@sjcrh/proteinpaint-client 2.207.0 → 2.207.1

package/dist/Violin-F3QS2EMJ.js

@@ -0,0 +1,1082 @@
+import {
+  getDefaultViolinSettings
+} from "./chunk-W4RYRU5D.js";
+import {
+  DownloadMenu,
+  ListSamples,
+  PlotBase,
+  controlsInit,
+  defaultUiLabels,
+  fillTermWrapper,
+  filterJoin,
+  getCombinedTermFilter,
+  getFilterItemByTag,
+  getMaxLabelWidth,
+  getSingleCellSpecialCase,
+  getT0T2defaultQ,
+  htmlLegend,
+  renderTable,
+  renderTerm1Label,
+  table2col
+} from "./chunk-PC4MFDHP.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-KV4W2ACA.js";
+import "./chunk-HPAW7XDM.js";
+import {
+  Menu
+} from "./chunk-ELJX3QIQ.js";
+import "./chunk-BZN2O76M.js";
+import "./chunk-EEB5VE2A.js";
+import "./chunk-6RRZRISL.js";
+import "./chunk-2KM4PRQM.js";
+import "./chunk-52QHIKH2.js";
+import "./chunk-A2ORIMUJ.js";
+import {
+  isNumericTw
+} from "./chunk-PPSWNLMG.js";
+import {
+  SINGLECELL_GENE_EXPRESSION
+} from "./chunk-RUBZCKIX.js";
+import {
+  copyMerge,
+  getCompInit
+} from "./chunk-WINIL2KN.js";
+import "./chunk-PF4DSFDR.js";
+import {
+  niceNumLabels
+} from "./chunk-7X6NF7NI.js";
+import {
+  getValueConversionFactor,
+  toUserUnit
+} from "./chunk-W5J3LTYS.js";
+import {
+  axisLeft,
+  axisTop,
+  basis_default,
+  line_default
+} from "./chunk-Z2ZITHT4.js";
+import {
+  format,
+  linear,
+  log
+} from "./chunk-4OLM3KSB.js";
+import "./chunk-FXQXCOII.js";
+import "./chunk-TLT4YIG3.js";
+import {
+  brushX,
+  brushY
+} from "./chunk-5R63Q5KH.js";
+import "./chunk-I6Y4O3RR.js";
+import {
+  rgb
+} from "./chunk-Q5RDQNIT.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-HS5PO5ZQ.js";
+
+// plots/violin/violin.renderer.ts
+function getNumericTerm(t1, t2) {
+  return t2?.q?.mode === "continuous" ? t2.term : t1?.term;
+}
+function setViolinRenderer(self) {
+  self.render = function() {
+    const settings = self.config.settings.violin;
+    const isH = settings.orientation === "horizontal";
+    const t1 = self.config.term;
+    const t2 = self.config.term2;
+    const termNum = t2?.term.type === "condition" || t2?.term.type === "samplelst" || t2?.term.type === "categorical" || (t2?.term.type === "float" || t2?.term.type === "integer") && t1.q.mode === "continuous" ? t2 : t1;
+    if (!termNum?.q.hiddenValues) termNum.q.hiddenValues = {};
+    if (termNum?.term?.values) {
+      for (const [k, val] of Object.entries(termNum.term.values)) {
+        const v = val;
+        if (v.uncomputable) {
+          if (termNum.q.hiddenValues[k]) {
+            termNum.q.hiddenValues[v.label] = 1;
+            delete termNum.q.hiddenValues[k];
+          }
+        }
+      }
+    }
+    self.dom.violinDiv.selectAll("*").remove();
+    const chartKeys = Object.keys(self.data.charts);
+    if (!chartKeys?.length) {
+      self.dom.banner.html(`<span>No visible violin plot data to render</span>`).style("display", "block");
+      self.dom.legendDiv.selectAll("*").remove();
+      return;
+    }
+    for (const chartKey of chartKeys) {
+      const chart = self.data.charts[chartKey];
+      const plots = chart.plots.filter((p) => !termNum?.q?.hiddenValues?.[p.label || p.seriesId]);
+      if (settings.orderByMedian == true) {
+        plots.sort(
+          (a, b) => a.summaryStats.find((x) => x.id === "median").value - b.summaryStats.find((x) => x.id === "median").value
+        );
+      }
+      if (self.legendRenderer) self.legendRenderer(getLegendGrps(termNum, self));
+      const chartDiv = self.dom.violinDiv.append("div").attr("class", "sjpp-vp-chartDiv").style("padding", Object.keys(self.data.charts).length > 1 ? "20px 20px 0px 0px" : "0px");
+      chart.chartDiv = chartDiv;
+      if (plots.length === 0) {
+        chartDiv.html(
+          ` <span style="opacity:.6;font-size:1em;margin-left:90px;">No visible violin plot data to render</span>`
+        );
+        return;
+      }
+      chartDiv.select(".sjpp-violin-plot").remove();
+      const chartWrapper = chartDiv.append("div").style("display", "inline-block");
+      if (chart.chartId) {
+        const totalCount = chart.plots.reduce((acc, plot) => acc + plot.plotValueCount, 0);
+        chartWrapper.append("div").attr("class", "pp-chart-title").style("display", "block").style("text-align", "center").style("font-size", "1.1em").style("margin-bottom", "5px").html(`${self.getChartTitle(chart.chartId)} (n=${totalCount})`);
+      }
+      const svgData = renderSvg(t1, plots, chartWrapper, self, isH, settings);
+      renderScale(t1, t2, settings, isH, svgData, self);
+      let y = 0;
+      const thickness = self.settings.plotThickness || self.getAutoThickness();
+      for (const plot of plots) {
+        const wScale = linear().domain([plot.density.densityMax, plot.density.densityMin]).range([thickness / 2, 0]);
+        let areaBuilder;
+        if (isH) {
+          areaBuilder = line_default().curve(basis_default).x((d) => svgData.axisScale(d.x0)).y((d) => wScale(d.density));
+        } else {
+          areaBuilder = line_default().curve(basis_default).x((d) => wScale(d.density)).y((d) => svgData.axisScale(d.x0));
+        }
+        const { violinG, height } = renderViolinPlot(svgData, plot, isH, wScale, areaBuilder, y);
+        y += height;
+        if (self.opts.mode != "minimal") renderLabels(t1, t2, violinG, plot, isH, settings);
