@sjcrh/proteinpaint-client 2.191.4 → 2.192.0

package/dist/chunk-BDIKFVWZ.js

@@ -1,443 +0,0 @@
-import {
-  getDefaultViolinSettings
-} from "./chunk-FFEIP5CT.js";
-import {
-  getDefaultScatterSettings
-} from "./chunk-OEDZHPBJ.js";
-import {
-  getDefaultBoxplotSettings
-} from "./chunk-PCZNTK74.js";
-import {
-  PlotBase,
-  defaultUiLabels,
-  fillTermWrapper,
-  filterRxCompInit,
-  getDefaultBarSettings,
-  term0_term2_defaultQ
-} from "./chunk-SA7APTJR.js";
-import {
-  importPlot
-} from "./chunk-SKREEF3H.js";
-import {
-  Menu
-} from "./chunk-HYOEWQ5P.js";
-import {
-  Tabs
-} from "./chunk-HBW42TDT.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-M3J4MINX.js";
-import {
-  isNumericTerm
-} from "./chunk-NOEAT6CX.js";
-
-// plots/summary.ts
-var SummaryPlot = class _SummaryPlot extends PlotBase {
-  constructor(opts, api) {
-    super(opts, api);
-    this.components = {};
-    // expected class-specific props
-    this.chartsByType = {};
-    this.configTermKeys = ["term", "term0", "term2"];
-    this.type = _SummaryPlot.type;
-    this.dom = this.getDom(opts);
-    this.tabsData = this.getTabsData();
-    this.chartToggles = new Tabs({ holder: this.dom.chartToggles, tabs: this.tabsData, noContent: true });
-    this.components = {
-      plots: {}
-    };
-  }
-  static {
-    this.type = "summary";
-  }
-  preApiFreeze(api) {
-    api.getError = () => {
-      return this.error;
-    };
-  }
-  getDom(opts) {
-    const holder = opts.holder;
-    holder.header.style("padding", 0);
-    const paneTitleDiv = holder.header.append("div").style("display", "inline-block").style("color", "#555").style("padding-left", "7px");
-    return {
-      tip: new Menu({ padding: "0px" }),
-      holder,
-      body: holder.body.style("white-space", "nowrap").style("overflow-x", "auto"),
-      // will hold no data notice or the page title in multichart views
-      errdiv: holder.body.append("div").attr("class", "sja_errorbar").style("display", "none").style("padding", "5px"),
-      loading: holder.body.append("div").style("display", "none").style("padding", "5px").html("Loading ..."),
-      // dom.viz will hold the rendered view
-      viz: holder.body.append("div"),
-      plotDivs: {},
-      paneTitleDiv,
-      paneTitleText: paneTitleDiv.append("div").classed("sjpp-term-header", true).style("display", "inline-block").style("vertical-align", "sub"),
-      chartToggles: paneTitleDiv.append("div").style("display", "inline-block").style("margin-left", "10px"),
-      localRecoverDiv: paneTitleDiv.append("div").style("display", "inline-block"),
-      filterDiv: holder.header.append("div").style("display", "inline-block").style("zoom", 0.9)
-    };
-  }
-  getTabsData() {
-    const callback = (event, tab) => this.tabClickCallback(event, tab);
-    return [
-      {
-        childType: "barchart",
-        label: "Barchart",
-        isVisible: () => true,
-        disabled: () => false,
-        getConfig: async () => {
-          if (!this.config) return;
-          const config = { id: this.id, childType: "barchart" };
-          const { term, term2 } = this.config || {};
-          if (term) {
-            const mode = isNumericTerm(term?.term) ? "discrete" : term?.q.mode || "discrete";
-            config.term = await this.getWrappedTermCopy(term, mode);
-          }
-          if (term2) {
