@sjcrh/proteinpaint-client 2.190.2 → 2.191.2

package/dist/chunk-WKMZ4ZQ3.js

@@ -1,407 +0,0 @@
-import {
-  getMaxLabelWidth,
-  renderTable,
-  table2col
-} from "./chunk-UK3PTE3P.js";
-import {
-  SINGLECELL_GENE_EXPRESSION
-} from "./chunk-XOCO3LVN.js";
-import {
-  basis_default,
-  line_default
-} from "./chunk-KSGA62R2.js";
-import {
-  axisLeft,
-  axisTop
-} from "./chunk-LOZEKOES.js";
-import {
-  format,
-  linear,
-  log
-} from "./chunk-OAWQ6LOO.js";
-import {
-  brushX,
-  brushY
-} from "./chunk-KYBIQBXE.js";
-import {
-  rgb
-} from "./chunk-OMR2DT66.js";
-
-// plots/violin.renderer.js
-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 && termNum.term?.values) {
-      for (const [k, v] of Object.entries(termNum.term.values)) {
-        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 [plotIdx, plot] of plots.entries()) {
-        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(d, event) {
-    if (!d.summaryStats) return;
-    self.dom.hovertip.clear().show(event.clientX, event.clientY);
-    const table = table2col({ holder: self.dom.hovertip.d.append("div") });
-    for (const { label, value } of Object.values(d.summaryStats)) table.addRow(label, value);
-  };
-  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 ticks = settings.isLogScale ? svg.axisScale.ticks(15) : (
-      // svg.axisScale.ticks().filter(tick => tick > 0 || tick < 0)
-      svg.axisScale.ticks()
-    );
-    g.call(
-      (isH ? axisTop : axisLeft)().scale(svg.axisScale).tickFormat((d, i) => {
-        if (settings.isLogScale) {
-          if (self2.app.vocabApi.termdbConfig.logscaleBase2) {
-            if (ticks.length > 10 && i % 2 !== 0) return "";
-            if (d < 0.1) return format(".3f")(d);
-            return format(".1f")(d);
-          } else {
-            if (ticks.length >= 12 && i % 5 !== 0) return "";
-            if (d < 50) return d;
-            return format(".1s")(d);
-          }
-        }
-        if (ticks.length >= 12 && i % 2 !== 0) return "";
-        return d;
-      }).tickValues(ticks)
-    );
-    if (self2.opts.mode != "minimal") {
-      const n = t2?.q?.mode === "continuous" ? t2.term.name : t1.term.name;
-      const lab = 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;
-    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);
-    }
-    let 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);
-      };
-    }
-  }
-  self.toggleLoadingDiv = function(display = "") {
-    if (display != "none") {
-      self.dom.loadingDiv.style("opacity", 0).style("display", display).transition().duration("loadingWait" in self ? self.loadingWait : 3e3).style("opacity", 1);
-    } else {
-      self.dom.loadingDiv.style("display", display);
-    }
-    self.loadingWait = 1e3;
-  };
-}
-function createNumericScale(self, settings, isH) {
-  let axisScale;
-  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]) : 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) {
-  if (term?.q.descrStats) {
-    const items = Object.values(term.q.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}">${title}</span>`;
-    legendGrps.push({ name, items });
-  }
-}
-function addUncomputableValues(term, legendGrps, headingStyle, self) {
-  if (term?.term.values) {
-    const items = [];
-    for (const k in term.term.values) {
-      if (self.data.uncomputableValues?.[term.term.values[k]?.label]) {
-        items.push({
-          text: `${term.term.values[k].label}, n = ${self.data.uncomputableValues[term.term.values[k].label]}`,
-          noIcon: true,
-          /** Need to specify that this is a hidden value for
-           * text styling in the legend but not a plot to avoid
-           * rendering a tooltip or click events.