+        if (self.config.term.term.type == SINGLECELL_GENE_EXPRESSION) {
+        } else {
+          if (self.opts.mode != "minimal") renderBrushing(t1, t2, violinG, settings, plot, isH, svgData);
+        }
+        self.labelHideLegendClicking(t2, plot);
+      }
+      if (self.settings.showAssociationTests) self.renderPvalueTable(chartDiv, chart);
+    }
+  };
+  self.displaySummaryStats = function(data, event) {
+    const d = data;
+    if (!d.summaryStats) return;
+    self.dom.hovertip.clear().show(event.clientX, event.clientY);
+    const table = table2col({ holder: self.dom.hovertip.d.append("div") });
+    const term = getNumericTerm(self.config.term, self.config.term2);
+    for (const { key, label, value } of Object.values(d.summaryStats))
+      table.addRow(label, key == "total" ? value : toUserUnit(value, term));
+  };
+  self.getAutoThickness = function() {
+    let maxPlotCount = 0;
+    for (const k of Object.keys(this.data.charts)) {
+      const chart = this.data.charts[k];
+      maxPlotCount = Math.max(maxPlotCount, chart.plots.length);
+    }
+    if (maxPlotCount == 1) return 150;
+    return Math.min(100, Math.max(40, 600 / maxPlotCount));
+  };
+  self.getPlotThicknessWithPadding = function() {
+    const plotThickness = self.settings.plotThickness || self.getAutoThickness();
+    return plotThickness + self.settings.rowSpace;
+  };
+  self.renderPvalueTable = function(chartDiv, chart) {
+    if (!chart.pvalues) return;
+    const tableHolder = chartDiv.append("div").classed("sjpp-tableHolder", true).style("display", "inline-block").style("padding", "10px").style("vertical-align", "top").style("margin-left", "0px").style("margin-top", "30px").style("margin-right", "30px");
+    const t1 = self.config.term;
+    const t2 = self.config.term2;
+    if (!t2) {
+      tableHolder.style("display", "none");
+      return;
+    }
+    const termNum = t2?.term.type === "condition" || t2?.term.type === "samplelst" || t2?.term.type === "categorical" || (t2?.term.type === "float" || t2?.term.type === "integer") && t1.q.mode === "continuous" ? t2 : t1;
+    const pvalues = chart.pvalues.filter((arr) => {
+      for (let i = 0; i < arr.length; i++) {
+        if (typeof arr[i].value === "string") {
+          if (termNum.q?.hiddenValues && arr[i].value in termNum.q.hiddenValues) {
+            return false;
+          }
+        }
+      }
+      return true;
+    });
+    tableHolder.style("display", "inline-block").style("vertical-align", "top").append("div").style("font-weight", "bold").text(pvalues.length > 0 ? "Group comparisons (Wilcoxon's rank sum test)" : "");
+    const columns = [{ label: "Group 1" }, { label: "Group 2" }, { label: "P-value" }];
+    const rows = pvalues;
+    const isH = this.settings.orientation === "horizontal";
+    const maxHeight = isH ? self.getPlotThicknessWithPadding() * chart.plots.length + 10 : this.settings.svgw + this.config.term.term.name.length;
+    renderTable({
+      rows,
+      columns,
+      div: tableHolder,
+      showLines: false,
+      maxWidth: "27vw",
+      maxHeight: `${maxHeight}px`,
+      resize: true
+    });
+  };
+  self.getChartTitle = function(chartId) {
+    if (!self.config.term0) return chartId;
+    return self.config.term0.term.values && chartId in self.config.term0.term.values ? self.config.term0.term.values[chartId].label : chartId;
+  };
+  function createMargins(labelsize, settings, isH, isMinimal) {
+    let margins;
+    if (isMinimal) {
+      margins = isH ? { left: 5, top: settings.axisHeight, right: settings.rightMargin, bottom: 10 } : { left: settings.axisHeight, top: 30, right: settings.rightMargin, bottom: 10 };
+    } else {
+      margins = isH ? { left: labelsize + 5, top: settings.axisHeight, right: settings.rightMargin, bottom: 10 } : { left: settings.axisHeight, top: 50, right: settings.rightMargin, bottom: labelsize };
+    }
+    return margins;
+  }
+  function renderSvg(t1, plots, chartDiv, self2, isH, settings) {
+    const violinDiv = chartDiv.append("div").style("display", "inline-block").style("padding", self2.opts.mode != "minimal" ? "5px" : "0px").style("overflow", "auto").style("scrollbar-width", "none");
+    const violinSvg = violinDiv.append("svg");
+    const labelsize = getMaxLabelWidth(
+      violinSvg,
+      plots.map((plot) => `${plot.label}, n=${plot.plotValueCount}`)
+    );
+    const margin = createMargins(labelsize, settings, isH, self2.opts.mode == "minimal");
+    const plotThickness = self2.getPlotThicknessWithPadding();
+    const width = margin.left + margin.top + (isH ? settings.svgw : plotThickness * plots.length + t1.term.name.length);
+    const height = margin.bottom + margin.top + (isH ? plotThickness * plots.length : settings.svgw + t1.term.name.length);
+    violinSvg.attr("width", width).attr("height", height).classed("sjpp-violin-plot", true).attr("data-testid", "sja_violin_plot");
+    const svgG = violinSvg.append("g").attr("transform", "translate(" + margin.left + "," + margin.top + ")");
+    return { margin, svgG, axisScale: createNumericScale(self2, settings, isH), violinSvg };
+  }
+  function renderScale(t1, t2, settings, isH, svg, self2) {
+    const g = svg.svgG.append("g").style("font-size", "12").classed(settings.isLogScale ? "sjpp-logscale" : "sjpp-linearscale", true);
