@sjcrh/proteinpaint-client 2.201.0 → 2.202.0

package/dist/chunk-OBRVYT5O.js

@@ -0,0 +1,187 @@
+import {
+  DATermTypes
+} from "./chunk-73PFJ2VF.js";
+import {
+  dofetch3
+} from "./chunk-X4QQRHFB.js";
+import {
+  rgb
+} from "./chunk-Q5RDQNIT.js";
+
+// plots/volcano/colors.ts
+function getGroupColors(config) {
+  const groups = config?.samplelst?.groups;
+  const termValues = config?.tw?.term?.values;
+  const rawDown = termValues?.[groups?.[0]?.name]?.color || "red";
+  const rawUp = termValues?.[groups?.[1]?.name]?.color || "blue";
+  return {
+    controlColor: toHex(rawDown, "red"),
+    caseColor: toHex(rawUp, "blue")
+  };
+}
+function toHex(color, fallback) {
+  const c = rgb(color || fallback);
+  return c.displayable() ? c.formatHex() : rgb(fallback).formatHex();
+}
+
+// plots/volcano/model/VolcanoModel.ts
+var VolcanoModel = class {
+  /** TODO: This model is used in both the volcano and gsea.
+   * In the future, create base model in DA and use specific
+   * classes for the volcano and gsea. */
+  constructor(plot, termType) {
+    this.plot = plot;
+    this.app = plot.app;
+    this.termType = termType;
+  }
+  /** May use mapper instead as more termTypes are added */
+  async getData(config, settings) {
+    this.config = config;
+    this.settings = settings;
+    if (this.termType === DATermTypes.GENE_EXPRESSION) {
+      const body = await this.getGERequestBody();
+      const response = await dofetch3("termdb/DE", { body, signal: this.plot.api?.getAbortSignal() });
+      if (response && !response.error) response.daRequest = body;
+      return response;
+    }
+    if (this.termType === DATermTypes.DNA_METHYLATION) {
+      const body = await this.getDMRequestBody();
+      const response = await dofetch3("termdb/diffMeth", { body, signal: this.plot.api?.getAbortSignal() });
+      if (response && !response.error) response.daRequest = body;
+      return response;
+    }
+    if (this.termType === DATermTypes.SINGLECELL_CELLTYPE) {
+      const body = await this.getSCCTRequestBody();
+      return await dofetch3("termdb/singlecellDEgenes", { body, signal: this.plot.api?.getAbortSignal() });
+    }
+    if (this.termType === DATermTypes.PROTEOME_DAP) {
+      const body = this.getDapRequestBody();
+      return await dofetch3("termdb/dapVolcano", { body, signal: this.plot.api?.getAbortSignal() });
+    }
+    if (this.termType === DATermTypes.SINGLECELL_GENE_EXPRESSION) {
+    }
+    throw new Error(`Volcano plot does not support route for termType='${this.termType}'`);
+  }
+  //Gene expression
+  async getGERequestBody() {
+    await this.getOtherSamples(this.config.samplelst);
+    const state = this.app.getState();
+    const body = {
+      kind: "DE",
+      genome: this.app.vocabApi.vocab.genome,
+      dslabel: this.app.vocabApi.vocab.dslabel,
+      method: this.settings.method,
+      min_count: this.settings.minCount,
+      min_total_count: this.settings.minTotalCount,
+      samplelst: this.config.samplelst,
+      filter: state.termfilter.filter,
+      filter0: state.termfilter.filter0,
+      cpm_cutoff: this.settings.cpmCutoff,
+      volcanoRender: this.getVolcanoRender()
+    };
+    const pseudobulk = this.config.tw?.pseudobulk;
+    if (pseudobulk) body.pseudobulk = pseudobulk;
+    this.addConfounderTw(body);
+    return body;
+  }
+  //DNA methylation
+  async getDMRequestBody() {
+    await this.getOtherSamples(this.config.samplelst);