-           */
-          isHidden: true,
-          isClickable: false,
-          hiddenOpacity: 1
-        });
-      }
-    }
-    if (items.length) {
-      const name = self.config.term2?.term.type === "float" || self.config.term2?.term.type === "integer" ? `<span style="${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 });
-}
-
-export {
-  setViolinRenderer,
-  createNumericScale
-};
-//# sourceMappingURL=chunk-WKMZ4ZQ3.js.map

package/dist/chunk-WKMZ4ZQ3.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../plots/violin.renderer.js"],
-  "sourcesContent": ["import { axisLeft, axisTop } from 'd3-axis'\nimport { scaleLinear, scaleLog } from 'd3-scale'\nimport { curveBasis, line } from 'd3-shape'\nimport { brushX, brushY } from 'd3-brush'\nimport { renderTable, getMaxLabelWidth, table2col } from '#dom'\nimport { rgb } from 'd3'\nimport { format as d3format } from 'd3-format'\nimport { SINGLECELL_GENE_EXPRESSION } from '#shared/terms.js'\n\nconst minSampleSize = 5 // a group below cutoff will not render a violin plot\n\nexport default function setViolinRenderer(self) {\n\tself.render = function () {\n\t\tconst settings = self.config.settings.violin\n\t\tconst isH = settings.orientation === 'horizontal'\n\t\tconst t1 = self.config.term\n\t\tconst t2 = self.config.term2\n\n\t\t//termsetting.js 'set_hiddenvalues()' adds uncomputable values from term.values to q.hiddenValues object. Since it will show up on the legend, delete that key-value pair from t2.q.hiddenValues object.\n\t\tconst termNum =\n\t\t\tt2?.term.type === 'condition' ||\n\t\t\tt2?.term.type === 'samplelst' ||\n\t\t\tt2?.term.type === 'categorical' ||\n\t\t\t((t2?.term.type === 'float' || t2?.term.type === 'integer') && t1.q.mode === 'continuous')\n\t\t\t\t? t2\n\t\t\t\t: t1\n\n\t\tif (termNum && termNum.term?.values) {\n\t\t\tfor (const [k, v] of Object.entries(termNum.term.values)) {\n\t\t\t\tif (v.uncomputable) {\n\t\t\t\t\tif (termNum.q.hiddenValues[k]) {\n\t\t\t\t\t\ttermNum.q.hiddenValues[v.label] = 1\n\t\t\t\t\t\tdelete termNum.q.hiddenValues[k]\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\t//filter out hidden values and only keep plots which are not hidden in term2.q.hiddenvalues\n\t\tself.dom.violinDiv.selectAll('*').remove()\n\t\tconst chartKeys = Object.keys(self.data.charts)\n\t\tif (!chartKeys?.length) {\n\t\t\tself.dom.banner.html(`<span>No visible violin plot data to render</span>`).style('display', 'block')\n\t\t\tself.dom.legendDiv.selectAll('*').remove()\n\t\t\treturn\n\t\t}\n\t\tfor (const chartKey of chartKeys) {\n\t\t\tconst chart = self.data.charts[chartKey]\n\t\t\tconst plots = chart.plots.filter(p => !termNum?.q?.hiddenValues?.[p.label || p.seriesId])\n\t\t\tif (settings.orderByMedian == true) {\n\t\t\t\tplots.sort(\n\t\t\t\t\t(a, b) =>\n\t\t\t\t\t\ta.summaryStats.find(x => x.id === 'median').value - b.summaryStats.find(x => x.id === 'median').value\n\t\t\t\t)\n\t\t\t}\n\t\t\tif (self.legendRenderer) self.legendRenderer(getLegendGrps(termNum, self))\n\n\t\t\tconst chartDiv = self.dom.violinDiv\n\t\t\t\t.append('div')\n\t\t\t\t.attr('class', 'sjpp-vp-chartDiv')\n\t\t\t\t.style('padding', Object.keys(self.data.charts).length > 1 ? '20px 20px 0px 0px' : '0px')\n\t\t\tchart.chartDiv = chartDiv\n\t\t\tif (plots.length === 0) {\n\t\t\t\tchartDiv.html(\n\t\t\t\t\t` <span style=\"opacity:.6;font-size:1em;margin-left:90px;\">No visible violin plot data to render</span>`\n\t\t\t\t)\n\t\t\t\treturn\n\t\t\t}\n\n\t\t\t// append the svg object to the body of the page\n\t\t\tchartDiv.select('.sjpp-violin-plot').remove()\n\n\t\t\t//Fix for centering the chart title over the chart,\n\t\t\t//not the entire div.