@sjcrh/proteinpaint-client 2.182.0 → 2.183.0

package/dist/chunk-CVBQWXLH.js

@@ -0,0 +1,455 @@
+import {
+  setViolinRenderer
+} from "./chunk-6C2SBTLR.js";
+import {
+  setInteractivity
+} from "./chunk-WGHO2NCP.js";
+import {
+  PlotBase,
+  controlsInit,
+  defaultUiLabels,
+  fillTermWrapper,
+  getCombinedTermFilter,
+  htmlLegend,
+  renderTerm1Label,
+  term0_term2_defaultQ
+} from "./chunk-OXJ2TWDO.js";
+import {
+  Menu
+} from "./chunk-A6TQGNDQ.js";
+import {
+  copyMerge,
+  getCompInit
+} from "./chunk-MVTCBVSX.js";
+import {
+  isNumericTerm,
+  isSingleCellTerm
+} from "./chunk-6ITDJ5UR.js";
+import {
+  plotColor
+} from "./chunk-XYFDBYOY.js";
+
+// plots/violin.js
+var ViolinPlot = class _ViolinPlot extends PlotBase {
+  static type = "violin";
+  constructor(opts) {
+    super(opts);
+    this.type = _ViolinPlot.type;
+  }
+  async init(appState) {
+    const controls = this.opts.holder.append("div").attr("class", "sjpp-plot-controls").style("display", "inline-block");
+    const config = appState.plots.find((p) => p.id === this.id);
+    const holder = this.opts.holder.append("div").style("display", "inline-block").style("padding", this.opts.mode != "minimal" ? "5px" : "0px").style("padding-left", this.opts.mode != "minimal" ? "20px" : "0px").attr("id", "sjpp-vp-holder");
+    this.dom = {
+      hovertip: new Menu({ padding: "3px" }),
+      // separate tips for hover & click on violin labels to avoid interfering
+      clicktip: new Menu({ padding: "0px" }),
+      sampletabletip: new Menu({ padding: "3px" }),
+      // sampletable is lauched from option shown in clicktip which closes on clicking, thus need its own menu..
+      header: this.opts.header,
+      controls,
+      banner: holder.append("div").attr("data-testid", "sjpp-violin-banner").style("display", "none").style("text-align", "center").style("padding", "24px").style("font-size", "16px"),
+      loadingDiv: holder.append("div").attr("data-testid", "sjpp-violin-loading-div").style("display", this.opts.mode != "minimal" ? "inline-block" : "none").style("padding", "24px").text("Loading ..."),
+      violinDiv: holder.append("div").attr("class", "sjpp-vp-violinDiv").attr("data-testid", "sjpp-violin-div").style("display", "flex").style("flex-direction", "row").style("flex-wrap", "wrap").style("max-width", "100vw"),
+      legendDiv: holder.append("div").classed("sjpp-vp-legend", true).attr("data-testid", "sjpp-violin-legend").style("margin-left", "-15px").style("padding-top", "20px")
+    };
+    setViolinRenderer(this);
+    setInteractivity(this);
+    if (this.opts.mode != "minimal") {
+      this.legendRenderer = htmlLegend(this.dom.legendDiv, {
+        settings: {
+          legendOrientation: "vertical"
+        },
+        handlers: {}
+      });
+    }
+  }
+  reactsTo(action) {
+    if (action.type.startsWith("plot_")) {
+      return (action.id === this.id || action.id == this.parentId) && (!action.config?.childType || action.config?.childType == this.type);
+    }
+    return true;
+  }
+  preApiFreeze(api) {
+    api.download = this.download;
+    api.getChartImages = () => this.getChartImages();
+  }
+  async setControls() {
+    if (this.components.controls) return;
+    this.dom.controls.selectAll("*").remove();
+    const controlLabels = this.state.config.controlLabels;
+    if (!controlLabels) throw "controls labels not found";
+    this.components = {};
+    if (this.opts.mode == "minimal") return;
+    let specialCase = "default";
+    if (isSingleCellTerm(this.config.term.term)) {
+      if (!this.config.term.term.sample)
+        console.error("single cell term without sample specified in config, unexpected");
+      else {
+        specialCase = {
+          type: "singleCell",
+          config: { sample: this.config.term.term.sample }
+        };
+      }
+    }
+    const inputs = [
+      {
+        type: "term",
+        configKey: "term",
+        chartType: "violin",
+        usecase: { target: "violin", detail: "term" },
