@sjcrh/proteinpaint-client 2.201.0 → 2.202.0

package/dist/chunk-UJN2RH5R.js

@@ -1,411 +0,0 @@
-import {
-  getMaxLabelWidth,
-  renderTable,
-  table2col
-} from "./chunk-K6OVOHIZ.js";
-import {
-  SINGLECELL_GENE_EXPRESSION
-} from "./chunk-GEQUQ3GG.js";
-import {
-  getValueConversionFactor,
-  toUserUnit
-} from "./chunk-75T7ESEO.js";
-import {
-  basis_default,
-  line_default
-} from "./chunk-2KXLYFAO.js";
-import {
-  axisLeft,
-  axisTop
-} from "./chunk-LOZEKOES.js";
-import {
-  format,
-  linear,
-  log
-} from "./chunk-UJELJXJG.js";
-import {
-  brushX,
-  brushY
-} from "./chunk-5R63Q5KH.js";
-import {
-  rgb
-} from "./chunk-Q5RDQNIT.js";
-
-// plots/violin.renderer.js
-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 && 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") });
-    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)().scale(uiScale).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 numTerm = getNumericTerm(t1, t2);
-      const n = numTerm.valueConversion ? `${numTerm.name} (${numTerm.valueConversion.toUnit}s)` : numTerm.name;
-      const lab = svg.svgG.append("text").text(n).classed("sjpp-numeric-term-label", true).attr("data-testid", `sjpp-violin-label-${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);
-      };
-    }
-  }
-}
-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-UJN2RH5R.js.map