\n\t\t\tconst chartWrapper = chartDiv.append('div').style('display', 'inline-block')\n\t\t\t// render chart title\n\t\t\tif (chart.chartId) {\n\t\t\t\tconst totalCount = chart.plots.reduce((acc, plot) => acc + plot.plotValueCount, 0)\n\t\t\t\tchartWrapper\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.attr('class', 'pp-chart-title')\n\t\t\t\t\t.style('display', 'block')\n\t\t\t\t\t.style('text-align', 'center')\n\t\t\t\t\t.style('font-size', '1.1em')\n\t\t\t\t\t.style('margin-bottom', '5px')\n\t\t\t\t\t.html(`${self.getChartTitle(chart.chartId)} (n=${totalCount})`)\n\t\t\t}\n\n\t\t\t// render chart data\n\t\t\tconst svgData = renderSvg(t1, plots, chartWrapper, self, isH, settings)\n\t\t\trenderScale(t1, t2, settings, isH, svgData, self)\n\t\t\tlet y = 0\n\t\t\tconst thickness = self.settings.plotThickness || self.getAutoThickness()\n\t\t\tfor (const [plotIdx, plot] of plots.entries()) {\n\t\t\t\t//R x values are not the same as the plot values, so we need to use a scale to map them to the plot values\n\t\t\t\t// The scale uses half of the plotThickness as the maximum value as the image is symmetrical\n\t\t\t\t// Only one half of the image is computed and the other half is mirrored\n\t\t\t\tconst wScale = scaleLinear()\n\t\t\t\t\t.domain([plot.density.densityMax, plot.density.densityMin])\n\t\t\t\t\t.range([thickness / 2, 0])\n\t\t\t\tlet areaBuilder\n\t\t\t\t//when doing this interpolation, the violin plot will be smoother and some padding may be added\n\t\t\t\t//between the plot and the axis\n\t\t\t\tif (isH) {\n\t\t\t\t\tareaBuilder = line()\n\t\t\t\t\t\t.curve(curveBasis)\n\t\t\t\t\t\t.x(d => svgData.axisScale(d.x0))\n\t\t\t\t\t\t.y(d => wScale(d.density))\n\t\t\t\t} else {\n\t\t\t\t\tareaBuilder = line()\n\t\t\t\t\t\t.curve(curveBasis)\n\t\t\t\t\t\t.x(d => wScale(d.density))\n\t\t\t\t\t\t.y(d => svgData.axisScale(d.x0))\n\t\t\t\t}\n\t\t\t\t//if only one plot pass area builder to calculate the exact height of the plot\n\t\t\t\tconst { violinG, height } = renderViolinPlot(svgData, plot, isH, wScale, areaBuilder, y)\n\t\t\t\ty += height\n\t\t\t\tif (self.opts.mode != 'minimal') renderLabels(t1, t2, violinG, plot, isH, settings)\n\n\t\t\t\tif (self.config.term.term.type == SINGLECELL_GENE_EXPRESSION) {\n\t\t\t\t\t// is sc data, disable brushing for now because 1) no use 2) avoid bug of listing cells\n\t\t\t\t} else {\n\t\t\t\t\t// enable brushing\n\t\t\t\t\tif (self.opts.mode != 'minimal') renderBrushing(t1, t2, violinG, settings, plot, isH, svgData)\n\t\t\t\t}\n\n\t\t\t\tself.labelHideLegendClicking(t2, plot) // FIXME\n\t\t\t}\n\n\t\t\t// render p-value table\n\t\t\tif (self.settings.showAssociationTests) self.renderPvalueTable(chartDiv, chart)\n\t\t}\n\t}\n\n\tself.displaySummaryStats = function (d, event) {\n\t\tif (!d.summaryStats) return\n\t\tself.dom.hovertip.clear().show(event.clientX, event.clientY)\n\t\tconst table = table2col({ holder: self.dom.hovertip.d.append('div') })\n\t\tfor (const { label, value } of Object.values(d.summaryStats)) table.addRow(label, value)\n\t}\n\tself.getAutoThickness = function () {\n\t\tlet maxPlotCount = 0\n\t\tfor (const k of Object.keys(this.data.charts)) {\n\t\t\tconst chart = this.data.charts[k]\n\t\t\tmaxPlotCount = Math.max(maxPlotCount, chart.plots.length)\n\t\t}\n\t\tif (maxPlotCount == 1) return 150\n\t\treturn Math.min(100, Math.max(40, 600 / maxPlotCount)) //clamp between 60 and 130\n\t}\n\n\tself.getPlotThicknessWithPadding = function () {\n\t\tconst plotThickness = self.settings.plotThickness || self.getAutoThickness()\n\t\treturn plotThickness + self.settings.rowSpace\n\t}\n\n\tself.renderPvalueTable = function (chartDiv, chart) {\n\t\tif (!chart.pvalues) return\n\t\tconst tableHolder = chartDiv\n\t\t\t.append('div')\n\t\t\t.classed('sjpp-tableHolder', true)\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('padding', '10px')\n\t\t\t.style('vertical-align', 'top')\n\t\t\t.style('margin-left', '0px')\n\t\t\t.style('margin-top', '30px')\n\t\t\t.style('margin-right', '30px')\n\n\t\tconst t1 = self.config.term\n\t\tconst t2 = self.config.term2\n\n\t\tif (!t2) {\n\t\t\t// no term2, no table to show\n\t\t\ttableHolder.style('display', 'none')\n\t\t\treturn\n\t\t}\n\n\t\tconst termNum =\n\t\t\tt2?.term.type === 'condition' ||\n\t\t\tt2?.term.type === 'samplelst' ||\n\t\t\tt2?.term.type === 'categorical' ||\n\t\t\t((t2?.term.type === 'float' || t2?.term.type === 'integer') && t1.q.mode === 'continuous')\n\t\t\t\t? t2\n\t\t\t\t: t1\n\n\t\t//hide p-values for categories that are hidden\n\t\tconst pvalues = chart.pvalues.filter(arr => {\n\t\t\tfor (let i = 0; i < arr.length; i++) {\n\t\t\t\tif (typeof arr[i].value === 'string') {\n\t\t\t\t\tif (termNum.q?.hiddenValues && arr[i].value in termNum.q.hiddenValues) {\n\t\t\t\t\t\treturn false\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t\treturn