-            const mode = isNumericTerm(term2.term) ? "discrete" : term2.q.mode || "discrete";
-            config.term2 = await this.getWrappedTermCopy(term2, mode);
-          }
-          return config;
-        },
-        active: true,
-        callback
-      },
-      {
-        childType: "violin",
-        label: "Violin",
-        disabled: () => false,
-        isVisible: () => isNumericTerm(this.config?.term?.term) || isNumericTerm(this.config?.term2?.term),
-        getConfig: async () => {
-          const term = this.config?.term;
-          const term2 = this.config.term2;
-          let _term, _term2;
-          this.violinContTerm = isNumericTerm(term?.term) ? "term" : "term2";
-          if (this.violinContTerm && this.violinContTerm === "term" || term.q?.mode == "continuous") {
-            _term = await this.getWrappedTermCopy(term, "continuous");
-            _term2 = await this.getWrappedTermCopy(term2, "discrete");
-            this.violinContTerm = "term";
-          } else if (this.violinContTerm && this.violinContTerm === "term2" || term2?.q?.mode == "continuous") {
-            _term = await this.getWrappedTermCopy(term, "discrete");
-            _term2 = await this.getWrappedTermCopy(term2, "continuous");
-            this.violinContTerm = "term2";
-          } else if (term2?.q?.mode == "discrete") {
-            _term = await this.getWrappedTermCopy(term, "discrete");
-            _term2 = await this.getWrappedTermCopy(term2, "continuous");
-            this.violinContTerm = "term2";
-          } else {
-            _term = await this.getWrappedTermCopy(term, "continuous");
-            _term2 = await this.getWrappedTermCopy(term2, "discrete");
-            this.violinContTerm = "term";
-          }
-          const config = { childType: "violin", term: _term, term2: _term2 };
-          return config;
-        },
-        active: false,
-        callback
-      },
-      {
-        childType: "boxplot",
-        label: "Boxplot",
-        disabled: () => false,
-        isVisible: () => isNumericTerm(this.config?.term?.term) || isNumericTerm(this.config?.term2?.term),
-        getConfig: async () => {
-          const _term = this.config?.term;
-          const _term2 = this.config.term2;
-          let termMode = "continuous", term2Mode = "discrete";
-          this.boxContTerm = isNumericTerm(_term?.term) ? "term" : "term2";
-          if (this.boxContTerm && this.boxContTerm === "term" || _term.q?.mode == "continuous") {
-            termMode = "continuous";
-            term2Mode = "discrete";
-            this.boxContTerm = "term";
-          } else if (this.boxContTerm && this.boxContTerm === "term2" || _term2?.q?.mode == "continuous") {
-            termMode = "discrete";
-            term2Mode = "continuous";
-            this.boxContTerm = "term2";
-          } else if (_term2?.q?.mode == "discrete") {
-            termMode = "discrete";
-            term2Mode = "continuous";
-            this.boxContTerm = "term2";
-          }
-          const term = await this.getWrappedTermCopy(_term, termMode);
-          const term2 = await this.getWrappedTermCopy(_term2, term2Mode);
-          const config = {
-            childType: "boxplot",
-            term,
-            term2
-          };
-          return config;
-        },
-        active: false,
-        callback
-      },
-      {