+        label: controlLabels.term1?.label || renderTerm1Label,
+        vocabApi: this.app.vocabApi,
+        menuOptions: "edit"
+      },
+      {
+        type: "term",
+        configKey: "term2",
+        chartType: "violin",
+        usecase: { target: "violin", detail: "term2", specialCase },
+        title: controlLabels.term2.title || controlLabels.term2.label,
+        label: controlLabels.term2.label,
+        vocabApi: this.app.vocabApi,
+        numericEditMenuVersion: this.opts.numericEditMenuVersion,
+        defaultQ4fillTW: term0_term2_defaultQ,
+        getDisplayStyle: (plot) => plot.config?.term?.term?.type === "termCollection" ? "none" : ""
+      },
+      {
+        type: "term",
+        configKey: "term0",
+        chartType: "violin",
+        usecase: { target: "violin", detail: "term0", specialCase },
+        title: controlLabels.term0.title || controlLabels.term0.label,
+        label: controlLabels.term0.label,
+        vocabApi: this.app.vocabApi,
+        // by default, do not allow continuous mode for divide-by term, since
+        // it will create a separate violin-overlay group per unique float or integer value
+        // and there will nonsensical tens/hundreds of these charts based on the cohort size
+        numericEditMenuVersion: this.opts.numericEditMenuVersion || ["discrete"],
+        defaultQ4fillTW: term0_term2_defaultQ,
+        getDisplayStyle: (plot) => plot.config?.term?.term?.type === "termCollection" ? "none" : ""
+      },
+      {
+        label: "Orientation",
+        title: "Orientation of the chart",
+        type: "radio",
+        chartType: "violin",
+        settingsKey: "orientation",
+        options: [
+          { label: "Vertical", value: "vertical" },
+          { label: "Horizontal", value: "horizontal" }
+        ]
+      },
+      {
+        label: "Data symbol",
+        title: "Symbol type",
+        type: "radio",
+        chartType: "violin",
+        settingsKey: "datasymbol",
+        options: [
+          { label: "Ticks", value: "rug" },
+          { label: "Circles", value: "bean" },
+          { label: "Off", value: "none" }
+        ]
+      },
+      {
+        label: "Scale",
+        title: "Axis scale",
+        type: "radio",
+        chartType: "violin",
+        settingsKey: "isLogScale",
+        options: [
+          { label: "Linear", value: false },
+          { label: "Log10", value: true }
+        ]
+      },
+      {
+        label: "Order by",
+        title: "Order violin plots by parameters",
+        type: "radio",
+        chartType: "violin",
+        settingsKey: "orderByMedian",
+        options: [
+          { label: "Default", value: false },
+          { label: "Median", value: true }
+        ],
+        getDisplayStyle: () => {
+          let style = "none";
+          const charts = this.data?.charts || {};
+          for (const k of Object.keys(charts)) {
+            const chart = charts[k];
+            if (chart?.plots.length > 1) style = "";
+          }
+          return style;
+        }
+      },
+      {
+        label: "Symbol size",
+        type: "number",
+        chartType: "violin",
+        settingsKey: "radius",
+        step: 1,
+        max: 30,
+        min: 4
+      },
+      {
+        label: "Bins",
+        type: "number",
+        chartType: "violin",
+        settingsKey: "ticks",
+        title: "Number of bins used to build the plot",
+        min: 1,
+        max: 50
+      },
+      {
+        label: "Plot length",
+        title: "Length of the plot",
+        type: "number",
+        chartType: "violin",
+        settingsKey: "svgw",
+        step: 10,
+        max: 1e3,
+        min: 200,
+        debounceInterval: 1e3
+      },
+      {
+        label: "Plot thickness",
+        title: "If not specified, the plot thickness is calculated based on the number of categories",
+        type: "number",
+        chartType: "violin",
+        settingsKey: "plotThickness",
+        step: 10,