true\n\t\t})\n\n\t\ttableHolder\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('vertical-align', 'top')\n\t\t\t.append('div')\n\t\t\t.style('font-weight', 'bold')\n\t\t\t.text(pvalues.length > 0 ? \"Group comparisons (Wilcoxon's rank sum test)\" : '')\n\n\t\tconst columns = [{ label: 'Group 1' }, { label: 'Group 2' }, { label: 'P-value' }]\n\t\tconst rows = pvalues\n\t\tconst isH = this.settings.orientation === 'horizontal'\n\t\tconst maxHeight = isH\n\t\t\t? self.getPlotThicknessWithPadding() * chart.plots.length + 10 //add axes height\n\t\t\t: this.settings.svgw + this.config.term.term.name.length\n\t\trenderTable({\n\t\t\trows,\n\t\t\tcolumns,\n\t\t\tdiv: tableHolder,\n\t\t\tshowLines: false,\n\t\t\tmaxWidth: '27vw',\n\t\t\tmaxHeight: `${maxHeight}px`,\n\t\t\tresize: true\n\t\t})\n\t}\n\n\tself.getChartTitle = function (chartId) {\n\t\tif (!self.config.term0) return chartId\n\t\treturn self.config.term0.term.values && chartId in self.config.term0.term.values\n\t\t\t? self.config.term0.term.values[chartId].label\n\t\t\t: chartId\n\t}\n\n\tfunction createMargins(labelsize, settings, isH, isMinimal) {\n\t\tlet margins\n\n\t\tif (isMinimal) {\n\t\t\tmargins = isH\n\t\t\t\t? { left: 5, top: settings.axisHeight, right: settings.rightMargin, bottom: 10 }\n\t\t\t\t: { left: settings.axisHeight, top: 30, right: settings.rightMargin, bottom: 10 }\n\t\t} else {\n\t\t\tmargins = isH\n\t\t\t\t? { left: labelsize + 5, top: settings.axisHeight, right: settings.rightMargin, bottom: 10 }\n\t\t\t\t: { left: settings.axisHeight, top: 50, right: settings.rightMargin, bottom: labelsize }\n\t\t}\n\t\treturn margins\n\t}\n\n\tfunction renderSvg(t1, plots, chartDiv, self, isH, settings) {\n\t\tconst violinDiv = chartDiv\n\t\t\t.append('div')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('padding', self.opts.mode != 'minimal' ? '5px' : '0px')\n\t\t\t.style('overflow', 'auto')\n\t\t\t.style('scrollbar-width', 'none')\n\n\t\tconst violinSvg = violinDiv.append('svg')\n\n\t\tconst labelsize = getMaxLabelWidth(\n\t\t\tviolinSvg,\n\t\t\tplots.map(plot => `${plot.label}, n=${plot.plotValueCount}`)\n\t\t)\n\n\t\tconst margin = createMargins(labelsize, settings, isH, self.opts.mode == 'minimal')\n\t\tconst plotThickness = self.getPlotThicknessWithPadding()\n\t\tconst width = margin.left + margin.top + (isH ? settings.svgw : plotThickness * plots.length + t1.term.name.length)\n\t\tconst height =\n\t\t\tmargin.bottom + margin.top + (isH ? plotThickness * plots.length : settings.svgw + t1.term.name.length)\n\n\t\tviolinSvg\n\t\t\t.attr('width', width)\n\t\t\t.attr('height', height)\n\t\t\t.classed('sjpp-violin-plot', true)\n\t\t\t.attr('data-testid', 'sja_violin_plot')\n\n\t\t// a <g> in which everything is rendered into\n\t\tconst svgG = violinSvg.append('g').attr('transform', 'translate(' + margin.left + ',' + margin.top + ')')\n\n\t\treturn { margin: margin, svgG: svgG, axisScale: createNumericScale(self, settings, isH), violinSvg: violinSvg }\n\t}\n\n\tfunction renderScale(t1, t2, settings, isH, svg, self) {\n\t\t// <g>: holder of numeric axis\n\t\tconst g = svg.svgG\n\t\t\t.append('g')\n\t\t\t.style('font-size', '12')\n\t\t\t.classed(settings.isLogScale ? 'sjpp-logscale' : 'sjpp-linearscale', true)\n\n\t\tconst ticks = settings.isLogScale\n\t\t\t? svg.axisScale.ticks(15)\n\t\t\t: // svg.axisScale.ticks().filter(tick => tick > 0 || tick < 0)\n\t\t\t  svg.axisScale.ticks()\n\n\t\tg.call(\n\t\t\t(isH ? axisTop : axisLeft)()\n\t\t\t\t.scale(svg.axisScale)\n\t\t\t\t.tickFormat((d, i) => {\n\t\t\t\t\tif (settings.isLogScale) {\n\t\t\t\t\t\tif (self.app.vocabApi.termdbConfig.logscaleBase2) {\n\t\t\t\t\t\t\tif (ticks.length > 10 && i % 2 !== 0) return ''\n\t\t\t\t\t\t\tif (d < 0.1) return d3format('.3f')(d)\n\t\t\t\t\t\t\treturn d3format('.1f')(d)\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\tif (ticks.length >= 12 && i % 5 !== 0) return ''\n\t\t\t\t\t\t\tif (d < 50) return d\n\t\t\t\t\t\t\treturn d3format('.1s')(d)\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t\tif (ticks.length >= 12 && i % 2 !