+    const f = getValueConversionFactor(getNumericTerm(t1, t2));
+    const uiScale = f == 1 ? svg.axisScale : svg.axisScale.copy().domain(svg.axisScale.domain().map((v) => v * f));
+    const ticks = settings.isLogScale ? uiScale.ticks(15) : (
+      // svg.axisScale.ticks().filter(tick => tick > 0 || tick < 0)
+      uiScale.ticks()
+    );
+    g.call(
+      (isH ? axisTop : axisLeft)(uiScale).scale(uiScale).tickFormat((d, i) => {
+        const value = Number(d);
+        if (settings.isLogScale) {
+          if (self2.app.vocabApi.termdbConfig.logscaleBase2) {
+            if (ticks.length > 10 && i % 2 !== 0) return "";
+            if (value < 0.1) return format(".3f")(value);
+            return format(".1f")(value);
+          } else {
+            if (ticks.length >= 12 && i % 5 !== 0) return "";
+            if (value < 50) return String(value);
+            return format(".1s")(value);
+          }
+        }
+        if (ticks.length >= 12 && i % 2 !== 0) return "";
+        return String(value);
+      }).tickValues(ticks)
+    );
+    if (self2.opts.mode != "minimal") {
+      const numTerm = getNumericTerm(t1, t2);
+      const n = numTerm.valueConversion ? `${numTerm.name} (${numTerm.valueConversion.toUnit}s)` : numTerm.name;
+      svg.svgG.append("text").text(n).classed("sjpp-numeric-term-label", true).attr("data-testid", `sjpp-violin-label-${n}`).style("font-weight", 600).attr("text-anchor", "middle").attr("x", isH ? settings.svgw / 2 : -settings.svgw / 2).attr("y", isH ? -30 : -45).style("opacity", 0).attr("transform", isH ? null : "rotate(-90)").style("opacity", 1);
+    }
+  }
+  function renderViolinPlot(svgData, plot, isH, wScale, areaBuilder, y) {
+    const label = plot.label?.split(",")[0];
+    const catTerm = self.config.term.q.mode == "discrete" ? self.config.term : self.config.term2;
+    const category = catTerm?.term.values ? Object.values(catTerm.term.values).find(
+      (o) => o.label == label
+    ) ?? null : null;
+    let color;
+    if (catTerm) {
+      if (catTerm.q.type == "predefined-groupset" || catTerm.q.type == "custom-groupset") {
+        const groupset = catTerm.q.type == "predefined-groupset" ? catTerm.term.groupsetting.lst[catTerm.q.predefined_groupset_idx] : catTerm.q.customset;
+        if (!groupset) throw "groupset is missing";
+        const group = groupset.groups.find((g) => g.name == label);
+        if (group?.color) color = group.color;
+      } else {
+        color = category?.color;
+      }
+    }
+    if (!color) color = self.config.settings.violin.defaultColor;
+    if (!plot.color) plot.color = color;
+    if (category && !category.color) category.color = color;
+    const svg = svgData.svgG;
+    const violinG = svg.append("g").datum(plot).attr("class", "sjpp-violinG");
+    renderArea(violinG, plot, areaBuilder);
+    renderArea(violinG, plot, isH ? areaBuilder.y((d) => -wScale(d.density)) : areaBuilder.x((d) => -wScale(d.density)));
+    renderSymbolImage(self, violinG, plot, isH);
+    if (self.opts.mode != "minimal") renderMedian(violinG, isH, plot, svgData, self);
+    renderLines(violinG, isH, self.config.settings.violin.lines, svgData);
+    if ("value" in self.state.config) {
+      const value = svgData.axisScale(self.state.config.value);
+      const s = self.config.settings.violin;
+      violinG.append("line").style("stroke", "black").style("stroke-width", s.medianThickness).attr("x1", 200).attr("x2", 200).attr("x1", isH ? value : -s.medianLength).attr("x2", isH ? value : s.medianLength).attr("y1", isH ? -s.medianLength : value).attr("y2", isH ? s.medianLength : value);
+    }
+    const height = self.getPlotThicknessWithPadding();
+    const translate = isH ? `translate(0, ${y + height / 2}) ` : `translate(${y + height / 2}, 0)`;
+    violinG.attr("transform", translate);
+    return { violinG, height };
+  }
+  function renderLabels(t1, t2, violinG, plot, isH, settings) {
+    violinG.append("text").attr("data-testid", "sjpp-violin-label").text(`${plot.label}, n=${plot.plotValueCount}`).style("cursor", "pointer").on("click", function(event) {
+      if (!event) return;
+      self.displayLabelClickMenu(t1, t2, plot, event);
+    }).on("mouseover", function(event, d) {
+      event.stopPropagation();
+      if (!event) return;
+      self.displaySummaryStats(d, event);
+    }).on("mouseout", function() {
+      self.dom.hovertip.hide();
+    }).style("opacity", 0).style("opacity", 1).attr("x", isH ? -5 : 0 - settings.svgw - 5).attr("y", 0).attr("text-anchor", "end").attr("dominant-baseline", "central").attr("transform", isH ? null : "rotate(-90)");
+  }
+  function renderArea(violinG, plot, areaBuilder) {
+    if (plot.density.densityMax == 0) return;
+    violinG.append("path").attr("class", "sjpp-vp-path").style("fill", self.opts.mode === "minimal" ? rgb(221, 221, 221) : plot.color).style("opacity", 0).attr("stroke", rgb(plot.color).darker()).attr("stroke-width", 1).attr("stroke-linejoin", "round").style("opacity", "0.8").attr("d", areaBuilder(plot.density.bins));
+  }
+  function renderSymbolImage(self2, violinG, plot, isH) {
+    const i = violinG.append("image").style("opacity", 0).classed(self2.config.settings.violin.datasymbol === "rug" ? "sjpp-rug-img" : "sjpp-beans-img", true).style("opacity", 1).attr("xlink:href", plot.src).attr(