+    const state = this.app.getState();
+    const body = {
+      kind: "DM",
+      genome: this.app.vocabApi.vocab.genome,
+      dslabel: this.app.vocabApi.vocab.dslabel,
+      samplelst: this.config.samplelst,
+      filter: state.termfilter.filter,
+      filter0: state.termfilter.filter0,
+      min_samples_per_group: this.settings.minSamplesPerGroup,
+      volcanoRender: this.getVolcanoRender()
+    };
+    this.addConfounderTw(body);
+    return body;
+  }
+  /** Parameters telling the server to run the `volcano` Rust renderer and return a
+   * volcano PNG + top-significant rows instead of the full dot list. */
+  getVolcanoRender() {
+    const dotRadius = Math.max(this.settings.width, this.settings.height) / 80;
+    const { caseColor, controlColor } = getGroupColors(this.config);
+    return {
+      significanceThresholds: {
+        pValueCutoff: this.settings.pValue,
+        pValueType: this.settings.pValueType,
+        foldChangeCutoff: this.settings.foldChangeCutoff
+      },
+      pixelWidth: this.settings.width,
+      pixelHeight: this.settings.height,
+      colorSignificant: toHex(this.settings.defaultSignColor, "red"),
+      colorSignificantUp: caseColor,
+      colorSignificantDown: controlColor,
+      colorNonsignificant: toHex(this.settings.defaultNonSignColor, "black"),
+      dotRadius,
+      maxInteractiveDots: this.settings.maxInteractiveDots,
+      // Render the PNG at device-pixel resolution so it stays sharp on
+      // retina screens. The server reports the plot extent in CSS-space,
+      // so SVG overlay coords are unaffected.
+      //
+      // Oversample by 2× so the PNG also stays sharp when the user
+      // *zooms in after* the initial render (the captured DPR is frozen
+      // at fetch time — bigger headroom = more tolerable post-render
+      // zoom before pixelation appears). The server clamp keeps the
+      // bitmap memory bounded.
+      devicePixelRatio: (typeof window !== "undefined" ? window.devicePixelRatio : 1) * 2
+    };
+  }
+  //This is a workaround until the server can accept an arr of confounder tws
+  addConfounderTw(body) {
+    const confounders = this.config?.confounderTws;
+    if (confounders?.length) {
+      body.tw = this.config.confounderTws[0];
+      if (confounders.length > 1) body.tw2 = this.config.confounderTws[1];
+    }
+  }
+  //Single cell cell type
+  getSCCTRequestBody() {
+    const body = {
+      genome: this.app.vocabApi.vocab.genome,
+      dslabel: this.app.vocabApi.vocab.dslabel,
+      sample: this.config.sample,
+      termId: this.config.termId,
+      categoryName: this.config.categoryName,
+      volcanoRender: this.getVolcanoRender()
+    };
+    return body;
+  }
+  getDapRequestBody() {
+    const { organism, assay, cohort } = this.config.proteomeDetails;
+    return {
+      genome: this.app.vocabApi.vocab.genome,
+      dslabel: this.app.vocabApi.vocab.dslabel,
+      organism,
+      assay,
+      cohort,
+      volcanoRender: this.getVolcanoRender()
+    };
+  }
+  /** retrieve the sampleId/sampleName for samples in
+   * the "others" group instead of using {in: false} */
+  async getOtherSamples(samplelst) {
+    const othersSamplesGroup = samplelst.groups.find((g) => !g.in);
+    if (!othersSamplesGroup) return;
+    const state = this.app.getState();
+    const samplesGroup = samplelst.groups.find((g) => g.in);
+    othersSamplesGroup.values = [];