== 0) return ''\n\t\t\t\t\treturn d\n\t\t\t\t})\n\t\t\t\t.tickValues(ticks)\n\t\t)\n\n\t\tif (self.opts.mode != 'minimal') {\n\t\t\t// TODO need to add term2 label onto the svg\n\t\t\tconst n = t2?.q?.mode === 'continuous' ? t2.term.name : t1.term.name\n\t\t\tconst lab = svg.svgG\n\t\t\t\t.append('text')\n\t\t\t\t.text(n)\n\t\t\t\t.classed('sjpp-numeric-term-label', true)\n\t\t\t\t.attr('data-testid', `sjpp-violin-label-${n}`)\n\t\t\t\t.style('font-weight', 600)\n\t\t\t\t.attr('text-anchor', 'middle')\n\t\t\t\t.attr('x', isH ? settings.svgw / 2 : -settings.svgw / 2)\n\t\t\t\t.attr('y', isH ? -30 : -45)\n\t\t\t\t.style('opacity', 0)\n\t\t\t\t.attr('transform', isH ? null : 'rotate(-90)')\n\t\t\t\t// .transition()\n\t\t\t\t// .delay(self.opts.mode == 'minimal' ? 0 : 100)\n\t\t\t\t// .duration(self.opts.mode == 'minimal' ? 0 : 200)\n\t\t\t\t.style('opacity', 1)\n\t\t}\n\t}\n\n\tfunction renderViolinPlot(svgData, plot, isH, wScale, areaBuilder, y) {\n\t\tconst label = plot.label?.split(',')[0]\n\t\tconst catTerm = self.config.term.q.mode == 'discrete' ? self.config.term : self.config.term2\n\t\tconst category = catTerm?.term.values ? Object.values(catTerm.term.values).find(o => o.label == label) : null\n\t\tlet color\n\t\tif (catTerm) {\n\t\t\tif (catTerm.q.type == 'predefined-groupset' || catTerm.q.type == 'custom-groupset') {\n\t\t\t\tconst groupset =\n\t\t\t\t\tcatTerm.q.type == 'predefined-groupset'\n\t\t\t\t\t\t? catTerm.term.groupsetting.lst[catTerm.q.predefined_groupset_idx]\n\t\t\t\t\t\t: catTerm.q.customset\n\t\t\t\tif (!groupset) throw 'groupset is missing'\n\t\t\t\tconst group = groupset.groups.find(g => g.name == label)\n\t\t\t\tif (group?.color) color = group.color\n\t\t\t} else {\n\t\t\t\tcolor = category?.color\n\t\t\t}\n\t\t}\n\n\t\tif (!color) color = self.config.settings.violin.defaultColor\n\n\t\tif (!plot.color) plot.color = color\n\t\tif (category && !category.color) category.color = color\n\t\t// <g> of one plot\n\t\t// adding .5 to plotIdx allows to anchor each plot <g> to the middle point\n\t\tconst svg = svgData.svgG\n\t\tconst violinG = svg.append('g').datum(plot).attr('class', 'sjpp-violinG')\n\t\trenderArea(violinG, plot, areaBuilder)\n\t\t//render symmetrical violin plot\n\t\trenderArea(violinG, plot, isH ? areaBuilder.y(d => -wScale(d.density)) : areaBuilder.x(d => -wScale(d.density)))\n\n\t\trenderSymbolImage(self, violinG, plot, isH)\n\t\tif (self.opts.mode != 'minimal') renderMedian(violinG, isH, plot, svgData, self)\n\t\trenderLines(violinG, isH, self.config.settings.violin.lines, svgData)\n\t\tif ('value' in self.state.config) {\n\t\t\tconst value = svgData.axisScale(self.state.config.value)\n\t\t\tconst s = self.config.settings.violin\n\t\t\tviolinG\n\t\t\t\t.append('line')\n\t\t\t\t.style('stroke', 'black')\n\t\t\t\t.style('stroke-width', s.medianThickness)\n\t\t\t\t.attr('x1', 200)\n\t\t\t\t.attr('x2', 200)\n\t\t\t\t.attr('x1', isH ? value : -s.medianLength)\n\t\t\t\t.attr('x2', isH ? value : s.medianLength)\n\t\t\t\t.attr('y1', isH ? -s.medianLength : value)\n\t\t\t\t.attr('y2', isH ? s.medianLength : value)\n\t\t}\n\t\tlet height = self.getPlotThicknessWithPadding()\n\t\tconst translate = isH ? `translate(0, ${y + height / 2}) ` : `translate(${y + height / 2}, 0)`\n\t\tviolinG.attr('transform', translate)\n\n\t\treturn { violinG, height }\n\t}\n\n\t// label for each violin (on left when horizontal)\n\tfunction renderLabels(t1, t2, violinG, plot, isH, settings) {\n\t\tviolinG\n\t\t\t.append('text')\n\t\t\t.attr('data-testid', 'sjpp-violin-label')\n\t\t\t.text(`${plot.label}, n=${plot.plotValueCount}`)\n\t\t\t.style('cursor', 'pointer')\n\t\t\t.on('click', function (event) {\n\t\t\t\tif (!event) return\n\t\t\t\tself.displayLabelClickMenu(t1, t2, plot, event)\n\t\t\t})\n\t\t\t.on('mouseover', function (event, d) {\n\t\t\t\tevent.stopPropagation()\n\t\t\t\tif (!event) return\n\t\t\t\tself.displaySummaryStats(d, event)\n\t\t\t})\n\t\t\t.on('mouseout', function () {\n\t\t\t\tself.dom.hovertip.hide()\n\t\t\t})\n\t\t\t.style('opacity', 0)\n\t\t\t.style('opacity', 1)\n\t\t\t.attr('x', isH ? -5 : 0 - settings.svgw - 5)\n\t\t\t.attr('y', 0)\n\t\t\t.attr('text-anchor', 'end')\n\t\t\t.attr('dominant-baseline', 'central')\n\t\t\t.attr('transform', isH ? null : 'rotate(-90)')\n\t}\n\n\tfunction renderArea(violinG, plot, areaBuilder) {\n\t\tif (plot.density.densityMax == 0) return\n\t\tviolinG\n\t\t\t.append('path')\n\t\t\t.attr('class', 'sjpp-vp-path')\n\t\t\t.style('fill', self.opts.mode === 'minimal' ? rgb(221, 221, 221) : plot.color)\n\t\t\t.style('opacity', 0)\n\t\t\t.attr('stroke', rgb(plot.color).darker())\n\t\t\t.attr('stroke-width', 1)\n\t\t\t.attr('stroke-linejoin', 'round')\n\t\t\t.style('opacity', '0.8')\n\t\t\t.attr('d', areaBuilder(plot.density.bins))\n\t}\n\n\tfunction renderSymbolImage(self, violinG, plot, isH) {\n\t\tconst i = violinG\n\t\t\t.append('image')\n\t\t\t.style('opacity', 0)\n\t\t\t.classed(self.config.settings.violin.datasymbol === 'rug' ? 