+      "transform",
+      isH ? `translate(0, -${self2.settings.radius / 2})` : `translate(-${self2.settings.radius / 2}, 0)`
+    );
+    if (self2.settings.orientation == "horizontal") {
+      i.attr("width", self2.settings.svgw);
+    } else if (self2.settings.orientation == "vertical") {
+      i.attr("height", self2.settings.svgw);
+    }
+  }
+  function renderMedian(violinG, isH, plot, svgData, self2) {
+    const s = self2.config.settings.violin;
+    const median = svgData.axisScale(plot.summaryStats.median.value);
+    if (plot.plotValueCount >= 2) {
+      violinG.append("line").attr("class", "sjpp-median-line").style("stroke-width", s.medianThickness).style("stroke", s.medianColor).style("opacity", "0.5").attr("y1", isH ? -s.medianLength : median).attr("y2", isH ? s.medianLength : median).attr("x1", isH ? median : -s.medianLength).attr("x2", isH ? median : s.medianLength);
+    } else return;
+  }
+  function renderLines(violinG, isH, lines, svgData) {
+    const plotThickness = self.settings.plotThickness;
+    violinG.selectAll(".sjpp-vp-line").remove();
+    if (!lines?.length) return;
+    for (const line of lines) {
+      violinG.append("line").attr("class", "sjpp-vp-line").style("stroke", self.opts.mode == "minimal" ? "red" : "black").attr("y1", isH ? -(plotThickness / 2) : svgData.axisScale(line)).attr("y2", isH ? plotThickness / 2 : svgData.axisScale(line)).attr("x1", isH ? svgData.axisScale(line) : -(plotThickness / 2)).attr("x2", isH ? svgData.axisScale(line) : plotThickness / 2);
+    }
+  }
+  function renderBrushing(t1, t2, violinG, settings, plot, isH, svgData) {
+    if (settings.datasymbol === "rug" || settings.datasymbol === "bean") {
+      const br = isH ? brushX().extent([
+        [0, -20],
+        [settings.svgw, 20]
+      ]).on("end", (event) => {
+        if (!event.selection) return;
+        self.displayBrushMenu(t1, t2, self, plot, event, svgData.axisScale, isH);
+        document.body.addEventListener("pointerdown", onClickOut, true);
+      }) : brushY().extent([
+        [-20, 0],
+        [20, settings.svgw]
+      ]).on("end", (event) => {
+        if (!event.selection) return;
+        self.displayBrushMenu(t1, t2, self, plot, event, svgData.axisScale, isH);
+        document.body.addEventListener("pointerdown", onClickOut, true);
+      });
+      const brushG = violinG.append("g").classed("sjpp-brush", true).call(br);
+      const onClickOut = (e) => {
+        if (!brushG || !br) return;
+        if (!brushG.node().contains(e.target)) br.clear(brushG);
+        document.body.removeEventListener("pointerdown", onClickOut, true);
+      };
+    }
+  }
+}
+function createNumericScale(self, settings, isH) {
+  let axisScale;
+  if (settings.isLogScale) {
+    axisScale = log().base(self.app.vocabApi.termdbConfig.logscaleBase2 ? 2 : 10).domain([self.data.min, self.data.max]).range(isH ? [0, settings.svgw] : [settings.svgw, 0]);
+  } else {
+    axisScale = linear().domain([self.data.min, self.data.max]).range(isH ? [0, settings.svgw] : [settings.svgw, 0]);
+  }
+  return axisScale;
+}
+function getLegendGrps(termNum, self) {
+  const legendGrps = [], t1 = self.config.term, t2 = self.config.term2, headingStyle = "color: #555; font-weight: 400";
+  if (self.settings.showStats) addDescriptiveStats(t1, legendGrps, headingStyle, self);
+  if (t2?.term.type === "float" || t2?.q.mode === "continuous" || t2?.term.type === "integer")
+    addDescriptiveStats(t2, legendGrps, headingStyle, self);
+  addUncomputableValues(
+    t1?.q.mode === "continuous" && t1?.q.hiddenValues && Object.keys(t1?.q.hiddenValues).length > 0 ? t1 : t2?.q.mode === "continuous" && t2?.q.hiddenValues && Object.keys(t2?.q.hiddenValues).length > 0 ? t2 : null,
+    legendGrps,
+    headingStyle,
+    self
+  );
+  if (t2) {
+    if (termNum.q.hiddenValues && Object.entries(termNum.q.hiddenValues).length != 0) {
+      addHiddenValues(termNum, legendGrps, headingStyle);
+    }
+  }
+  return legendGrps;
+}
+function addDescriptiveStats(term, legendGrps, headingStyle, self) {
+  const descrStats = term?.q?.descrStats;
+  if (descrStats) {
+    const items = Object.values(descrStats).map((stat) => {
+      return {
+        text: `${stat.label}: ${stat.value}`,
+        noIcon: true
+      };
+    });
+    const title = self.config.term2?.term.type === "float" || self.config.term2?.term.type === "integer" ? `Descriptive statistics: ${term.term.name}` : `Descriptive statistics`;
+    const name = `<span style="${headingStyle}">${title}</span>`;
+    legendGrps.push({ name, items });
+  }
+}
+function addUncomputableValues(term, legendGrps, headingStyle, self) {
+  if (term?.term.values) {
+    const items = [];
+    const values = term.term.values;
+    for (const k in values) {
+      const label = values[k]?.label;
+      if (!label) continue;
+      if (self.data.uncomputableValues?.[label]) {
+        items.push({
+          text: `${label}, n = ${self.data.uncomputableValues[label]}`,
+          noIcon: true,
+          /** Need to specify that this is a hidden value for
+           * text styling in the legend but not a plot to avoid
+           * rendering a tooltip or click events.
