@sjcrh/proteinpaint-client 2.219.1 → 2.221.0

package/dist/BoxPlot-22RXMPRL.js

@@ -1,1229 +0,0 @@
-import {
-  getDefaultBoxplotSettings
-} from "./chunk-GX6G2SSW.js";
-import {
-  CustomDownloadMenu,
-  ListSamples,
-  PlotBase,
-  axisstyle,
-  controlsInit,
-  defaultUiLabels,
-  descrStatsToTSV,
-  drawBoxplot,
-  fillTermWrapper,
-  getChartTitle,
-  getCombinedTermFilter,
-  getMaxLabelWidth,
-  getSingleCellSpecialCase,
-  getT0T2defaultQ,
-  joinToFilterUiRoot,
-  renderTable,
-  renderTerm1Label,
-  setDescrStatsByTerm,
-  testRowsToTSV
-} from "./chunk-BKW35Z4U.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-ETXOEP4N.js";
-import {
-  Menu
-} from "./chunk-CNFTQSNE.js";
-import "./chunk-5NI77Z3O.js";
-import "./chunk-TVJOSRCH.js";
-import "./chunk-3CIL7KH7.js";
-import "./chunk-T4XPCSLP.js";
-import "./chunk-CJHNPYFQ.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-NR6WFCPF.js";
-import {
-  isNumTermCollection,
-  isNumericTerm
-} from "./chunk-GN2A5NL5.js";
-import {
-  axisLeft,
-  axisTop,
-  isErrorResponse
-} from "./chunk-ME3HB3V6.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-HBNB5TRH.js";
-import "./chunk-PF4DSFDR.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-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 sampleList = this.initListSamples(plot);
-    const filter = joinToFilterUiRoot(this.app.getState().termfilter.filter, [sampleList.tvslst]);
-    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-22RXMPRL.js.map