'sjpp-rug-img' : 'sjpp-beans-img', true)\n\t\t\t.style('opacity', 1)\n\t\t\t.attr('xlink:href', plot.src)\n\t\t\t.attr(\n\t\t\t\t'transform',\n\t\t\t\tisH ? `translate(0, -${self.settings.radius / 2})` : `translate(-${self.settings.radius / 2}, 0)`\n\t\t\t)\n\t\t// set image dimension for crisp look\n\t\tif (self.settings.orientation == 'horizontal') {\n\t\t\ti.attr('width', self.settings.svgw)\n\t\t} else if (self.settings.orientation == 'vertical') {\n\t\t\ti.attr('height', self.settings.svgw)\n\t\t}\n\t}\n\n\tfunction renderMedian(violinG, isH, plot, svgData, self) {\n\t\tconst s = self.config.settings.violin\n\t\t//render median values on plots\n\t\tconst median = svgData.axisScale(plot.summaryStats.median.value)\n\t\tif (plot.plotValueCount >= 2) {\n\t\t\tviolinG\n\t\t\t\t.append('line')\n\t\t\t\t.attr('class', 'sjpp-median-line')\n\t\t\t\t.style('stroke-width', s.medianThickness)\n\t\t\t\t.style('stroke', s.medianColor)\n\t\t\t\t.style('opacity', '0.5')\n\t\t\t\t.attr('y1', isH ? -s.medianLength : median)\n\t\t\t\t.attr('y2', isH ? s.medianLength : median)\n\t\t\t\t.attr('x1', isH ? median : -s.medianLength)\n\t\t\t\t.attr('x2', isH ? median : s.medianLength)\n\t\t} else return\n\t}\n\n\tfunction renderLines(violinG, isH, lines, svgData) {\n\t\t// render straight lines on plot\n\t\tconst plotThickness = self.settings.plotThickness\n\n\t\tviolinG.selectAll('.sjpp-vp-line').remove()\n\t\tif (!lines?.length) return\n\t\tfor (const line of lines) {\n\t\t\tviolinG\n\t\t\t\t.append('line')\n\t\t\t\t.attr('class', 'sjpp-vp-line')\n\t\t\t\t.style('stroke', self.opts.mode == 'minimal' ? 'red' : 'black') // if not minimal, then red median line will also appear\n\t\t\t\t.attr('y1', isH ? -(plotThickness / 2) : svgData.axisScale(line))\n\t\t\t\t.attr('y2', isH ? plotThickness / 2 : svgData.axisScale(line))\n\t\t\t\t.attr('x1', isH ? svgData.axisScale(line) : -(plotThickness / 2))\n\t\t\t\t.attr('x2', isH ? svgData.axisScale(line) : plotThickness / 2)\n\t\t}\n\t}\n\n\tfunction renderBrushing(t1, t2, violinG, settings, plot, isH, svgData) {\n\t\t//brushing on data points\n\t\tif (settings.datasymbol === 'rug' || settings.datasymbol === 'bean') {\n\t\t\tconst br = isH\n\t\t\t\t? brushX()\n\t\t\t\t\t\t.extent([\n\t\t\t\t\t\t\t[0, -20],\n\t\t\t\t\t\t\t[settings.svgw, 20]\n\t\t\t\t\t\t])\n\t\t\t\t\t\t.on('end', event => {\n\t\t\t\t\t\t\tif (!event.selection) return\n\t\t\t\t\t\t\tself.displayBrushMenu(t1, t2, self, plot, event, svgData.axisScale, isH)\n\t\t\t\t\t\t\tdocument.body.addEventListener('pointerdown', onClickOut, true)\n\t\t\t\t\t\t})\n\t\t\t\t: brushY()\n\t\t\t\t\t\t.extent([\n\t\t\t\t\t\t\t[-20, 0],\n\t\t\t\t\t\t\t[20, settings.svgw]\n\t\t\t\t\t\t])\n\t\t\t\t\t\t.on('end', event => {\n\t\t\t\t\t\t\tif (!event.selection) return\n\t\t\t\t\t\t\tself.displayBrushMenu(t1, t2, self, plot, event, svgData.axisScale, isH)\n\t\t\t\t\t\t\tdocument.body.addEventListener('pointerdown', onClickOut, true)\n\t\t\t\t\t\t})\n\n\t\t\tconst brushG = violinG.append('g').classed('sjpp-brush', true).call(br)\n\n\t\t\t// clear brush when clicking outside of it\n\t\t\tconst onClickOut = e => {\n\t\t\t\tif (!brushG || !br) return\n\t\t\t\tif (!brushG.node().contains(e.target)) br.clear(brushG)\n\t\t\t\tdocument.body.removeEventListener('pointerdown', onClickOut, true)\n\t\t\t}\n\t\t}\n\t}\n\n\tself.toggleLoadingDiv = function (display = '') {\n\t\tif (display != 'none') {\n\t\t\tself.dom.loadingDiv\n\t\t\t\t.style('opacity', 0)\n\t\t\t\t.style('display', display)\n\t\t\t\t.transition()\n\t\t\t\t.duration('loadingWait' in self ? self.loadingWait : 3000)\n\t\t\t\t.style('opacity', 1)\n\t\t} else {\n\t\t\tself.dom.loadingDiv.style('display', display)\n\t\t}\n\t\tself.loadingWait = 1000\n\t}\n}\n\n// creates numeric axis\nexport function createNumericScale(self, settings, isH) {\n\tlet axisScale\n\tsettings.isLogScale\n\t\t? (axisScale = scaleLog()\n\t\t\t\t.base(self.app.vocabApi.termdbConfig.logscaleBase2 ? 