+    for (const s of await this.plot.vocabApi.getFilteredSampleList(state.termfilter.filter)) {
+      if (!samplesGroup.values.some((i) => i.sampleId == s.id)) {
+        othersSamplesGroup.values.push({ sampleId: s.id, sample: s.name });
+      }
+    }
+    othersSamplesGroup.in = true;
+  }
+};
+
+export {
+  getGroupColors,
+  VolcanoModel
+};
+//# sourceMappingURL=chunk-OBRVYT5O.js.map

package/dist/chunk-OBRVYT5O.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/volcano/colors.ts", "../plots/volcano/model/VolcanoModel.ts"],
+  "sourcesContent": ["import { rgb } from 'd3-color'\n\n/** Resolve the case/control dot colors for a volcano plot in one place so the\n * interactive SVG overlay (VolcanoViewModel) and the server-rendered PNG\n * (VolcanoModel \u2192 Rust) paint each dot the same color.\n *\n * `caseColor` maps to points with `fold_change > 0` (group 2 in samplelst),\n * `controlColor` to `fold_change < 0` (group 1). Every returned color is a\n * `#rrggbb` hex string \u2014 CSS names like `'red'` are normalized via d3-color\n * so the Rust renderer's hex-only parser doesn't fall back to a muted tuple.\n */\nexport function getGroupColors(config: any): { caseColor: string; controlColor: string } {\n\tconst groups = config?.samplelst?.groups\n\tconst termValues = config?.tw?.term?.values\n\tconst rawDown = termValues?.[groups?.[0]?.name]?.color || 'red'\n\tconst rawUp = termValues?.[groups?.[1]?.name]?.color || 'blue'\n\treturn {\n\t\tcontrolColor: toHex(rawDown, 'red'),\n\t\tcaseColor: toHex(rawUp, 'blue')\n\t}\n}\n\n/** Normalize any CSS-accepted color string into `#rrggbb`. */\nexport function toHex(color: string | undefined, fallback: string): string {\n\tconst c = rgb(color || fallback)\n\treturn c.displayable() ? c.formatHex() : rgb(fallback).formatHex()\n}\n", "import type { MassAppApi } from '#mass/types/mass'\nimport { dofetch3 } from '#common/dofetch'\nimport type { DERequest, DiffMethRequest, TermdbSingleCellDEgenesRequest, VolcanoRenderRequest } from '#types'\nimport { DATermTypes as tt } from '../../diffAnalysis/enabledTermTypes'\nimport { getGroupColors, toHex } from '../colors'\n// import type { Volcano } from '../Volcano'\n\nexport class VolcanoModel {\n\tplot: any\n\tapp: MassAppApi\n\tconfig!: any\n\tsettings!: any\n\ttermType: string\n\n\t/** TODO: This model is used in both the volcano and gsea.\n\t * In the future, create base model in DA and use specific\n\t * classes for the volcano and gsea. */\n\tconstructor(plot: any, termType: string) {\n\t\tthis.plot = plot\n\t\tthis.app = plot.app\n\t\tthis.termType = termType\n\t}\n\n\t/** May use mapper instead as more termTypes are added */\n\tasync getData(config: any, settings: any) {\n\t\tthis.config = config\n\t\tthis.settings = settings\n\n\t\tif (this.termType === tt.GENE_EXPRESSION) {\n\t\t\tconst body = await this.getGERequestBody()\n\t\t\tconst response = await dofetch3('termdb/DE', { body, signal: this.plot.api?.getAbortSignal() })\n\t\t\t// Surface the DE request so downstream plots (GSEA) can snapshot\n\t\t\t// it and later ask the server to recompute the DA cache if the\n\t\t\t// file is missing on a peer node or after TTL eviction.\n\t\t\tif (response && !response.error) response.daRequest = body\n\t\t\treturn response\n\t\t}\n\t\tif (this.termType === tt.DNA_METHYLATION) {\n\t\t\tconst body = await this.getDMRequestBody()\n\t\t\tconst response = await dofetch3('termdb/diffMeth', { body, signal: this.plot.api?.getAbortSignal() })\n\t\t\t// Surface the DM request the same way the GE branch above does so\n\t\t\t// the GSEA tab can snapshot it and the server can recompute the DM\n\t\t\t// cache if the file is missing on a peer node or after TTL.