-        childType: "sampleScatter",
-        label: "Scatter",
-        disabled: () => false,
-        isVisible: () => {
-          return isNumericTerm(this.config?.term.term) && isNumericTerm(this.config?.term2?.term);
-        },
-        getConfig: async () => {
-          const _term = await this.getWrappedTermCopy(this.config?.term, "continuous");
-          const _term2 = await this.getWrappedTermCopy(this.config?.term2, "continuous");
-          const config = {
-            childType: "sampleScatter",
-            term: _term,
-            term2: _term2,
-            groups: [],
-            term0: this.config.term0
-          };
-          return config;
-        },
-        active: false,
-        callback
-      }
-    ];
-  }
-  async init(appState) {
-    const state = this.getState(appState);
-    const config = structuredClone(state.config);
-    this.initUi(this.opts, config);
-    this.components.filter = await filterRxCompInit({
-      app: this.app,
-      vocabApi: this.app.vocabApi,
-      parentId: this.id,
-      holder: this.dom.filterDiv,
-      hideLabel: true,
-      emptyLabel: "+Add new filter",
-      callback: (filter) => {
-        this.app.dispatch({
-          id: this.id,
-          type: "plot_edit",
-          config: { filter }
-        });
-      }
-    });
-  }
-  reactsTo(action) {
-    if (action.type.includes("cache_termq")) return true;
-    if (action.type.startsWith("plot_")) {
-      if (action.type.startsWith("plot_")) {
-        return action.id === this.id || action.id == this.parentId;
-      }
-    }
-    if (action.type.startsWith("filter")) return true;
-    if (action.type.startsWith("cohort")) return true;
-    if (action.type == "app_refresh") return true;
-    return false;
-  }
-  getState(appState) {
-    const config = appState.plots.find((p) => p.id === this.id);
-    if (!config) {
-      throw `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`;
-    }
-    return {
-      termfilter: appState.termfilter,
-      config,
-      // quick fix to skip history tracking as needed
-      _scope_: appState._scope_
-    };
-  }
-  async main() {
-    delete this.error;
-    this.dom.errdiv.style("display", "none").html("");
-    this.dom.loading.style("display", "");
-    this.config = await this.getMutableConfig();
-    this.maySetSandboxHeader();
-    if (!this.components.plots[this.config.childType]) {
-      await this.setComponent(this.config);
-    }
-    this.dom.loading.style("display", "none");
-    this.render();
-    const activeTabIndex = this.tabsData.findIndex((tab) => tab.childType == this.config.childType);
-    this.chartToggles.update(activeTabIndex);
-    const numVisTabs = this.tabsData.filter((d) => d.isVisible()).length;
-    if (numVisTabs > 1) this.dom.chartToggles.style("display", "inline-block");
-    else this.dom.chartToggles.style("display", "none");
-  }
-  maySetSandboxHeader() {
-    const { term, term2, headerText, assayCohortTitle } = this.config;
-    const mainTerm = term.getTitleText?.() || term.term.name;
-    const _headerPretext = headerText ? `${headerText} ` : "";
-    const _headerSuffix = assayCohortTitle ? ` (${assayCohortTitle})` : "";
-    const titleBase = mainTerm + _headerSuffix;
-    if (term2?.type) {
-      this.dom.paneTitleText.html(`${_headerPretext}${term2.getTitleText?.() || term2.term.name} vs ${titleBase}`);