+           */
+          isHidden: true,
+          isClickable: false,
+          hiddenOpacity: 1
+        });
+      }
+    }
+    if (items.length) {
+      const name = self.config.term2?.term.type === "float" || self.config.term2?.term.type === "integer" ? `<span style="${headingStyle}">${term.term.name}</span>` : `<span style="${headingStyle}">Other categories</span>`;
+      legendGrps.push({ name, items });
+    }
+  }
+}
+function addHiddenValues(term, legendGrps, headingStyle) {
+  const items = [];
+  for (const key of Object.keys(term.q.hiddenValues || {})) {
+    items.push({
+      text: `${key}`,
+      noIcon: true,
+      /** Need to specify that this is a hidden value for
+       * text styling in the legend and  a plot for
+       * rendering a tooltip or click events.
+       */
+      isHidden: true,
+      isClickable: true,
+      hiddenOpacity: 1
+    });
+  }
+  const title = `${term.term.name}`;
+  const name = `<span style="${headingStyle}">${title}</span>`;
+  legendGrps.push({ name, items });
+}
+
+// plots/violin/violin.interactivity.ts
+function setInteractivity(self) {
+  self.getChartImages = function() {
+    const charts = [];
+    for (const chart of Object.values(self.data.charts)) {
+      const title = self.getChartTitle(chart.chartId);
+      const name = `${self.config.term.term.name}  ${title}`;
+      const chartDiv = chart.chartDiv;
+      charts.push({ name, svg: chartDiv.select("svg") });
+    }
+    return charts;
+  };
+  self.download = function(event) {
+    if (!self.state) return;
+    const name2svg = self.getChartImages();
+    const dm = new DownloadMenu(name2svg, self.config.term.term.name);
+    dm.show(event.clientX, event.clientY, void 0);
+  };
+  self.displayLabelClickMenu = function(t1, t2, plot, event) {
+    if (!t2) return;
+    if (self.config.term.term.type == SINGLECELL_GENE_EXPRESSION) return;
+    const label = t1.q.mode === "continuous" ? "term2" : "term";
+    const options = [];
+    if (this.app.getState().nav.header_mode !== "only_buttons")
+      options.push({
+        label: `Add filter: ${plot.label.split(",")[0]}`,
+        testid: "sjpp-violinLabOpt-addf",
+        callback: getAddFilterCallback(self, plot)
+      });
+    options.push({
+      label: `Hide: ${plot.label}`,
+      testid: "sjpp-violinLabOpt-hide",
+      callback: () => {
+        const term = self.config[label];
+        const isHidden = true;
+        self.app.dispatch({
+          type: "plot_edit",
+          id: self.id,
+          config: {
+            [label]: {
+              isAtomic: true,
+              term: term.term,
+              q: getUpdatedQfromClick(plot, term, isHidden)
+            }
+          }
+        });
+      }
+    });
+    const { samples } = self.config.controlLabels;
+    if (self.state.displaySampleIds && self.state.hasVerifiedToken) {
+      options.push({
+        label: `List ${samples}`,
+        testid: "sjpp-violinLabOpt-list",
+        callback: async () => {
+          const [start, end] = [self.data.min, self.data.max];
+          await self.callListSamples(event, plot, start, end);
+        }
+      });
+      if (self.opts.allow2selectSamples) {
+        const ss = self.opts.allow2selectSamples;
+        options.push({
+          label: ss.buttonText,
+          callback: async () => {
+            const [start, end] = [self.data.min, self.data.max];
+            await self.selectSamples(plot, start, end, ss);
+          }
+        });
+      }
+    }
+    self.displayMenu(event, options);
+  };
+  self.displayBrushMenu = function(t1, t2, self2, plot, event, scale, isH) {
+    const selection = event.selection;
+    const [start, end] = isH ? [scale.invert(selection[0]), scale.invert(selection[1])] : [scale.invert(selection[1]), scale.invert(selection[0])];
+    const options = [];
+    if (this.app.getState().nav.header_mode === "with_tabs")
+      options.push({
+        label: `Add filter`,
+        testid: "sjpp-violinBrushOpt-addf",
+        callback: getAddFilterCallback(self2, plot, start, end)
+      });
+    const { samples } = self2.config.controlLabels;
+    if (self2.state.displaySampleIds && self2.state.hasVerifiedToken) {
+      options.push({
+        label: `List ${samples}`,
+        testid: "sjpp-violinBrushOpt-list",
+        callback: async () => self2.callListSamples(event.sourceEvent, plot, start, end)
+      });
+      if (self2.opts.allow2selectSamples) {
+        const ss = self2.opts.allow2selectSamples;
+        options.push({
+          label: ss.buttonText,
+          callback: async () => {
+            await self2.selectSamples(plot, start, end, ss);
+          }
+        });
+      }
+    }
+    self2.displayMenu(event.sourceEvent, options, start, end);
+  };
+  self.displayMenu = function(event, options, start, end) {
+    const tip = self.dom.clicktip.clear().show(event.clientX, event.clientY);
+    const isBrush = start != null && end != null;
+    if (isBrush) {
+      const [niceStart, niceEnd] = self.config.term.term.type == "integer" ? [Math.round(start), Math.round(end)] : niceNumLabels([start, end]);