\n\t\t\tif (response && !response.error) response.daRequest = body\n\t\t\treturn response\n\t\t}\n\t\tif (this.termType === tt.SINGLECELL_CELLTYPE) {\n\t\t\tconst body = await this.getSCCTRequestBody()\n\t\t\treturn await dofetch3('termdb/singlecellDEgenes', { body, signal: this.plot.api?.getAbortSignal() })\n\t\t}\n\t\tif (this.termType === tt.PROTEOME_DAP) {\n\t\t\tconst body = this.getDapRequestBody()\n\t\t\treturn await dofetch3('termdb/dapVolcano', { body, signal: this.plot.api?.getAbortSignal() })\n\t\t}\n\t\tif (this.termType === tt.SINGLECELL_GENE_EXPRESSION) {\n\t\t\t//TODO\n\t\t}\n\t\tthrow new Error(`Volcano plot does not support route for termType='${this.termType}'`)\n\t}\n\n\t//Gene expression\n\tasync getGERequestBody() {\n\t\tawait this.getOtherSamples(this.config.samplelst)\n\t\tconst state = this.app.getState()\n\t\tconst body = {\n\t\t\tkind: 'DE',\n\t\t\tgenome: this.app.vocabApi.vocab.genome,\n\t\t\tdslabel: this.app.vocabApi.vocab.dslabel,\n\t\t\tmethod: this.settings.method,\n\t\t\tmin_count: this.settings.minCount,\n\t\t\tmin_total_count: this.settings.minTotalCount,\n\t\t\tsamplelst: this.config.samplelst,\n\t\t\tfilter: state.termfilter.filter,\n\t\t\tfilter0: state.termfilter.filter0,\n\t\t\tcpm_cutoff: this.settings.cpmCutoff,\n\t\t\tvolcanoRender: this.getVolcanoRender()\n\t\t} as Partial<DERequest> //remove Partial when storage_type is removed from DERequest\n\t\tconst pseudobulk = this.config.tw?.pseudobulk\n\t\tif (pseudobulk) body.pseudobulk = pseudobulk\n\n\t\tthis.addConfounderTw(body)\n\n\t\treturn body\n\t}\n\n\t//DNA methylation\n\tasync getDMRequestBody() {\n\t\tawait this.getOtherSamples(this.config.samplelst)\n\t\tconst state = this.app.getState()\n\t\tconst body = {\n\t\t\tkind: 'DM',\n\t\t\tgenome: this.app.vocabApi.vocab.genome,\n\t\t\tdslabel: this.app.vocabApi.vocab.dslabel,\n\t\t\tsamplelst: this.config.samplelst,\n\t\t\tfilter: state.termfilter.filter,\n\t\t\tfilter0: state.termfilter.filter0,\n\t\t\tmin_samples_per_group: this.settings.minSamplesPerGroup,\n\t\t\tvolcanoRender: this.getVolcanoRender()\n\t\t} as Partial<DiffMethRequest>\n\n\t\tthis.addConfounderTw(body)\n\n\t\treturn body\n\t}\n\n\t/** Parameters telling the server to run the `volcano` Rust renderer and return a\n\t * volcano PNG + top-significant rows instead of the full dot list. */\n\tgetVolcanoRender(): VolcanoRenderRequest {\n\t\t// Match the client overlay's radius (see VolcanoViewModel.setPointData)\n\t\t// so the PNG rings and the interactive overlay rings line up; otherwise\n\t\t// a smaller PNG ring sits inside the larger overlay ring and looks like\n\t\t// a stray dot at the center.\n\t\tconst dotRadius = Math.max(this.settings.width, this.settings.height) / 80\n\t\t// Resolve case/control colors via the shared helper (see colors.ts) so the\n\t\t// PNG and the SVG overlay paint each side with the exact same hex string.