-    } else {
-      this.dom.paneTitleText.html(`${_headerPretext}${titleBase}`);
-    }
-  }
-  async setComponent(config) {
-    const _ = await importPlot(config.childType, `unsupported childType='${config.childType}'`);
-    this.dom.plotDivs[config.childType] = this.dom.viz.append("div");
-    this.components.plots[config.childType] = await _.componentInit({
-      app: this.app,
-      holder: this.dom.plotDivs[config.childType],
-      id: this.id,
-      parent: this.api
-    });
-  }
-  destroy() {
-    this.dom.holder.app_div.selectAll("*").remove();
-    this.dom.holder.app_div.remove();
-    for (const key in this.dom) {
-      delete this.dom[key];
-    }
-  }
-  initUi(opts, config) {
-    this.dom.paneTitleText.html(config.term.term.name);
-    this.chartToggles.main();
-  }
-  async tabClickCallback(event, tab) {
-    if (!tab || !tab.getConfig) return;
-    let config;
-    try {
-      this.dom.viz.style("display", "none");
-      this.dom.loading.style("display", "");
-      config = await tab.getConfig();
-      this.dom.loading.style("display", "none");
-      this.dom.viz.style("display", "");
-      if (config)
-        this.app.dispatch({
-          type: "plot_edit",
-          id: this.id,
-          config
-        });
-    } catch (e) {
-      this.dom.loading.style("display", "none");
-      this.error = e;
-      this.dom.errdiv.style("display", "").html(`Error: ${e.message || e.error || e}`);
-    }
-  }
-  async getWrappedTermCopy(term, mode) {
-    if (!term) return;
-    const tw = structuredClone(term);
-    tw.q.mode = mode;
-    await fillTermWrapper(tw, this.app.vocabApi);
-    return tw;
-  }
-  render() {
-    for (const childType of Object.keys(this.components.plots)) {
-      const chart = this.components.plots[childType];
-      if (chart.type != this.config.childType) {
-        this.dom.plotDivs[chart.type].style("display", "none");
-      }
-    }
-    this.dom.plotDivs[this.config.childType].style("display", "");
-  }
-  getChartImages() {
-    const chart = this.components.plots[this.config.childType];
-    if (chart?.getChartImages) {
-      return chart.getChartImages();
-    }
-    return null;
-  }
-};
-var summaryInit = getCompInit(SummaryPlot);
-var componentInit = summaryInit;
-async function getPlotConfig(opts, app) {
-  if (!opts.term) throw "summary getPlotConfig: opts.term{} missing";
-  try {
-    opts.term = await fillTermWrapper(
-      opts.term,
-      app.vocabApi,
-      opts.term.q || { geneVariant: { type: "predefined-groupset" } }
-    );
-    if (opts.term2)
-      opts.term2 = await fillTermWrapper(
-        opts.term2,
-        app.vocabApi,
-        opts.term2.bins || opts.term2.q ? void 0 : term0_term2_defaultQ
-      );
-    if (opts.term0)
-      opts.term0 = await fillTermWrapper(
-        opts.term0,
-        app.vocabApi,
-        opts.term0.bins || opts.term0.q ? void 0 : term0_term2_defaultQ
-      );
-    if (opts.colorTW) opts.colorTW = await fillTermWrapper(opts.colorTW, app.vocabApi);
-    if (opts.shapeTW) opts.shapeTW = await fillTermWrapper(opts.shapeTW, app.vocabApi);
-    if (opts.scaleDotTW) opts.scaleDotTW = await fillTermWrapper(opts.scaleDotTW, app.vocabApi);
-  } catch (e) {
-    if (e.stack) console.log(e.stack);
-    throw `${e} [summary getPlotConfig()]`;
-  }
-  const config = {
-    chartType: "summary",