+        max: 200,
+        min: 20,
+        debounceInterval: 1e3
+      },
+      {
+        label: "Plot padding",
+        type: "number",
+        chartType: "violin",
+        settingsKey: "rowSpace",
+        step: 1,
+        max: 20,
+        min: 0,
+        debounceInterval: 1e3
+      },
+      {
+        label: "Median length",
+        title: "Length of median",
+        type: "number",
+        chartType: "violin",
+        settingsKey: "medianLength",
+        step: 1,
+        max: 50,
+        min: 3,
+        debounceInterval: 1e3
+      },
+      {
+        label: "Median color",
+        title: "color of median",
+        type: "color",
+        chartType: "violin",
+        settingsKey: "medianColor"
+      },
+      {
+        label: "Median thickness",
+        title: "Width of median",
+        type: "number",
+        chartType: "violin",
+        settingsKey: "medianThickness",
+        step: 1,
+        max: 10,
+        min: 3,
+        debounceInterval: 100
+      },
+      {
+        label: "Default violin color",
+        type: "color",
+        chartType: "violin",
+        settingsKey: "defaultColor"
+      },
+      {
+        label: "Show stats",
+        type: "checkbox",
+        chartType: "violin",
+        settingsKey: "showStats",
+        boxLabel: "Yes"
+      },
+      {
+        label: "Show association tests",
+        type: "checkbox",
+        chartType: "violin",
+        settingsKey: "showAssociationTests",
+        boxLabel: "Yes",
+        getDisplayStyle: (plot) => plot.term2 ? "table-row" : "none"
+      }
+    ];
+    this.components.controls = await controlsInit({
+      app: this.app,
+      id: this.id,
+      holder: this.dom.controls,
+      inputs
+    });
+    this.components.controls.on("downloadClick.violin", this.download);
+  }
+  getState(appState) {
+    const config = appState.plots.find((p) => p.id === this.id);
+    if (!config) {
+      throw `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`;
+    }
+    const parentConfig = appState.plots.find((p) => p.id === this.parentId);
+    const termfilter = getCombinedTermFilter(appState, config.filter || parentConfig?.filter);
+    return {
+      termfilter,
+      config,
+      displaySampleIds: appState.termdbConfig.displaySampleIds,
+      hasVerifiedToken: this.app.vocabApi.hasVerifiedToken()
+    };
+  }
+  async main() {
+    this.config = structuredClone(this.state.config);
+    this.settings = this.config.settings.violin;
+    await this.setControls();
+    if (this.config.chartType != this.type && this.config.childType != this.type) return;
+    if (this.dom.header)
+      this.dom.header.html(
+        this.config.term.term.name + ` <span style="opacity:.6;font-size:1em;margin-left:10px;">Violin Plot</span>`
+      );
+    const existingMsg = this.dom.banner.style("display", "none").select("span");
+    if (!existingMsg.empty()) existingMsg.remove();
+    const args = this.validateArgs();
+    let data;
+    try {
+      this.toggleLoadingDiv();
+      data = await this.app.vocabApi.getViolinBox(args, null, this.api.getAbortSignal());
+    } catch (e) {
+      this.toggleLoadingDiv("none");
+      if (this.app.isAbortError(e)) return;
+      throw e;
+    }
+    this.data = data;
+    if (this.data.error) {
+      this.toggleLoadingDiv("none");
+      throw this.data.error;
+    }
+    args.tw.q.descrStats = this.data.descrStats;
+    this.toggleLoadingDiv(this.opts.mode == "minimal" ? "none" : "");
+    setTimeout(
+      () => {
+        this.render();
+      },
+      this.opts.mode == "minimal" ? 0 : 500
+    );
+    this.toggleLoadingDiv("none");
+  }
+  validateArgs() {
+    const { term, term2, term0, settings } = this.config;
+    const s = this.settings;
+    const arg = {
+      plotType: "violin",
+      svgw: s.svgw,
+      orientation: s.orientation,
+      devicePixelRatio: window.devicePixelRatio,
+      datasymbol: s.datasymbol,
+      radius: s.radius,
+      axisHeight: s.axisHeight,
