tip
+      };
+      if (chart.plotDim.subtitle.text) {
+        chartDom.subtitle = svg.append("text");
+      }
+      chartDom.title = svg.append("text");
+      chartDom.axis = svg.append("g");
+      chartDom.boxplots = svg.append("g").attr("class", "sjpp-boxplot-boxplots");
+      if (chart.wilcoxon) {
+        chartDom.assocTableDiv = chartWrapper.append("div").attr("class", "sjpp-boxplot-wilcoxon").style("display", "inline-block");
+      }
+      new ChartRender(
+        chartDom,
+        this.settings,
+        this.app,
+        this.interactions,
+        chart,
+        viewData.backgroundColor,
+        viewData.textColor
+      );
+    }
+    new LegendRenderer(dom.legend, viewData.legend, interactions, viewData.textColor);
+  }
+};
+
+// plots/boxplot/BoxPlotControlInputs.ts
+function setBoxPlotControlInputs(state, app, opts, getCharts, useDefaultSettings) {
+  const controlLabels = state.config.controlLabels;
+  if (!controlLabels) throw new Error("controls labels not found");
+  const specialCase = getSingleCellSpecialCase(state.config);
+  const inputs = [
+    {
+      type: "term",
+      configKey: "term",
+      chartType: "boxplot",
+      usecase: { target: "boxplot", detail: "term" },
+      label: controlLabels.term1?.label || renderTerm1Label,
+      vocabApi: app.vocabApi,
+      menuOptions: "edit",
+      // Hide term1 control for termCollection; later reenable when tw edit menu works to allow choosing subset of member terms
+      // and take into account state changes.
+      getDisplayStyle: (plot) => isNumTermCollection(plot.config.term?.term) ? "none" : ""
+    },
+    {
+      type: "term",
+      configKey: "term2",
+      chartType: "boxplot",
+      usecase: { target: "boxplot", detail: "term2", specialCase },
+      title: controlLabels.term2.title || controlLabels.term2.label,
+      label: controlLabels.term2.label,
+      vocabApi: app.vocabApi,
+      numericEditMenuVersion: opts.numericEditMenuVersion || ["continuous", "discrete"],
+      defaultQ4fillTW: getT0T2defaultQ(),
+      // Hide term2 control when numeric termCollection is detected
+      // and take into account state changes.
+      getDisplayStyle: (plot) => isNumTermCollection(plot.config.term?.term) ? "none" : ""
+    },
+    {
+      type: "term",
+      configKey: "term0",
+      chartType: "boxplot",
+      usecase: { target: "boxplot", detail: "term0", specialCase },
+      title: controlLabels.term0.title || controlLabels.term0.label,
+      label: controlLabels.term0.label,
+      vocabApi: app.vocabApi,
+      // by default, do not allow continuous mode for divide-by term, since
+      // it will create a separate violin-overlay group per unique float or integer value
+      // and there will nonsensical tens/hundreds of these charts based on the cohort size
+      numericEditMenuVersion: opts.numericEditMenuVersion || ["discrete"],
+      defaultQ4fillTW: getT0T2defaultQ(),
+      // Hide term0 control when numeric termCollection is detected
+      // and take into account state changes.