-    childType: "barchart",
-    term: opts.term,
-    groups: [],
-    controlLabels: Object.assign({}, defaultUiLabels, app.vocabApi.termdbConfig.uiLabels || {}),
-    settings: {
-      controls: {
-        isOpen: false
-      },
-      common: {
-        use_logscale: false,
-        // flag for y-axis scale type, 0=linear, 1=log
-        use_percentage: false
-        // Move to barchart settings
-        // barheight: 300, // maximum bar length
-        // barwidth: 20, // bar thickness
-        // barspace: 2 // space between two bars
-      },
-      barchart: getDefaultBarSettings(app),
-      violin: getDefaultViolinSettings(app),
-      boxplot: getDefaultBoxplotSettings(app),
-      sampleScatter: getDefaultScatterSettings(opts)
-    },
-    mayAdjustConfig(config2, edits = {}) {
-      return mayAdjustConfig(config2, opts, edits);
-    }
-  };
-  if (config.term.term.type == "geneVariant") config.settings.barchart.colorBars = true;
-  copyMerge(config, opts);
-  Object.assign(config.controlLabels, app.vocabApi.termdbConfig.uiLabels || {});
-  return config;
-}
-var discreteByContinuousPlots = /* @__PURE__ */ new Set(["violin", "boxplot"]);
-function mayAdjustConfig(config, opts, edits = {}) {
-  if (edits.childType) {
-    if (config.childType != edits.childType) throw `action.config.childType was not applied in mass store.plot_edit()`;
-    return;
-  }
-  if (config.term?.q?.mode == "continuous" && config.term2?.q?.mode == "continuous") {
-    config.childType = "sampleScatter";
-  } else if (config.term?.term?.type == "termCollection") {
-    if (config.term.term.memberType == "categorical") {
-      config.childType = "barchart";
-    } else if (config.term.term.memberType == "numeric") {
-      if (config.childType) {
-        if (config.childType == "barchart") {
-          config.childType = "violin";
-        } else {
-        }
-      } else {
-        config.childType = "violin";
-      }
-    } else {
-      throw new Error("config.term.term.memberType not categorical or numeric");
-    }
-  } else if (config.term?.q?.mode == "continuous" || config.term2?.q?.mode == "continuous") {
-    if (!discreteByContinuousPlots.has(config.childType)) {
-      if (opts.childType && !discreteByContinuousPlots.has(opts.childType)) {
-        console.warn(
-          `ignoring summary opts.childType='${opts.childType}' since it does not support plotting discrete by continuous tw's`
-        );
-        config.childType = "violin";
-      } else {
-        config.childType = opts.childType || "violin";
-      }
-    }
-  } else {
-    config.childType = "barchart";
-  }
-}
-
-export {
-  summaryInit,
-  componentInit,
-  getPlotConfig,
-  mayAdjustConfig
-};
-//# sourceMappingURL=chunk-BDIKFVWZ.js.map

package/dist/chunk-BDIKFVWZ.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../plots/summary.ts"],