+      rightMargin: s.rightMargin,
+      isLogScale: s.isLogScale,
+      ticks: s.ticks,
+      orderByMedian: s.orderByMedian,
+      filter: this.state.termfilter.filter
+    };
+    if (this.opts.mode == "minimal") {
+      arg.tw = term;
+      if (term2 || term0) throw "only a single term allowed for minimal plot";
+      if (term.q.mode == "spline") {
+        s.lines = term.q.knots.map((x) => Number(x.value));
+      } else {
+        s.lines = [];
+      }
+      if (term.q.scale) {
+        arg.scale = term.q.scale;
+      }
+    } else if (term.term?.type === "termCollection" && term.term?.memberType === "numeric") {
+      arg.tw = term;
+    } else if (isNumericTerm(term.term) && term.q.mode === "continuous") {
+      arg.tw = term;
+      if (term2) arg.overlayTw = term2;
+    } else if (isNumericTerm(term2?.term) && term2.q.mode === "continuous") {
+      arg.tw = term2;
+      arg.overlayTw = term;
+    } else {
+      throw "both term1 and term2 are not numeric/continuous";
+    }
+    if (term0) arg.divideTw = term0;
+    return arg;
+  }
+};
+var violinInit = getCompInit(ViolinPlot);
+var componentInit = violinInit;
+function getDefaultViolinSettings(app, overrides = {}) {
+  const defaults = {
+    orientation: "horizontal",
+    rowlabelw: 250,
+    brushRange: null,
+    //object with start and end if there is a brush selection
+    svgw: 500,
+    // span length of a plot/svg, not including margin
+    datasymbol: "rug",
+    radius: 10,
+    axisHeight: 60,
+    rightMargin: 50,
+    lines: [],
+    isLogScale: false,
+    // false: linear scale, true: log scale
+    rowSpace: 10,
+    medianLength: 7,
+    medianColor: "#FF0000",
+    medianThickness: 3,
+    ticks: 15,
+    defaultColor: plotColor,
+    method: 0,
+    orderByMedian: false,
+    showStats: true,
+    showAssociationTests: true
+  };
+  return Object.assign(defaults, overrides);
+}
+async function getPlotConfig(opts, app) {
+  if (!opts.term) throw "violin getPlotConfig: opts.term{} missing";
+  try {
+    await fillTermWrapper(opts.term, app.vocabApi);
+    if (opts.term2) await fillTermWrapper(opts.term2, app.vocabApi);
+    if (opts.term0) await fillTermWrapper(opts.term0, app.vocabApi);
+  } catch (e) {
+    throw `${e} [violin getPlotConfig()]`;
+  }
+  const config = {
+    id: opts.term.term.id,
+    controlLabels: Object.assign({}, defaultUiLabels, app.vocabApi.termdbConfig.uiLabels || {}),
+    settings: {
+      controls: {
+        term2: null,
+        // the previous overlay value may be displayed as a convenience for toggling
+        term0: null
+      },
+      // common: {
+      // 	use_logscale: false, // flag for y-axis scale type, 0=linear, 1=log
+      // 	use_percentage: false,
+      // 	barheight: 300, // maximum bar length
+      // 	barwidth: 20, // bar thickness
+      // 	barspace: 2 // space between two bars
+      // },
+      violin: getDefaultViolinSettings(app)
+    }
+  };
+  return copyMerge(config, opts);
+}
+
+export {
+  violinInit,
+  componentInit,
+  getDefaultViolinSettings,
+  getPlotConfig
+};
+//# sourceMappingURL=chunk-CVBQWXLH.js.map

package/dist/chunk-CVBQWXLH.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/violin.js"],
+  "sourcesContent": ["import { getCompInit, copyMerge } from '../rx'\nimport { controlsInit, term0_term2_defaultQ, renderTerm1Label } from './controls'\nimport setViolinRenderer from './violin.renderer'\n//import htmlLegend from '../dom/html.legend'\nimport { htmlLegend, Menu } from '#dom'\nimport { fillTermWrapper } from '#termsetting'\nimport { setInteractivity } from './violin.interactivity'\nimport { plotColor } from '#shared/common.js'\nimport { isNumericTerm, isSingleCellTerm } from '#shared/terms.js'\nimport { getCombinedTermFilter } from '#filter'\nimport { PlotBase, defaultUiLabels } from '#plots/PlotBase.js'\n/*\nwhen opts.mode = 'minimal', a minimal violin plot will be rendered that will have a single term and minimal features (i.e. no controls, legend, labels, brushing, transitions, etc.)