+      getDisplayStyle: (plot) => isNumTermCollection(plot.config.term?.term) ? "none" : ""
+    },
+    {
+      label: "Order by",
+      title: "Order box plots by parameters",
+      type: "radio",
+      chartType: "boxplot",
+      settingsKey: "orderByMedian",
+      options: [
+        { label: "Default", value: false },
+        { label: "Median values", value: true }
+      ],
+      getDisplayStyle: () => {
+        const charts = getCharts();
+        let style = "none";
+        for (const k of Object.keys(charts)) {
+          const chart = charts[k];
+          if (chart.plots.length > 1) style = "";
+        }
+        return style;
+      }
+    },
+    {
+      label: "Scale",
+      title: "Change the axis scale",
+      type: "radio",
+      chartType: "boxplot",
+      settingsKey: "isLogScale",
+      options: [
+        { label: "Linear", value: false },
+        { label: "Log10", value: true }
+      ]
+    },
+    {
+      label: "Orientation",
+      title: "Change the orientation of the box plots",
+      type: "radio",
+      chartType: "boxplot",
+      settingsKey: "isVertical",
+      options: [
+        { label: "Horizontal", value: false },
+        { label: "Vertical", value: true }
+      ]
+    },
+    {
+      label: "Plot length",
+      title: "Set the plot length of the entire plot in pixels, >=200",
+      type: "number",
+      chartType: "boxplot",
+      settingsKey: "plotLength",
+      debounceInterval: 500,
+      min: 200,
+      step: 10
+    },
+    {
+      label: "Box size",
+      title: "Set the box size or thickness in pixels of each box plot between 20 and 50",
+      type: "number",
+      chartType: "boxplot",
+      settingsKey: "rowHeight",
+      step: 1,
+      max: 50,
+      min: 20,
+      debounceInterval: 500,
+      processInput: (val) => {
+        if (useDefaultSettings == true) useDefaultSettings = false;
+        return val;
+      }
+    },
+    {
+      label: "Plots padding",
+      title: "Set the space between each box plot. Number must be between 10 and 20",
+      type: "number",
+      chartType: "boxplot",
+      settingsKey: "rowSpace",
+      step: 1,
+      max: 20,
+      min: 10,
+      debounceInterval: 500,
+      processInput: (val) => {
+        if (useDefaultSettings == true) useDefaultSettings = false;
+        return val;
+      }
+    },
+    {
+      label: "Default color",
+      type: "color",
+      chartType: "boxplot",
+      settingsKey: "color",
+      getDisplayStyle: () => {
+        const charts = getCharts();
+        let style = "";
+        for (const k of Object.keys(charts)) {
+          const chart = charts[k];
+          if (chart.plots.length > 1) style = "none";
+        }
+        return style;
+      }
+    },
+    {
+      label: "Display mode",
+      title: "Apply a dark theme to the plot",
+      type: "radio",
+      chartType: "boxplot",
+      settingsKey: "displayMode",
+      options: [
+        { label: "Default", value: "default" },
+        { label: "Filled", value: "filled" },
+        { label: "Dark mode", value: "dark" }
+      ]
+    },
+    {
+      label: "Show association tests",
+      boxLabel: "",
+      type: "checkbox",
+      chartType: "boxplot",
+      settingsKey: "showAssocTests",
+      title: `Show association tests next to the box plots.`,
+      getDisplayStyle: (plot) => {
+        return plot?.term2 ? "" : "none";
+      }
+    }
+  ];
+  if (state.termdbConfig?.boxplots?.removeOutliers) {
+    inputs.push({
+      label: "Remove outliers",
+      boxLabel: "",
+      type: "checkbox",
+      chartType: "boxplot",
+      settingsKey: "removeOutliers",
+      title: `Option to remove outliers from the analysis`
+    });
+  }
+  return inputs;
+}
+
+// plots/boxplot/BoxPlot.ts
+var TdbBoxplot = class _TdbBoxplot extends PlotBase {
+  constructor(opts, api) {
+    super(opts, api);
+    this.useDefaultSettings = true;
+    this.configTermKeys = ["term", "term0", "term2"];
+    this.type = _TdbBoxplot.type;
+    this.components = {
+      controls: {}
+    };