+      tip.d.append("div").style("margin", "10px").text(`From ${niceStart} to ${niceEnd}`);
+    }
+    tip.d.append("div").selectAll("div").data(options).enter().append("div").attr("class", "sja_menuoption sja_sharp_border").attr("data-testid", (d) => d.testid).text((d) => d.label).on("click", async (event2, d) => {
+      const target = event2.target;
+      if (target._clicked) return;
+      target._clicked = true;
+      target.textContent = "Loading...";
+      try {
+        await d.callback();
+      } catch (e) {
+        if (self.app.isAbortError(e) || self.app.isAbortError(e?.message)) {
+          tip.hide();
+          return;
+        }
+        throw e;
+      }
+      tip.hide();
+    });
+  };
+  self.selectSamples = async function(plot, start, end, ss) {
+    const ls = self.getSampleList(plot, start, end);
+    const data = await ls.getData();
+    const table = ls.setTableData(data);
+    const samples = table[2];
+    ss.callback({
+      samples: await self.app.vocabApi.convertSampleId(samples, ss.attributes),
+      source: ss.defaultSelectionLabel || `Selected from violin`
+    });
+  };
+  self.getSampleList = function(plot, start, end) {
+    const { term, term2, term0 } = self.config;
+    const bins = self.data.bins;
+    const rangeStart = start !== void 0 ? start : null;
+    const rangeStop = end !== void 0 ? end : null;
+    const ls = new ListSamples({
+      app: self.app,
+      termfilter: self.state.termfilter,
+      term,
+      term2,
+      term0,
+      plot,
+      bins,
+      start: rangeStart,
+      end: rangeStop
+    });
+    return ls;
+  };
+  self.callListSamples = async function(event, plot, start, end) {
+    const ls = self.getSampleList(plot, start, end);
+    const data = await ls.getData();
+    const [rows, columns] = ls.setTableData(data);
+    const tip = self.dom.sampletabletip;
+    tip.clear().show(event.clientX, event.clientY, false);
+    renderTable({
+      rows,
+      columns,
+      div: tip.d,
+      showLines: true,
+      maxHeight: "40vh",
+      resize: true,
+      dataTestId: "sjpp-listsampletable"
+    });
+  };
+  self.labelHideLegendClicking = function(t2, plot) {
+    self.dom.legendDiv.selectAll(".sjpp-htmlLegend").on("click", (event) => {
+      event.stopPropagation();
+      const d = event.target.__data__;
+      const termNum = t2?.term.type === "condition" || t2?.term.type === "samplelst" || t2?.term.type === "categorical" || (t2?.term.type === "float" || t2?.term.type === "integer") && self.config.term?.q.mode === "continuous" ? "term2" : "term";
+      const term = self.config[termNum];
+      if (t2) {
+        for (const key of Object.keys(term?.q?.hiddenValues)) {
+          if (d.text === key) {
+            delete term.q.hiddenValues[key];
+          }
+        }
+        const isHidden = false;
+        self.app.dispatch({
+          type: "plot_edit",
+          id: self.id,
+          config: {
+            [termNum]: {
+              isAtomic: true,
+              term: term.term,
+              q: getUpdatedQfromClick(plot, term, isHidden)
+            }
+          }
+        });
+      }
+    }).on("mouseover", (event) => {
+      const q = event.target.__data__;
+      if (q === void 0) return;
+      if (q.isHidden === true && q.isClickable === true) {
+        self.dom.hovertip.clear().show(event.clientX, event.clientY).d.append("span").text("Click to unhide plot");
+      }
+    }).on("mouseout", function() {
+      self.dom.hovertip.hide();
+    });
+  };
+}
+function getAddFilterCallback(self, plot, rangeStart, rangeStop) {
+  const ls = self.getSampleList(plot, rangeStart, rangeStop);
+  return () => {
+    const filterUiRoot = getFilterItemByTag(self.state.termfilter.filter, "filterUiRoot");
+    const filter = filterJoin([filterUiRoot, ls.tvslst]);
+    filter.tag = "filterUiRoot";
+    self.app.dispatch({
+      type: "filter_replace",
+      filter
+    });
+  };
+}
+function getUpdatedQfromClick(plot, term, isHidden = false) {
+  const label = plot.label;
+  const valueId = term?.term?.values ? term?.term?.values?.[label]?.label : label;
+  const id = !valueId ? label : valueId;
+  const q = term.q;
+  if (!q.hiddenValues) q.hiddenValues = {};
+  if (isHidden) q.hiddenValues[id] = 1;
+  else delete q.hiddenValues[id];
+  return q;
+}
+
+// plots/violin/Violin.ts
+var ViolinPlot = class _ViolinPlot extends PlotBase {
+  static {
+    this.type = "violin";
+  }
+  constructor(opts, api) {
+    super(opts, api);
+    this.type = _ViolinPlot.type;
+  }
+  async init() {
+    const holder = this.opts.holder.append("div").attr("id", "sjpp-vp-holder");
+    const { controls, errdiv, loadingDiv, banner, renderedData, charts, legendDiv } = this.getStandardDomLayout(
+      holder,
+      this.opts
+    );
+    this.dom = {
+      hovertip: new Menu({ padding: "3px" }),
+      // separate tips for hover & click on violin labels to avoid interfering
+      clicktip: new Menu({ padding: "0px" }),
+      sampletabletip: new Menu({ padding: "3px" }),
+      // sampletable is lauched from option shown in clicktip which closes on clicking, thus need its own menu..
