@sjcrh/proteinpaint-client 2.191.0 → 2.191.2

package/dist/chunk-QOE7MB4X.js

@@ -1,454 +0,0 @@
-import {
-  setViolinRenderer
-} from "./chunk-RRJGFE2S.js";
-import {
-  setInteractivity
-} from "./chunk-T2CG7BVN.js";
-import {
-  PlotBase,
-  controlsInit,
-  defaultUiLabels,
-  fillTermWrapper,
-  getCombinedTermFilter,
-  htmlLegend,
-  renderTerm1Label,
-  term0_term2_defaultQ
-} from "./chunk-6FF5VLGO.js";
-import {
-  Menu
-} from "./chunk-HYOEWQ5P.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-5V43Y2RC.js";
-import {
-  isNumericTerm,
-  isSingleCellTerm
-} from "./chunk-TVADJLMF.js";
-import {
-  plotColor
-} from "./chunk-EBKERML3.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 = {
-    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-QOE7MB4X.js.map

package/dist/chunk-QOE7MB4X.js.map

@@ -1,7 +0,0 @@
-{
-  "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\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"],
-  "mappings": 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package/dist/chunk-QSMU6K5D.js

@@ -1,34 +0,0 @@
-import {
-  appInit
-} from "./chunk-6FF5VLGO.js";
-import {
-  TermTypes
-} from "./chunk-TVADJLMF.js";
-
-// termdb/handlers/ssGSEA.ts
-var SearchHandler = class {
-  async init(opts) {
-    this.callback = opts.callback;
-    this.app = opts.app;
-    const genesetDbName = Object.keys(opts.genomeObj.termdbs || {})[0];
-    if (!genesetDbName) throw "genesetDbName missing";
-    await appInit({
-      holder: opts.holder,
-      state: {
-        dslabel: genesetDbName,
-        genome: opts.genomeObj.name,
-        nav: { header_mode: "search_only" }
-      },
-      tree: {
-        click_term: (term) => {
-          this.callback({ id: term.id, type: TermTypes.SSGSEA, name: term.name });
-        }
-      }
-    });
-  }
-};
-
-export {
-  SearchHandler
-};
-//# sourceMappingURL=chunk-QSMU6K5D.js.map

package/dist/chunk-RBIBHQTL.js

@@ -1,54 +0,0 @@
-import {
-  addGeneSearchbox
-} from "./chunk-6FF5VLGO.js";
-import {
-  Menu
-} from "./chunk-HYOEWQ5P.js";
-
-// termdb/handlers/snp.ts
-var SearchHandler = class {
-  init(opts) {
-    this.callback = opts.callback;
-    const geneSearch = addGeneSearchbox({
-      tip: new Menu({ padding: "0px" }),
-      genome: opts.genomeObj,
-      row: opts.holder,
-      searchOnly: "snp",
-      allowVariant: true,
-      callback: () => this.selectSnp(geneSearch)
-    });
-  }
-  async selectSnp(geneSearch) {
-    const { chr, ref, alt, fromWhat } = geneSearch;
-    if (!chr || !ref || !alt || !fromWhat) throw "missing chr, ref, alt, or fromWhat of snp";
-    let start, stop;
-    if (!geneSearch.start && !geneSearch.stop) {
-      if (geneSearch.pos) {
-        start = geneSearch.pos - 1;
-        stop = geneSearch.pos;
-      } else {
-        throw "missing coordinate of snp";
-      }
-    } else {
-      start = geneSearch.start;
-      stop = geneSearch.stop;
-    }
-    const term = {
-      id: fromWhat,
-      chr,
-      start,
-      stop,
-      name: fromWhat,
-      ref,
-      alt: typeof alt == "string" ? [alt] : alt,
-      // is string if input to geneSearch was in variant or hgvs format // TODO: update genesearch.ts to parse alternative alleles from any input format into arrays
-      type: "snp"
-    };
-    this.callback(term);
-  }
-};
-
-export {
-  SearchHandler
-};
-//# sourceMappingURL=chunk-RBIBHQTL.js.map