+    const holder = opts.holder.classed("sjpp-boxplot-main", true);
+    const { controls, errdiv, loadingDiv, mainDiv, renderedData, charts, legendDiv } = this.getStandardDomLayout(
+      holder,
+      opts
+    );
+    this.dom = {
+      controls,
+      div: mainDiv,
+      error: errdiv,
+      loading: loadingDiv,
+      renderedData,
+      charts: charts.attr("class", "sjpp-boxplot-charts").style("display", "flex").style("flex-direction", "row").style("flex-wrap", "wrap").style("max-width", "100vw"),
+      legend: legendDiv.append("div").attr("class", "sjpp-boxplot-legend").style("margin-top", "25px"),
+      tip: new Menu()
+    };
+    if (opts.header) this.dom.header = opts.header.html("Box plot");
+  }
+  static {
+    this.type = "boxplot";
+  }
+  async setControls() {
+    const state = this.getState(this.app.getState());
+    const inputs = setBoxPlotControlInputs(
+      state,
+      this.app,
+      this.opts,
+      () => {
+        return this.data?.charts || [];
+      },
+      this.useDefaultSettings
+    );
+    this.components.controls = await controlsInit({
+      app: this.app,
+      id: this.id,
+      holder: this.dom.controls.style("display", "inline-block"),
+      inputs
+    });
+    this.components.controls.on("downloadClick.boxplot", (event) => {
+      this.download(event);
+    });
+    this.components.controls.on("helpClick.boxplot", () => {
+      this.interactions.help();
+    });
+    if (state.termdbConfig?.hidePlotDocumentation) {
+      this.dom.controls.select('div[aria-label="Documentation"]').remove();
+    }
+  }
+  reactsTo(action) {
+    if (action.type.startsWith("plot_")) {
+      return (action.id === this.id || action.id == this.parentId) && (!action.config?.childType || action.config?.childType == this.type);
+    }
+    return true;
+  }
+  getState(appState) {
+    const config = appState.plots.find((p) => p.id === this.id);
+    if (!config) {
+      throw new Error(
+        `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`
+      );
+    }
+    const parentConfig = appState.plots.find((p) => p.id === this.parentId);
+    const termfilter = getCombinedTermFilter(appState, config.filter || parentConfig?.filter);
+    return {
+      termdbConfig: appState.termdbConfig,
+      termfilter,
+      vocab: appState.vocab,
+      config: Object.assign({}, config, {
+        settings: {
+          boxplot: config.settings.boxplot
+        }
+      })
+    };
+  }
+  async init() {
+    this.dom.div.style("display", "inline-block").style("margin-left", "20px");
+    this.interactions = new BoxPlotInteractions(this, () => this.data);
+    await this.setControls();
+  }
+  async main() {
+    const c = this.state.config;
+    if (c.childType != this.type && c.chartType != this.type) return;
+    if (!this.interactions) throw new Error("Interactions not initialized [box plot main()]");
+    const config = await this.getMutableConfig();
+    const settings = config.settings.boxplot;
+    const model = new Model(this, config);
+    try {
+      this.toggleLoadingDiv("block", "block");
+      const data = await model.getData();
+      if (isErrorResponse(data)) throw new Error(data.error);
+      setDescrStatsByTerm([config.term, config.term2], data.descrStats);
+      config.bins = data.bins;
+      if (!data.charts || !Object.keys(data.charts).length) {
+        this.interactions.clearDom();
+        this.dom.error.style("padding", "20px 20px 20px 60px").text("No visible box plot data to render");
+        this.toggleLoadingDiv("none");
+        return;
+      }
+      this.data = data;
+    } catch (e) {
+      this.toggleLoadingDiv("none", "none");
+      if (this.app.isAbortError(e)) return;
+      if (e.stack) console.log(e.stack);
+      if (e instanceof Error) console.error(e.message || e);
+      throw new Error(e);
+    }
+    this.interactions.clearDom();
+    const labels = Object.values(this.data.charts).reduce((labels2, chart) => {
+      const chartLabels = chart.plots.filter((p) => !p.isHidden).map((p) => p.boxplot.label);
+      labels2.push(...chartLabels);