2 : 10)\n\t\t\t\t.domain([self.data.min, self.data.max])\n\t\t\t\t.range(isH ? [0, settings.svgw] : [settings.svgw, 0]))\n\t\t: (axisScale = scaleLinear()\n\t\t\t\t.domain([self.data.min, self.data.max])\n\t\t\t\t.range(isH ? [0, settings.svgw] : [settings.svgw, 0]))\n\treturn axisScale\n}\n\nfunction getLegendGrps(termNum, self) {\n\tconst legendGrps = [],\n\t\tt1 = self.config.term,\n\t\tt2 = self.config.term2,\n\t\t// changed color from #aaa to address Section 508 contrast issue\n\t\theadingStyle = 'color: #555; font-weight: 400'\n\tif (self.settings.showStats) addDescriptiveStats(t1, legendGrps, headingStyle, self)\n\tif (t2?.term.type === 'float' || t2?.q.mode === 'continuous' || t2?.term.type === 'integer')\n\t\taddDescriptiveStats(t2, legendGrps, headingStyle, self)\n\n\taddUncomputableValues(\n\t\tt1?.q.mode === 'continuous' && t1?.q.hiddenValues && Object.keys(t1?.q.hiddenValues).length > 0\n\t\t\t? t1\n\t\t\t: t2?.q.mode === 'continuous' && t2?.q.hiddenValues && Object.keys(t2?.q.hiddenValues).length > 0\n\t\t\t? t2\n\t\t\t: null,\n\t\tlegendGrps,\n\t\theadingStyle,\n\t\tself\n\t)\n\n\tif (t2) {\n\t\tif (termNum.q.hiddenValues && Object.entries(termNum.q.hiddenValues).length != 0) {\n\t\t\taddHiddenValues(termNum, legendGrps, headingStyle)\n\t\t}\n\t}\n\treturn legendGrps\n}\n\nfunction addDescriptiveStats(term, legendGrps, headingStyle, self) {\n\tif (term?.q.descrStats) {\n\t\tconst items = Object.values(term.q.descrStats).map(stat => {\n\t\t\treturn {\n\t\t\t\ttext: `${stat.label}: ${stat.value}`,\n\t\t\t\tnoIcon: true\n\t\t\t}\n\t\t})\n\n\t\tconst title =\n\t\t\tself.config.term2?.term.type === 'float' || self.config.term2?.term.type === 'integer'\n\t\t\t\t? `Descriptive statistics: ${term.term.name}`\n\t\t\t\t: `Descriptive statistics`\n\t\tconst name = `<span style=\"${headingStyle}\">${title}</span>`\n\t\tlegendGrps.push({ name, items })\n\t}\n}\n\nfunction addUncomputableValues(term, legendGrps, headingStyle, self) {\n\tif (term?.term.values) {\n\t\tconst items = []\n\t\tfor (const k in term.term.values) {\n\t\t\tif (self.data.uncomputableValues?.[term.term.values[k]?.label]) {\n\t\t\t\titems.push({\n\t\t\t\t\ttext: `${term.term.values[k].label}, n = ${self.data.uncomputableValues[term.term.values[k].label]}`,\n\t\t\t\t\tnoIcon: true,\n\t\t\t\t\t/** Need to specify that this is a hidden value for\n\t\t\t\t\t * text styling in the legend but not a plot to avoid\n\t\t\t\t\t * rendering a tooltip or click events.\n\t\t\t\t\t */\n\t\t\t\t\tisHidden: true,\n\t\t\t\t\tisClickable: false,\n\t\t\t\t\thiddenOpacity: 1\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\t\tif (items.length) {\n\t\t\tconst name =\n\t\t\t\tself.config.term2?.term.type === 'float' || self.config.term2?.term.type === 'integer'\n\t\t\t\t\t? `<span style=\"${headingStyle}\">${term.term.name}</span>`\n\t\t\t\t\t: `<span style=\"${headingStyle}\">Other categories</span>`\n\t\t\tlegendGrps.push({ name, items })\n\t\t}\n\t}\n}\n\nfunction addHiddenValues(term, legendGrps, headingStyle) {\n\tconst items = []\n\tfor (const key of Object.keys(term.q.hiddenValues)) {\n\t\titems.push({\n\t\t\ttext: `${key}`,\n\t\t\tnoIcon: true,\n\t\t\t/** Need to specify that this is a hidden value for\n\t\t\t * text styling in the legend and  a plot for\n\t\t\t * rendering a tooltip or click events.\n\t\t\t */\n\t\t\tisHidden: true,\n\t\t\tisClickable: true,\n\t\t\thiddenOpacity: 1\n\t\t})\n\t}\n\tconst title = `${term.term.name}`\n\tconst name = `<span style=\"${headingStyle}\">${title}</span>`\n\tlegendGrps.push({ name, items })\n}\n"],
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-  "names": ["self"]
-}

package/dist/chunk-X27TRPIZ.js

@@ -1,119 +0,0 @@
-import {
-  GENE_EXPRESSION,
-  METABOLITE_INTENSITY,
-  PROTEOME_ABUNDANCE,
-  SINGLECELL_GENE_EXPRESSION
-} from "./chunk-XOCO3LVN.js";
-
-// common/termutils.js
-function sample_match_termvaluesetting(row, filter, geneVariant$ids) {
-  const lst = !filter ? [] : filter.type == "tvslst" ? filter.lst : [filter];
-  let numberofmatchedterms = 0;
-  for (const item of lst) {