\n\n*/\n\nclass ViolinPlot extends PlotBase {\n\tstatic type = 'violin'\n\n\tconstructor(opts) {\n\t\tsuper(opts)\n\t\tthis.type = ViolinPlot.type\n\t}\n\n\tasync init(appState) {\n\t\tconst controls = this.opts.holder.append('div').attr('class', 'sjpp-plot-controls').style('display', 'inline-block')\n\t\tconst config = appState.plots.find(p => p.id === this.id)\n\n\t\tconst holder = this.opts.holder\n\t\t\t.append('div')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('padding', this.opts.mode != 'minimal' ? '5px' : '0px')\n\t\t\t.style('padding-left', this.opts.mode != 'minimal' ? '20px' : '0px')\n\t\t\t.attr('id', 'sjpp-vp-holder')\n\n\t\tthis.dom = {\n\t\t\thovertip: new Menu({ padding: '3px' }), // separate tips for hover & click on violin labels to avoid interfering\n\t\t\tclicktip: new Menu({ padding: '0px' }),\n\t\t\tsampletabletip: new Menu({ padding: '3px' }), // sampletable is lauched from option shown in clicktip which closes on clicking, thus need its own menu..\n\t\t\theader: this.opts.header,\n\t\t\tcontrols,\n\t\t\tbanner: holder\n\t\t\t\t.append('div')\n\t\t\t\t.attr('data-testid', 'sjpp-violin-banner')\n\t\t\t\t.style('display', 'none')\n\t\t\t\t.style('text-align', 'center')\n\t\t\t\t.style('padding', '24px')\n\t\t\t\t.style('font-size', '16px'),\n\t\t\tloadingDiv: holder\n\t\t\t\t.append('div')\n\t\t\t\t.attr('data-testid', 'sjpp-violin-loading-div')\n\t\t\t\t.style('display', this.opts.mode != 'minimal' ? 'inline-block' : 'none')\n\t\t\t\t.style('padding', '24px')\n\t\t\t\t.text('Loading ...'),\n\t\t\tviolinDiv: holder\n\t\t\t\t.append('div')\n\t\t\t\t.attr('class', 'sjpp-vp-violinDiv')\n\t\t\t\t.attr('data-testid', 'sjpp-violin-div')\n\t\t\t\t.style('display', 'flex')\n\t\t\t\t.style('flex-direction', 'row')\n\t\t\t\t.style('flex-wrap', 'wrap')\n\t\t\t\t.style('max-width', '100vw'),\n\t\t\tlegendDiv: holder\n\t\t\t\t.append('div')\n\t\t\t\t.classed('sjpp-vp-legend', true)\n\t\t\t\t.attr('data-testid', 'sjpp-violin-legend')\n\t\t\t\t.style('margin-left', '-15px')\n\t\t\t\t.style('padding-top', '20px')\n\t\t}\n\n\t\tsetViolinRenderer(this)\n\t\tsetInteractivity(this)\n\n\t\tif (this.opts.mode != 'minimal') {\n\t\t\tthis.legendRenderer = htmlLegend(this.dom.legendDiv, {\n\t\t\t\tsettings: {\n\t\t\t\t\tlegendOrientation: 'vertical'\n\t\t\t\t},\n\t\t\t\thandlers: {}\n\t\t\t})\n\t\t}\n\t}\n\n\treactsTo(action) {\n\t\tif (action.type.startsWith('plot_')) {\n\t\t\treturn (\n\t\t\t\t(action.id === this.id || action.id == this.parentId) &&\n\t\t\t\t(!action.config?.childType || action.config?.childType == this.type)\n\t\t\t)\n\t\t}\n\t\treturn true\n\t}\n\n\tpreApiFreeze(api) {\n\t\tapi.download = this.download\n\t\tapi.getChartImages = () => this.getChartImages()\n\t}\n\n\tasync setControls() {\n\t\t// do not replace this.components.controls on every re-render,\n\t\t// that could lead to missing control.state if there are errors\n\t\t// with config.terms filling, etc. Better to set getDisplayStyle()\n\t\t// option for an input that doesn't have to be rendered for a given\n\t\t// term/term2/term0 combination.\n\t\tif (this.components.controls) return\n\t\tthis.dom.controls.selectAll('*').remove()\n\t\tconst controlLabels = this.state.config.controlLabels\n\t\tif (!controlLabels) throw 'controls labels not found'\n\t\tthis.components = {}\n\t\tif (this.opts.mode == 'minimal') return\n\n\t\tlet specialCase = 'default'\n\t\tif (isSingleCellTerm(this.config.term.term)) {\n\t\t\t//Do not prevent loading if no sample is specified but log the error.