+      return labels2;
+    }, []);
+    const tempsvg = this.dom.charts.append("svg");
+    const maxLabelLgth = getMaxLabelWidth(tempsvg.append("g"), labels);
+    tempsvg.remove();
+    const viewModel = new ViewModel(config, this.data, settings, maxLabelLgth, this.useDefaultSettings);
+    if (!viewModel.viewData) throw new Error("No viewData from ViewModel");
+    if ((viewModel.rowSpace !== settings.rowSpace || viewModel.rowHeight !== settings.rowHeight) && this.useDefaultSettings == true) {
+      settings.rowSpace = viewModel.rowSpace;
+      settings.rowHeight = viewModel.rowHeight;
+      this.app.save({
+        type: "plot_edit",
+        id: this.id,
+        config: {
+          settings: {
+            boxplot: {
+              rowSpace: viewModel.rowSpace,
+              rowHeight: viewModel.rowHeight
+            }
+          }
+        }
+      });
+    }
+    this.toggleLoadingDiv("none");
+    this.dom.renderedData.style("display", "");
+    new View(viewModel.viewData, settings, this.dom, this.app, this.interactions);
+    this.data.charts = viewModel.viewData.charts;
+  }
+  getChartImages() {
+    const chartImages = [];
+    const charts = this.data.charts;
+    for (const [key, chart] of Object.entries(charts)) {
+      const svg = chart.svg;
+      const title = getChartTitle(this.state.config, key);
+      const name = `${this.state.config.term.term.name}  ${title}`;
+      chartImages.push({ name, svg });
+    }
+    return chartImages;
+  }
+  download(event) {
+    if (!this.state) return;
+    const config = this.state.config;
+    const name2svg = this.getChartImages();
+    const filename = config.term.term.name;
+    const extraOptions = [];
+    const descrStatsByTerm = this.data?.descrStats || {};
+    const statTerms = [config.term, config.term2].filter(
+      (tw) => tw?.$id && descrStatsByTerm[tw.$id] && tw.term.type != "termCollection"
+    );
+    if (statTerms.length) {
+      extraOptions.push({
+        label: "Descriptive statistics",
+        testid: "sjpp-download-descrstats",
+        filename: `${filename}_descriptive_stats`,
+        callback: () => descrStatsToTSV(statTerms.map((tw) => ({ name: tw.term.name, stats: descrStatsByTerm[tw.$id] })))
+      });
+    }
+    const charts = Object.entries(this.data?.charts || {});
+    if (charts.some(([, chart]) => chart.wilcoxon?.length)) {
+      extraOptions.push({
+        label: "Group comparisons",
+        testid: "sjpp-download-comparison",
+        filename: `${filename}_wilcoxon_group_comparisons`,
+        callback: () => testRowsToTSV(
+          "Wilcoxon's rank sum test",
+          ["Group 1", "Group 2", "P-value"],
+          charts.filter(([, chart]) => chart.wilcoxon).map(([chartId, chart]) => ({ chartLabel: getChartTitle(config, chartId), rows: chart.wilcoxon }))
+        )
+      });
+    }
+    const dm = new CustomDownloadMenu({ chartImages: name2svg, filename, extraOptions });
+    dm.show(event.clientX, event.clientY, event.target);
+  }
+};
+var boxplotInit = getCompInit(TdbBoxplot);
+var componentInit = boxplotInit;
+async function getPlotConfig(opts, app) {
+  try {
+    if (!opts.term) throw new Error("opts.term{} missing");
+    if (opts.term.term?.type == "termCollection") {
+    }
+    await fillTermWrapper(opts.term, app.vocabApi);
+    if (opts.term2) await fillTermWrapper(opts.term2, app.vocabApi);
+    if (opts.term0) await fillTermWrapper(opts.term0, app.vocabApi);
+  } catch (e) {
+    console.error(new Error(`${e} [boxplot getPlotConfig()]`));
+    throw new Error(`boxplot getPlotConfig() failed`);
+  }
+  const config = {
+    id: opts.term.term.id || opts.term.$id,
+    controlLabels: Object.assign({}, defaultUiLabels, app.vocabApi.termdbConfig.uiLabels || {}),
+    settings: {
+      controls: {
+        term2: null,
+        term0: null
+      },
+      boxplot: getDefaultBoxplotSettings(app, opts.overrides || {})
+    }
+  };
+  return copyMerge(config, opts);
+}
+export {
+  TdbBoxplot,
+  boxplotInit,
+  componentInit,
+  getPlotConfig
+};
+//# sourceMappingURL=BoxPlot-6UOLWXPV.js.map