-  "sourcesContent": ["import { getCompInit, copyMerge, type ComponentApi, type RxComponent } from '#rx'\nimport { PlotBase, defaultUiLabels } from './PlotBase.ts'\nimport { Menu, Tabs } from '#dom'\nimport { fillTermWrapper } from '#termsetting'\n// import { recoverInit } from '../rx/src/recover'\nimport { getDefaultViolinSettings } from './violin.js'\nimport { getDefaultBarSettings } from './barchart.js'\nimport { getDefaultBoxplotSettings } from './boxplot/defaults'\nimport { getDefaultScatterSettings } from './scatter/settings/defaults'\nimport { isNumericTerm } from '#shared/terms.js'\nimport { term0_term2_defaultQ } from './controls'\nimport { importPlot } from './importPlot.js'\nimport { filterRxCompInit } from '#filter'\n\nclass SummaryPlot extends PlotBase implements RxComponent {\n\tstatic type = 'summary'\n\n\t// expected RxComponent props, some are already declared/set in PlotBase\n\ttype: string\n\tparentId?: string\n\tdom!: {\n\t\t[index: string]: any\n\t}\n\tcomponents: {\n\t\t[name: string]: ComponentApi | { [name: string]: ComponentApi }\n\t} = {}\n\n\terror: any\n\n\t// expected class-specific props\n\tchartsByType: { [chartType: string]: ComponentApi } = {}\n\tconfigTermKeys = ['term', 'term0', 'term2']\n\tconfig: any\n\ttabsData: any[]\n\tchartToggles: Tabs\n\n\tviolinContTerm?: 'term' | 'term2'\n\tboxContTerm?: 'term' | 'term2'\n\n\tconstructor(opts, api) {\n\t\tsuper(opts, api)\n\t\tthis.type = SummaryPlot.type\n\t\tthis.dom = this.getDom(opts)\n\t\tthis.tabsData = this.getTabsData()\n\t\tthis.chartToggles = new Tabs({ holder: this.dom.chartToggles, tabs: this.tabsData, noContent: true })\n\t\tthis.components = {\n\t\t\tplots: {}\n\t\t}\n\t}\n\n\tpreApiFreeze(api) {\n\t\tapi.getError = () => {\n\t\t\treturn this.error\n\t\t}\n\t}\n\n\tgetDom(opts) {\n\t\tconst holder = opts.holder\n\t\tholder.header.style('padding', 0)\n\n\t\tconst paneTitleDiv = holder.header\n\t\t\t.append('div')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('color', '#555') // changed from #999 to address Section 508 contrast issue\n\t\t\t.style('padding-left', '7px')\n\n\t\treturn {\n\t\t\ttip: new Menu({ padding: '0px' }),\n\t\t\tholder,\n\t\t\tbody: holder.body\n\t\t\t\t// .style('margin-top', '-1px')\n\t\t\t\t.style('white-space', 'nowrap')\n\t\t\t\t.style('overflow-x', 'auto'),\n\n\t\t\t// will hold no data notice or the page title in multichart views\n\t\t\terrdiv: holder.body.append('div').attr('class', 'sja_errorbar').style('display', 'none').style('padding', '5px'),\n\n\t\t\tloading: holder.body.append('div').style('display', 'none').style('padding', '5px').html('Loading ...'),\n\n\t\t\t// dom.viz will hold the rendered view\n\t\t\tviz: holder.body.append('div'),\n\t\t\tplotDivs: {},\n\t\t\tpaneTitleDiv,\n\t\t\tpaneTitleText: paneTitleDiv\n\t\t\t\t.append('div')\n\t\t\t\t.classed('sjpp-term-header', true)\n\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t.style('vertical-align', 'sub'),\n\t\t\tchartToggles: paneTitleDiv.append('div').style('display', 'inline-block').style('margin-left', '10px'),\n\t\t\tlocalRecoverDiv: paneTitleDiv.append('div').style('display', 'inline-block'),\n\t\t\tfilterDiv: holder.header.append('div').style('display', 'inline-block').style('zoom', 0.9)\n\t\t}\n\t}\n\n\tgetTabsData() {\n\t\tconst callback = (event, tab) => this.tabClickCallback(event, tab)\n\t\treturn [\n\t\t\t{\n\t\t\t\tchildType: 'barchart',\n\t\t\t\tlabel: 'Barchart',\n\t\t\t\tisVisible: () => true,\n\t\t\t\tdisabled: () => false,\n\t\t\t\tgetConfig: async () => {\n\t\t\t\t\tif (!this.config) return\n\t\t\t\t\tconst config: any = { id: this.id, childType: 'barchart' }\n\t\t\t\t\tconst { term, term2 } = this.config || {}\n\t\t\t\t\tif (term) {\n\t\t\t\t\t\tconst mode = isNumericTerm(term?.term) ? 'discrete' : term?.q.mode || 'discrete'\n\t\t\t\t\t\tconfig.term = await this.getWrappedTermCopy(term, mode)\n\t\t\t\t\t}\n\t\t\t\t\tif (term2) {\n\t\t\t\t\t\tconst mode = isNumericTerm(term2.term) ? 