\n\t\t\tif (!this.config.term.term.sample)\n\t\t\t\tconsole.error('single cell term without sample specified in config, unexpected')\n\t\t\telse {\n\t\t\t\tspecialCase = {\n\t\t\t\t\ttype: 'singleCell',\n\t\t\t\t\tconfig: { sample: this.config.term.term.sample }\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\tconst inputs = [\n\t\t\t{\n\t\t\t\ttype: 'term',\n\t\t\t\tconfigKey: 'term',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tusecase: { target: 'violin', detail: 'term' },\n\t\t\t\tlabel: controlLabels.term1?.label || renderTerm1Label,\n\t\t\t\tvocabApi: this.app.vocabApi,\n\t\t\t\tmenuOptions: 'edit'\n\t\t\t},\n\t\t\t{\n\t\t\t\ttype: 'term',\n\t\t\t\tconfigKey: 'term2',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tusecase: { target: 'violin', detail: 'term2', specialCase },\n\t\t\t\ttitle: controlLabels.term2.title || controlLabels.term2.label,\n\t\t\t\tlabel: controlLabels.term2.label,\n\t\t\t\tvocabApi: this.app.vocabApi,\n\t\t\t\tnumericEditMenuVersion: this.opts.numericEditMenuVersion,\n\t\t\t\tdefaultQ4fillTW: term0_term2_defaultQ,\n\t\t\t\tgetDisplayStyle: plot => (plot.config?.term?.term?.type === 'termCollection' ? 'none' : '')\n\t\t\t},\n\t\t\t{\n\t\t\t\ttype: 'term',\n\t\t\t\tconfigKey: 'term0',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tusecase: { target: 'violin', detail: 'term0', specialCase },\n\t\t\t\ttitle: controlLabels.term0.title || controlLabels.term0.label,\n\t\t\t\tlabel: controlLabels.term0.label,\n\t\t\t\tvocabApi: this.app.vocabApi,\n\t\t\t\t// by default, do not allow continuous mode for divide-by term, since\n\t\t\t\t// it will create a separate violin-overlay group per unique float or integer value\n\t\t\t\t// and there will nonsensical tens/hundreds of these charts based on the cohort size\n\t\t\t\tnumericEditMenuVersion: this.opts.numericEditMenuVersion || ['discrete'],\n\t\t\t\tdefaultQ4fillTW: term0_term2_defaultQ,\n\t\t\t\tgetDisplayStyle: plot => (plot.config?.term?.term?.type === 'termCollection' ? 'none' : '')\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Orientation',\n\t\t\t\ttitle: 'Orientation of the chart',\n\t\t\t\ttype: 'radio',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'orientation',\n\t\t\t\toptions: [\n\t\t\t\t\t{ label: 'Vertical', value: 'vertical' },\n\t\t\t\t\t{ label: 'Horizontal', value: 'horizontal' }\n\t\t\t\t]\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Data symbol',\n\t\t\t\ttitle: 'Symbol type',\n\t\t\t\ttype: 'radio',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'datasymbol',\n\t\t\t\toptions: [\n\t\t\t\t\t{ label: 'Ticks', value: 'rug' },\n\t\t\t\t\t{ label: 'Circles', value: 'bean' },\n\t\t\t\t\t{ label: 'Off', value: 'none' }\n\t\t\t\t]\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Scale',\n\t\t\t\ttitle: 'Axis scale',\n\t\t\t\ttype: 'radio',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'isLogScale',\n\t\t\t\toptions: [\n\t\t\t\t\t{ label: 'Linear', value: false },\n\t\t\t\t\t{ label: 'Log10', value: true }\n\t\t\t\t]\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Order by',\n\t\t\t\ttitle: 'Order violin plots by parameters',\n\t\t\t\ttype: 'radio',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'orderByMedian',\n\t\t\t\toptions: [\n\t\t\t\t\t{ label: 'Default', value: false },\n\t\t\t\t\t{ label: 'Median', value: true }\n\t\t\t\t],\n\t\t\t\tgetDisplayStyle: () => {\n\t\t\t\t\tlet style = 'none'\n\t\t\t\t\tconst charts = this.data?.charts || {}\n\t\t\t\t\tfor (const k of Object.keys(charts)) {\n\t\t\t\t\t\tconst chart = charts[k]\n\t\t\t\t\t\tif (chart?.plots.length > 1) style = ''\n\t\t\t\t\t}\n\t\t\t\t\treturn style\n\t\t\t\t}\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Symbol size',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'radius',\n\t\t\t\tstep: 1,\n\t\t\t\tmax: 30,\n\t\t\t\tmin: 4\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Bins',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'ticks',\n\t\t\t\ttitle: 'Number of bins used to build the plot',\n\t\t\t\tmin: 1,\n\t\t\t\tmax: 50\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Plot length',\n\t\t\t\ttitle: 'Length of the plot',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'svgw',\n\t\t\t\tstep: 10,\n\t\t\t\tmax: 1000,\n\t\t\t\tmin: 200,\n\t\t\t\tdebounceInterval: 1000\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Plot thickness',\n\t\t\t\ttitle: 'If not specified, the plot thickness is calculated based on the number of