+      header: this.opts.header,
+      controls: controls.attr("class", "sjpp-plot-controls").style("display", "inline-block"),
+      banner: banner.attr("data-testid", "sjpp-violin-banner"),
+      errdiv,
+      loadingDiv: loadingDiv.attr("data-testid", "sjpp-violin-loading-div").style("display", this.opts.mode != "minimal" ? "inline-block" : "none"),
+      renderedData,
+      violinDiv: charts.append("div").attr("class", "sjpp-vp-violinDiv").attr("data-testid", "sjpp-violin-div").style("display", "flex").style("flex-direction", "row").style("flex-wrap", "wrap").style("max-width", "100vw"),
+      legendDiv: legendDiv.classed("sjpp-vp-legend", true).attr("data-testid", "sjpp-violin-legend").style("margin-left", "-15px").style("padding-top", "20px")
+    };
+    setViolinRenderer(this);
+    setInteractivity(this);
+    if (this.opts.mode != "minimal") {
+      this.legendRenderer = htmlLegend(this.dom.legendDiv, {
+        settings: {
+          legendOrientation: "vertical"
+        },
+        handlers: {}
+      });
+    }
+  }
+  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;
+  }
+  preApiFreeze(api) {
+    api.download = this.download;
+    api.getChartImages = () => this.getChartImages();
+  }
+  async setControls() {
+    if (this.components.controls) return;
+    this.dom.controls.selectAll("*").remove();
+    const controlLabels = this.state.config.controlLabels;
+    if (!controlLabels) throw "controls labels not found";
+    this.components = {};
+    if (this.opts.mode == "minimal") return;
+    const specialCase = getSingleCellSpecialCase(this.config);
+    const inputs = [
+      {
+        type: "term",
+        configKey: "term",
+        chartType: "violin",
+        usecase: { target: "violin", detail: "term" },
+        label: controlLabels.term1?.label || renderTerm1Label,
+        vocabApi: this.app.vocabApi,
+        menuOptions: "edit"
+      },
+      {
+        type: "term",
+        configKey: "term2",
+        chartType: "violin",
+        usecase: { target: "violin", detail: "term2", specialCase },
+        title: controlLabels.term2.title || controlLabels.term2.label,
+        label: controlLabels.term2.label,
+        vocabApi: this.app.vocabApi,
+        numericEditMenuVersion: this.opts.numericEditMenuVersion,
+        defaultQ4fillTW: getT0T2defaultQ(),
+        getDisplayStyle: (plot) => plot.config?.term?.term?.type === "termCollection" ? "none" : ""
+      },
+      {
+        type: "term",
+        configKey: "term0",
+        chartType: "violin",
+        usecase: { target: "violin", detail: "term0", specialCase },
+        title: controlLabels.term0.title || controlLabels.term0.label,
+        label: controlLabels.term0.label,
+        vocabApi: this.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: this.opts.numericEditMenuVersion || ["discrete"],
+        defaultQ4fillTW: getT0T2defaultQ(),
+        getDisplayStyle: (plot) => plot.config?.term?.term?.type === "termCollection" ? "none" : ""
+      },
+      {
+        label: "Orientation",
+        title: "Orientation of the chart",
+        type: "radio",
+        chartType: "violin",
+        settingsKey: "orientation",
+        options: [
+          { label: "Vertical", value: "vertical" },
+          { label: "Horizontal", value: "horizontal" }
+        ]
+      },
+      {
+        label: "Data symbol",
+        title: "Symbol type",
+        type: "radio",
+        chartType: "violin",
+        settingsKey: "datasymbol",
+        options: [
+          { label: "Ticks", value: "rug" },
+          { label: "Circles", value: "bean" },
+          { label: "Off", value: "none" }
+        ]
+      },
+      {
+        label: "Scale",
+        title: "Axis scale",
+        type: "radio",
+        chartType: "violin",
+        settingsKey: "isLogScale",
+        options: [
+          { label: "Linear", value: false },
+          { label: "Log10", value: true }
+        ]
+      },
+      {
+        label: "Order by",
+        title: "Order violin plots by parameters",
+        type: "radio",
+        chartType: "violin",
+        settingsKey: "orderByMedian",
+        options: [
+          { label: "Default", value: false },
+          { label: "Median", value: true }
+        ],
+        getDisplayStyle: () => {
+          let style = "none";
+          const charts = this.data?.charts || {};
+          for (const k of Object.keys(charts)) {
+            const chart = charts[k];
+            if (chart?.plots.length > 1) style = "";
+          }
+          return style;
+        }
+      },
+      {
+        label: "Symbol size",
+        type: "number",
+        chartType: "violin",
+        settingsKey: "radius",
+        step: 1,
+        max: 30,
+        min: 4
+      },
+      {
+        label: "Bins",
+        type: "number",
+        chartType: "violin",
+        settingsKey: "ticks",
+        title: "Number of bins used to build the plot",
+        min: 1,
+        max: 50
+      },
+      {
+        label: "Plot length",
+        title: "Length of the plot",
+        type: "number",
+        chartType: "violin",
+        settingsKey: "svgw",
+        step: 10,
+        max: 1e3,
+        min: 200,
+        debounceInterval: 1e3
+      },
+      {
+        label: "Plot thickness",
+        title: "If not specified, the plot thickness is calculated based on the number of categories",
+        type: "number",
+        chartType: "violin",
+        settingsKey: "plotThickness",
+        step: 10,
+        max: 200,
+        min: 20,
+        debounceInterval: 1e3
+      },
+      {
+        label: "Plot padding",
+        type: "number",
+        chartType: "violin",
+        settingsKey: "rowSpace",
+        step: 1,
+        max: 20,
+        min: 0,
+        debounceInterval: 1e3
+      },
+      {
+        label: "Median length",