\n\t\tconst { caseColor, controlColor } = getGroupColors(this.config)\n\t\treturn {\n\t\t\tsignificanceThresholds: {\n\t\t\t\tpValueCutoff: this.settings.pValue,\n\t\t\t\tpValueType: this.settings.pValueType,\n\t\t\t\tfoldChangeCutoff: this.settings.foldChangeCutoff\n\t\t\t},\n\t\t\tpixelWidth: this.settings.width,\n\t\t\tpixelHeight: this.settings.height,\n\t\t\tcolorSignificant: toHex(this.settings.defaultSignColor, 'red'),\n\t\t\tcolorSignificantUp: caseColor,\n\t\t\tcolorSignificantDown: controlColor,\n\t\t\tcolorNonsignificant: toHex(this.settings.defaultNonSignColor, 'black'),\n\t\t\tdotRadius,\n\t\t\tmaxInteractiveDots: this.settings.maxInteractiveDots,\n\t\t\t// Render the PNG at device-pixel resolution so it stays sharp on\n\t\t\t// retina screens. The server reports the plot extent in CSS-space,\n\t\t\t// so SVG overlay coords are unaffected.\n\t\t\t//\n\t\t\t// Oversample by 2\u00D7 so the PNG also stays sharp when the user\n\t\t\t// *zooms in after* the initial render (the captured DPR is frozen\n\t\t\t// at fetch time \u2014 bigger headroom = more tolerable post-render\n\t\t\t// zoom before pixelation appears). The server clamp keeps the\n\t\t\t// bitmap memory bounded.\n\t\t\tdevicePixelRatio: (typeof window !== 'undefined' ? window.devicePixelRatio : 1) * 2\n\t\t}\n\t}\n\n\t//This is a workaround until the server can accept an arr of confounder tws\n\taddConfounderTw(body) {\n\t\tconst confounders = this.config?.confounderTws\n\t\tif (confounders?.length) {\n\t\t\tbody.tw = this.config.confounderTws[0]\n\t\t\tif (confounders.length > 1) body.tw2 = this.config.confounderTws[1]\n\t\t}\n\t}\n\n\t//Single cell cell type\n\tgetSCCTRequestBody(): TermdbSingleCellDEgenesRequest {\n\t\tconst body = {\n\t\t\tgenome: this.app.vocabApi.vocab.genome,\n\t\t\tdslabel: this.app.vocabApi.vocab.dslabel,\n\t\t\tsample: this.config.sample,\n\t\t\ttermId: this.config.termId,\n\t\t\tcategoryName: this.config.categoryName,\n\t\t\tvolcanoRender: this.getVolcanoRender()\n\t\t}\n\t\treturn body\n\t}\n\n\tgetDapRequestBody() {\n\t\tconst { organism, assay, cohort } = this.config.proteomeDetails\n\t\treturn {\n\t\t\tgenome: this.app.vocabApi.vocab.genome,\n\t\t\tdslabel: this.app.vocabApi.vocab.dslabel,\n\t\t\torganism,\n\t\t\tassay,\n\t\t\tcohort,\n\t\t\tvolcanoRender: this.getVolcanoRender()\n\t\t}\n\t}\n\n\t/** retrieve the sampleId/sampleName for samples in\n\t * the \"others\" group instead of using {in: false} */\n\tasync getOtherSamples(samplelst) {\n\t\tconst othersSamplesGroup = samplelst.groups.find(g => !g.in)\n\t\tif (!othersSamplesGroup) return\n\n\t\tconst state = this.app.getState()\n\t\tconst samplesGroup = samplelst.groups.find(g => g.in)\n\t\tothersSamplesGroup.values = []\n\t\t// retrieve full list of samples based on current filter. put samples not in samplesGroup in \"others\" group.\n\t\t// the plot-scoped vocabApi from PlotBase is used, so that an unrelated app dispatch does not cancel this request\n\t\tfor (const s of await this.plot.vocabApi.getFilteredSampleList(state.termfilter.filter)) {\n\t\t\t// s={id,name}, samplelst.groups[].values[]={sampleId,sample}\n\t\t\t// NOTE: must not use indexOf() here, it compares by strict equality and not by predicate,\n\t\t\t// which would never match and would put every sample in the \"others\" group\n\t\t\tif (!samplesGroup.values.some(i => i.sampleId == s.id)) {\n\t\t\t\tothersSamplesGroup.values.push({ sampleId: s.id, sample: s.name })\n\t\t\t}\n\t\t}\n\t\tothersSamplesGroup.in = true\n\t}\n}\n"],
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+  "names": []
+}

package/dist/chunk-OCC5HEPR.js

@@ -0,0 +1,411 @@
+import {
+  getMaxLabelWidth,
+  renderTable,
+  table2col
+} from "./chunk-73PFJ2VF.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-OCC5HEPR.js.map