categories',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'plotThickness',\n\t\t\t\tstep: 10,\n\t\t\t\tmax: 200,\n\t\t\t\tmin: 20,\n\t\t\t\tdebounceInterval: 1000\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Plot padding',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'rowSpace',\n\t\t\t\tstep: 1,\n\t\t\t\tmax: 20,\n\t\t\t\tmin: 0,\n\t\t\t\tdebounceInterval: 1000\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Median length',\n\t\t\t\ttitle: 'Length of median',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'medianLength',\n\t\t\t\tstep: 1,\n\t\t\t\tmax: 50,\n\t\t\t\tmin: 3,\n\t\t\t\tdebounceInterval: 1000\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Median color',\n\t\t\t\ttitle: 'color of median',\n\t\t\t\ttype: 'color',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'medianColor'\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Median thickness',\n\t\t\t\ttitle: 'Width of median',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'medianThickness',\n\t\t\t\tstep: 1,\n\t\t\t\tmax: 10,\n\t\t\t\tmin: 3,\n\t\t\t\tdebounceInterval: 100\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Default violin color',\n\t\t\t\ttype: 'color',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'defaultColor'\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Show stats',\n\t\t\t\ttype: 'checkbox',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'showStats',\n\t\t\t\tboxLabel: 'Yes'\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Show association tests',\n\t\t\t\ttype: 'checkbox',\n\t\t\t\tchartType: 'violin',\n\t\t\t\tsettingsKey: 'showAssociationTests',\n\t\t\t\tboxLabel: 'Yes',\n\t\t\t\tgetDisplayStyle: plot => (plot.term2 ? 'table-row' : 'none')\n\t\t\t}\n\t\t]\n\n\t\tthis.components.controls = await controlsInit({\n\t\t\tapp: this.app,\n\t\t\tid: this.id,\n\t\t\tholder: this.dom.controls,\n\t\t\tinputs\n\t\t})\n\n\t\tthis.components.controls.on('downloadClick.violin', this.download)\n\t}\n\n\tgetState(appState) {\n\t\tconst config = appState.plots.find(p => p.id === this.id)\n\t\tif (!config) {\n\t\t\tthrow `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`\n\t\t}\n\t\tconst parentConfig = appState.plots.find(p => p.id === this.parentId)\n\n\t\tconst termfilter = getCombinedTermFilter(appState, config.filter || parentConfig?.filter)\n\t\treturn {\n\t\t\ttermfilter,\n\t\t\tconfig,\n\t\t\tdisplaySampleIds: appState.termdbConfig.displaySampleIds,\n\t\t\thasVerifiedToken: this.app.vocabApi.hasVerifiedToken()\n\t\t}\n\t}\n\n\tasync main() {\n\t\tthis.config = structuredClone(this.state.config)\n\t\tthis.settings = this.config.settings.violin\n\t\tawait this.setControls()\n\n\t\tif (this.config.chartType != this.type && this.config.childType != this.type) return\n\t\tif (this.dom.header)\n\t\t\tthis.dom.header.html(\n\t\t\t\tthis.config.term.term.name + ` <span style=\"opacity:.6;font-size:1em;margin-left:10px;\">Violin Plot</span>`\n\t\t\t)\n\n\t\t//Fix for rm'ing error message when plot re-renders\n\t\t//Leave in main() so the message doesn't linger whilst\n\t\t//the plot is rendering\n\t\tconst existingMsg = this.dom.banner.style('display', 'none').select('span')\n\t\tif (!existingMsg.empty()) existingMsg.remove()\n\n\t\tconst args = this.validateArgs()\n\t\tlet data\n\t\ttry {\n\t\t\tthis.toggleLoadingDiv()\n\t\t\tdata = await this.app.vocabApi.getViolinBox(args, null, this.api.getAbortSignal())\n\t\t} catch (e) {\n\t\t\tthis.toggleLoadingDiv('none')\n\t\t\tif (this.app.isAbortError(e)) return\n\t\t\tthrow e\n\t\t}\n\n\t\tthis.data = data\n\t\tif (this.data.error) {\n\t\t\tthis.toggleLoadingDiv('none')\n\t\t\tthrow this.data.error\n\t\t}\n\t\targs.tw.q.descrStats = this.data.descrStats\n\n\t\tthis.toggleLoadingDiv(this.opts.mode == 'minimal' ? 'none' : '')\n\t\tsetTimeout(\n\t\t\t() => {\n\t\t\t\tthis.render()\n\t\t\t},\n\t\t\tthis.opts.mode == 'minimal' ? 