+        title: "Length of median",
+        type: "number",
+        chartType: "violin",
+        settingsKey: "medianLength",
+        step: 1,
+        max: 50,
+        min: 3,
+        debounceInterval: 1e3
+      },
+      {
+        label: "Median color",
+        title: "color of median",
+        type: "color",
+        chartType: "violin",
+        settingsKey: "medianColor"
+      },
+      {
+        label: "Median thickness",
+        title: "Width of median",
+        type: "number",
+        chartType: "violin",
+        settingsKey: "medianThickness",
+        step: 1,
+        max: 10,
+        min: 3,
+        debounceInterval: 100
+      },
+      {
+        label: "Default violin color",
+        type: "color",
+        chartType: "violin",
+        settingsKey: "defaultColor"
+      },
+      {
+        label: "Show stats",
+        type: "checkbox",
+        chartType: "violin",
+        settingsKey: "showStats",
+        boxLabel: "Yes"
+      },
+      {
+        label: "Show association tests",
+        type: "checkbox",
+        chartType: "violin",
+        settingsKey: "showAssociationTests",
+        boxLabel: "Yes",
+        getDisplayStyle: (plot) => plot.term2 ? "table-row" : "none"
+      }
+    ];
+    this.components.controls = await controlsInit({
+      app: this.app,
+      id: this.id,
+      holder: this.dom.controls,
+      inputs
+    });
+    this.components.controls.on("downloadClick.violin", this.download);
+  }
+  getState(appState) {
+    const config = appState.plots.find((p) => p.id === this.id);
+    if (!config) {
+      throw `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`;
+    }
+    const parentConfig = appState.plots.find((p) => p.id === this.parentId);
+    const termfilter = getCombinedTermFilter(appState, config.filter || parentConfig?.filter);
+    return {
+      termfilter,
+      config,
+      displaySampleIds: appState.termdbConfig.displaySampleIds,
+      hasVerifiedToken: this.app.vocabApi.hasVerifiedToken()
+    };
+  }
+  async main() {
+    this.config = structuredClone(this.state.config);
+    this.settings = this.config.settings.violin;
+    await this.setControls();
+    if (this.config.chartType != this.type && this.config.childType != this.type) return;
+    if (this.dom.header)
+      this.dom.header.html(
+        this.config.term.term.name + ` <span style="opacity:.6;font-size:1em;margin-left:10px;">Violin Plot</span>`
+      );
+    const existingMsg = this.dom.banner.style("display", "none").select("span");
+    if (!existingMsg.empty()) existingMsg.remove();
+    const args = this.validateArgs();
+    let data;
+    try {
+      this.toggleLoadingDiv("block", "block");
+      data = await this.app.vocabApi.getViolinBox(args, null, this.api?.getAbortSignal());
+    } catch (e) {
+      this.toggleLoadingDiv("none", "none");
+      if (this.app.isAbortError(e)) return;
+      throw e;
+    }
+    this.data = data;
+    if (this.data.error) {
+      this.toggleLoadingDiv("none", "none");
+      throw this.data.error;
+    }
+    args.tw.q.descrStats = this.data.descrStats;
+    setTimeout(
+      () => {
+        this.render();
+        this.toggleLoadingDiv("none");
+      },
+      this.opts.mode == "minimal" ? 0 : 500
+    );
+  }
+  validateArgs() {
+    const {
+      term,
+      term2,
+      term0
+      /*settings*/
+    } = this.config;
+    const s = this.settings;
+    const arg = {
+      plotType: "violin",
+      svgw: s.svgw,
+      orientation: s.orientation,
+      devicePixelRatio: window.devicePixelRatio,
+      datasymbol: s.datasymbol,
+      radius: s.radius,
+      axisHeight: s.axisHeight,
+      rightMargin: s.rightMargin,
+      isLogScale: s.isLogScale,
+      ticks: s.ticks,
+      orderByMedian: s.orderByMedian,
+      filter: this.state.termfilter.filter
+    };
+    if (this.opts.mode == "minimal") {
+      arg.tw = term;
+      if (term2 || term0) throw "only a single term allowed for minimal plot";
+      if (term.q.mode == "spline") {
+        s.lines = term.q.knots.map((x) => Number(x.value));
+      } else {
+        s.lines = [];
+      }
+      if (term.q.scale) {
+        arg.scale = term.q.scale;
+      }
+    } else if (term.term?.type === "termCollection" && term.term?.memberType === "numeric" && term.type !== "TermCollectionTWFraction") {
+      arg.tw = term;
+    } else if (isNumericTw(term) && term.q.mode === "continuous") {
+      arg.tw = term;
+      if (term2) arg.overlayTw = term2;
+    } else if (isNumericTw(term2) && term2.q.mode === "continuous") {
+      arg.tw = term2;
+      arg.overlayTw = term;
+    } else {
+      throw "both term1 and term2 are not numeric/continuous";
+    }
+    if (term0) arg.divideTw = term0;
+    return arg ? arg : arg;
+  }
+};
+var violinInit = getCompInit(ViolinPlot);
+var componentInit = violinInit;
+async function getPlotConfig(opts, app) {
+  if (!opts.term) throw "violin getPlotConfig: opts.term{} missing";
+  try {
+    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) {
+    throw `${e} [violin getPlotConfig()]`;
+  }
+  const config = {
+    controlLabels: Object.assign({}, defaultUiLabels, app.vocabApi.termdbConfig.uiLabels || {}),
+    settings: {
+      controls: {
+        term2: null,
+        // the previous overlay value may be displayed as a convenience for toggling
+        term0: null
+      },
+      // common: {
+      // 	use_logscale: false, // flag for y-axis scale type, 0=linear, 1=log
+      // 	use_percentage: false,
+      // 	barheight: 300, // maximum bar length
+      // 	barwidth: 20, // bar thickness
+      // 	barspace: 2 // space between two bars
+      // },
+      violin: getDefaultViolinSettings(app)
+    }
+  };
+  return copyMerge(config, opts);
+}
+export {
+  componentInit,
+  getPlotConfig,
+  violinInit
+};
+//# sourceMappingURL=Violin-F3QS2EMJ.js.map