-    if (item.type == "tvslst") {
-      if (sample_match_termvaluesetting(row, item)) {
-        numberofmatchedterms++;
-      }
-    } else {
-      const t = item.tvs;
-      let samplevalue;
-      if (t.term.type == "geneVariant") {
-        samplevalue = geneVariant$ids.map((g) => row[g]).filter((s) => s);
-      } else if (t.term.type == "integer" || t.term.type == "float" || t.term.type == GENE_EXPRESSION || t.term.type == METABOLITE_INTENSITY || t.term.type == PROTEOME_ABUNDANCE) {
-        samplevalue = row[t.term.id] || row[t.term.$id]?.key;
-      } else if (t.term.type == "survival") {
-        samplevalue = row[t.term.$id]?.key;
-      } else {
-        samplevalue = row[t.term.id] || row[t.term.$id]?.value;
-      }
-      let thistermmatch;
-      if (t.term.type == "categorical") {
-        if (samplevalue === void 0) {
-          if (t.isnot) thistermmatch = !thistermmatch;
-          if (thistermmatch) numberofmatchedterms++;
-          continue;
-        }
-        const valueset = t.valueset ? t.valueset : new Set(t.values.map((i) => i.key));
-        thistermmatch = valueset.has(samplevalue);
-      } else if (t.term.type == "integer" || t.term.type == "float" || t.term.type == GENE_EXPRESSION || t.term.type == METABOLITE_INTENSITY || t.term.type == PROTEOME_ABUNDANCE) {
-        if (samplevalue === void 0) {
-          if (t.isnot) thistermmatch = !thistermmatch;
-          if (thistermmatch) numberofmatchedterms++;
-          continue;
-        }
-        for (const range of t.ranges) {
-          if ("value" in range) {
-            thistermmatch = samplevalue === range.value;
-            if (thistermmatch) break;
-          } else if (samplevalue == range.name) {
-            thistermmatch = true;
-            break;
-          } else {
-            if (t.term.values) {
-              const v = t.term.values[samplevalue.toString()];
-              if (v && v.uncomputable) {
-                continue;
-              }
-            }
-            let left, right;
-            if (range.startunbounded) {
-              left = true;
-            } else if ("start" in range) {
-              if (range.startinclusive) {
-                left = samplevalue >= range.start;
-              } else {
-                left = samplevalue > range.start;
-              }
-            }
-            if (range.stopunbounded) {
-              right = true;
-            } else if ("stop" in range) {
-              if (range.stopinclusive) {
-                right = samplevalue <= range.stop;
-              } else {
-                right = samplevalue < range.stop;
-              }
-            }
-            thistermmatch = left && right;
-          }
-          if (thistermmatch) break;
-        }
-      } else if (t.term.type == "condition") {
-        const key = getPrecomputedKey(t);
-        const anno = samplevalue && samplevalue[key];
-        if (anno) {
-          thistermmatch = Array.isArray(anno) ? t.values.find((d) => anno.includes(d.key)) : t.values.find((d) => d.key == anno);
-        }
-      } else if (t.term.type == "survival") {
-        if (samplevalue === void 0) {
-          if (t.isnot) thistermmatch = !thistermmatch;
-          if (thistermmatch) numberofmatchedterms++;
-          continue;
-        }
-        const valueset = t.valueset ? t.valueset : new Set(t.values.map((i) => i.key));
-        thistermmatch = valueset.has(samplevalue);
-      } else if (t.term.type == "geneVariant" && t.legendFilterType == "geneVariant_hard") {
-        const f = t.values[0];
-        thistermmatch = samplevalue.find((s) => {
-          for (const v of s.values) {
-            if (v.dt == f.dt && (!v.origin || v.origin == f.origin) && f.mclasslst.includes(v.class)) return true;
-          }
-        }) && true;
-      } else if (t.term.type == SINGLECELL_GENE_EXPRESSION) {
-      } else {
-        throw "unknown term type";
-      }
-      if (t.isnot) {
-        thistermmatch = !thistermmatch;
-      }
-      if (thistermmatch) numberofmatchedterms++;
-    }
-    if (filter.join == "or" && numberofmatchedterms) return true;
-  }
-  if (numberofmatchedterms == lst.length) return true;
-}
-
-export {
-  sample_match_termvaluesetting
-};
-//# sourceMappingURL=chunk-X27TRPIZ.js.map