0 : 500\n\t\t)\n\t\tthis.toggleLoadingDiv('none')\n\t}\n\n\tvalidateArgs() {\n\t\tconst { term, term2, term0, settings } = this.config\n\t\tconst s = this.settings\n\t\tconst arg = {\n\t\t\tplotType: 'violin',\n\t\t\tsvgw: s.svgw,\n\t\t\torientation: s.orientation,\n\t\t\tdevicePixelRatio: window.devicePixelRatio,\n\t\t\tdatasymbol: s.datasymbol,\n\t\t\tradius: s.radius,\n\t\t\taxisHeight: s.axisHeight,\n\t\t\trightMargin: s.rightMargin,\n\t\t\tisLogScale: s.isLogScale,\n\t\t\tticks: s.ticks,\n\t\t\torderByMedian: s.orderByMedian,\n\t\t\tfilter: this.state.termfilter.filter\n\t\t}\n\n\t\tif (this.opts.mode == 'minimal') {\n\t\t\targ.tw = term\n\t\t\t// assume a single term for minimal plot\n\t\t\tif (term2 || term0) throw 'only a single term allowed for minimal plot'\n\t\t\tif (term.q.mode == 'spline') {\n\t\t\t\t/** FIXME bad design; should not modify setting or even plot state in runtime, \n\t\t\t\tinstead supply this in constructor arg and generalize it beyond spline\n\t\t\t\t// term may be cubic spline from regression analysis\n\t\t\t\t// render knot values as vertical lines on the plot\n\t\t\t\t*/\n\t\t\t\ts.lines = term.q.knots.map(x => Number(x.value))\n\t\t\t} else {\n\t\t\t\ts.lines = []\n\t\t\t}\n\t\t\tif (term.q.scale) {\n\t\t\t\t// term may be scaled from regression analysis\n\t\t\t\t// scale the data on the server-side\n\t\t\t\targ.scale = term.q.scale\n\t\t\t}\n\t\t} else if (term.term?.type === 'termCollection' && term.term?.memberType === 'numeric') {\n\t\t\t// numeric termCollection: server-side expandNumericTermCollection creates a\n\t\t\t// synthetic overlay from member terms, so don't send term2/term0\n\t\t\targ.tw = term\n\t\t} else if (isNumericTerm(term.term) && term.q.mode === 'continuous') {\n\t\t\targ.tw = term\n\t\t\tif (term2) arg.overlayTw = term2\n\t\t} else if (isNumericTerm(term2?.term) && term2.q.mode === 'continuous') {\n\t\t\targ.tw = term2\n\t\t\targ.overlayTw = term\n\t\t} else {\n\t\t\tthrow 'both term1 and term2 are not numeric/continuous'\n\t\t}\n\n\t\tif (term0) arg.divideTw = term0\n\t\treturn arg\n\t}\n}\n\nexport const violinInit = getCompInit(ViolinPlot)\nexport const componentInit = violinInit\n\nexport function getDefaultViolinSettings(app, overrides = {}) {\n\tconst defaults = {\n\t\torientation: 'horizontal',\n\t\trowlabelw: 250,\n\t\tbrushRange: null, //object with start and end if there is a brush selection\n\t\tsvgw: 500, // span length of a plot/svg, not including margin\n\t\tdatasymbol: 'rug',\n\t\tradius: 10,\n\t\taxisHeight: 60,\n\t\trightMargin: 50,\n\t\tlines: [],\n\t\tisLogScale: false, // false: linear scale, true: log scale\n\t\trowSpace: 10,\n\t\tmedianLength: 7,\n\t\tmedianColor: '#FF0000',\n\t\tmedianThickness: 3,\n\t\tticks: 15,\n\t\tdefaultColor: plotColor,\n\t\tmethod: 0,\n\t\torderByMedian: false,\n\t\tshowStats: true,\n\t\tshowAssociationTests: true\n\t}\n\treturn Object.assign(defaults, overrides)\n}\n\nexport async function getPlotConfig(opts, app) {\n\tif (!opts.term) throw 'violin getPlotConfig: opts.term{} missing'\n\ttry {\n\t\tawait fillTermWrapper(opts.term, app.vocabApi)\n\t\tif (opts.term2) await fillTermWrapper(opts.term2, app.vocabApi)\n\t\tif (opts.term0) await fillTermWrapper(opts.term0, app.vocabApi)\n\t} catch (e) {\n\t\tthrow `${e} [violin getPlotConfig()]`\n\t}\n\n\tconst config = {\n\t\tid: opts.term.term.id,\n\t\tcontrolLabels: Object.assign({}, defaultUiLabels, app.vocabApi.termdbConfig.uiLabels || {}),\n\t\tsettings: {\n\t\t\tcontrols: {\n\t\t\t\tterm2: null, // the previous overlay value may be displayed as a convenience for toggling\n\t\t\t\tterm0: null\n\t\t\t},\n\t\t\t// common: {\n\t\t\t// \tuse_logscale: false, // flag for y-axis scale type, 0=linear, 1=log\n\t\t\t// \tuse_percentage: false,\n\t\t\t// \tbarheight: 300, // maximum bar length\n\t\t\t// \tbarwidth: 20, // bar thickness\n\t\t\t// \tbarspace: 2 // space between two bars\n\t\t\t// },\n\t\t\tviolin: getDefaultViolinSettings(app)\n\t\t}\n\t}\n\n\t// may apply term-specific changes to the default object\n\treturn copyMerge(config, opts)\n}\n"],
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