'discrete' : term2.q.mode || 'discrete'\n\t\t\t\t\t\tconfig.term2 = await this.getWrappedTermCopy(term2, mode)\n\t\t\t\t\t}\n\t\t\t\t\treturn config\n\t\t\t\t},\n\t\t\t\tactive: true,\n\t\t\t\tcallback\n\t\t\t},\n\t\t\t{\n\t\t\t\tchildType: 'violin',\n\t\t\t\tlabel: 'Violin',\n\t\t\t\tdisabled: () => false,\n\t\t\t\tisVisible: () => isNumericTerm(this.config?.term?.term) || isNumericTerm(this.config?.term2?.term),\n\t\t\t\tgetConfig: async () => {\n\t\t\t\t\tconst term = this.config?.term\n\t\t\t\t\tconst term2 = this.config.term2\n\n\t\t\t\t\tlet _term, _term2\n\t\t\t\t\tthis.violinContTerm = isNumericTerm(term?.term) ? 'term' : 'term2'\n\n\t\t\t\t\t//If the first term was continuous or is coming as continuous\n\t\t\t\t\tif ((this.violinContTerm && this.violinContTerm === 'term') || term.q?.mode == 'continuous') {\n\t\t\t\t\t\t// must mean coming from scatter plot\n\t\t\t\t\t\t_term = await this.getWrappedTermCopy(term, 'continuous')\n\t\t\t\t\t\t_term2 = await this.getWrappedTermCopy(term2, 'discrete')\n\t\t\t\t\t\tthis.violinContTerm = 'term'\n\t\t\t\t\t}\n\t\t\t\t\t//If the second term was continuous or is coming as continuous\n\t\t\t\t\telse if ((this.violinContTerm && this.violinContTerm === 'term2') || term2?.q?.mode == 'continuous') {\n\t\t\t\t\t\t// must mean coming from barchart\n\t\t\t\t\t\t_term = await this.getWrappedTermCopy(term, 'discrete')\n\t\t\t\t\t\t_term2 = await this.getWrappedTermCopy(term2, 'continuous')\n\t\t\t\t\t\tthis.violinContTerm = 'term2'\n\t\t\t\t\t}\n\t\t\t\t\t//If the second term is coming as discrete from the scatter\n\t\t\t\t\telse if (term2?.q?.mode == 'discrete') {\n\t\t\t\t\t\t// must mean coming from barchart\n\t\t\t\t\t\t_term = await this.getWrappedTermCopy(term, 'discrete')\n\t\t\t\t\t\t_term2 = await this.getWrappedTermCopy(term2, 'continuous')\n\t\t\t\t\t\tthis.violinContTerm = 'term2'\n\t\t\t\t\t}\n\t\t\t\t\t//by default\n\t\t\t\t\telse {\n\t\t\t\t\t\t_term = await this.getWrappedTermCopy(term, 'continuous')\n\t\t\t\t\t\t_term2 = await this.getWrappedTermCopy(term2, 'discrete')\n\t\t\t\t\t\tthis.violinContTerm = 'term'\n\t\t\t\t\t}\n\t\t\t\t\tconst config = { childType: 'violin', term: _term, term2: _term2 }\n\t\t\t\t\treturn config\n\t\t\t\t},\n\t\t\t\tactive: false,\n\t\t\t\tcallback\n\t\t\t},\n\t\t\t{\n\t\t\t\tchildType: 'boxplot',\n\t\t\t\tlabel: 'Boxplot',\n\t\t\t\tdisabled: () => false,\n\t\t\t\tisVisible: () => isNumericTerm(this.config?.term?.term) || isNumericTerm(this.config?.term2?.term),\n\t\t\t\tgetConfig: async () => {\n\t\t\t\t\tconst _term = this.config?.term\n\t\t\t\t\tconst _term2 = this.config.term2\n\n\t\t\t\t\tlet termMode = 'continuous',\n\t\t\t\t\t\tterm2Mode = 'discrete'\n\t\t\t\t\tthis.boxContTerm = isNumericTerm(_term?.term) ? 'term' : 'term2'\n\n\t\t\t\t\t//If the first term was continuous or is coming as continuous\n\t\t\t\t\tif ((this.boxContTerm && this.boxContTerm === 'term') || _term.q?.mode == 'continuous') {\n\t\t\t\t\t\t// must mean coming from scatter plot\n\t\t\t\t\t\ttermMode = 'continuous'\n\t\t\t\t\t\tterm2Mode = 'discrete'\n\t\t\t\t\t\tthis.boxContTerm = 'term'\n\t\t\t\t\t}\n\t\t\t\t\t//If the second term was continuous or is coming as continuous\n\t\t\t\t\telse if ((this.boxContTerm && this.boxContTerm === 'term2') || _term2?.q?.mode == 'continuous') {\n\t\t\t\t\t\t// must mean coming from barchart\n\t\t\t\t\t\ttermMode = 'discrete'\n\t\t\t\t\t\tterm2Mode = 'continuous'\n\t\t\t\t\t\tthis.boxContTerm = 'term2'\n\t\t\t\t\t}\n\t\t\t\t\t//If the second term is coming as discrete from the scatter\n\t\t\t\t\telse if (_term2?.q?.mode == 'discrete') {\n\t\t\t\t\t\t// must mean coming from barchart\n\t\t\t\t\t\ttermMode = 'discrete'\n\t\t\t\t\t\tterm2Mode = 'continuous'\n\t\t\t\t\t\tthis.boxContTerm = 'term2'\n\t\t\t\t\t}\n\n\t\t\t\t\tconst term = await this.getWrappedTermCopy(_term, termMode)\n\t\t\t\t\tconst term2 = await this.getWrappedTermCopy(_term2, term2Mode)\n\t\t\t\t\tconst config = {\n\t\t\t\t\t\tchildType: 'boxplot',\n\t\t\t\t\t\tterm,\n\t\t\t\t\t\tterm2\n\t\t\t\t\t}\n\t\t\t\t\treturn config\n\t\t\t\t},\n\t\t\t\tactive: false,\n\t\t\t\tcallback\n\t\t\t},\n\t\t\t{\n\t\t\t\tchildType: 'sampleScatter',\n\t\t\t\tlabel: 'Scatter',\n\t\t\t\tdisabled: () => false,\n\t\t\t\tisVisible: () => {\n\t\t\t\t\treturn isNumericTerm(this.config?.term.term) && isNumericTerm(this.config?.term2?.term)\n\t\t\t\t},\n\t\t\t\tgetConfig: async () => {\n\t\t\t\t\tconst _term = await this.getWrappedTermCopy(this.config?.term, 'continuous')\n\t\t\t\t\tconst _term2 = await this.getWrappedTermCopy(this.config?.term2, 'continuous')\n\t\t\t\t\tconst config = {\n\t\t\t\t\t\tchildType: 'sampleScatter',\n\t\t\t\t\t\tterm: _term,\n\t\t\t\t\t\tterm2: _term2,\n\t\t\t\t\t\tgroups: [],\n\t\t\t\t\t\tterm0: this.config.term0\n\t\t\t\t\t}\n\t\t\t\t\treturn config\n\t\t\t\t},\n\t\t\t\tactive: false,\n\t\t\t\tcallback\n\t\t\t}\n\t\t]\n\t}\n\n\tasync init(appState) {\n\t\tconst state = this.getState(appState)\n\t\tconst config = structuredClone(state.config)\n\t\tthis.initUi(this.opts, config)\n\n\t\t// this.components.recover = await recoverInit({\n\t\t// \tapp: this.app,\n\t\t// \tholder: this.dom.localRecoverDiv,\n\t\t// \tgetState: appState => this.getState(appState),\n\t\t// \treactsTo: action => action.id == this.id && action.type == 'plot_edit' && action._scope_ != 'none',\n\t\t// \tplot_id: this.id,\n\t\t// \tmaxHistoryLen: 10,\n\t\t// \tmargin: '5px 10px' //Prevents a gap appearing between the tabs and sandbox content\n\t\t// })\n\t\tthis.components.filter = await filterRxCompInit({\n\t\t\tapp: this.app,\n\t\t\tvocabApi: this.app.vocabApi,\n\t\t\tparentId: this.id,\n\t\t\tholder: this.dom.filterDiv,\n\t\t\thideLabel: true,\n\n\t\t\temptyLabel: '+Add new filter',\n\t\t\tcallback: filter => {\n\t\t\t\tthis.app.dispatch({\n\t\t\t\t\tid: this.id,\n\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\tconfig: { filter }\n\t\t\t\t})\n\t\t\t}\n\t\t})\n\t}\n\n\treactsTo(action) {\n\t\tif (action.type.includes('cache_termq')) return true\n\t\tif (action.type.startsWith('plot_')) {\n\t\t\tif (action.type.startsWith('plot_')) {\n\t\t\t\treturn action.id === this.id || action.id == this.parentId\n\t\t\t}\n\t\t}\n\t\tif (action.type.startsWith('filter')) return true\n\t\tif (action.type.startsWith('cohort')) return true\n\t\tif (action.type == 'app_refresh') return true\n\t\treturn false\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='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`\n\t\t}\n\t\treturn {\n\t\t\ttermfilter: appState.termfilter,\n\t\t\tconfig,\n\t\t\t// quick fix to skip history tracking as needed\n\t\t\t_scope_: appState._scope_\n\t\t}\n\t}\n\n\tasync main() {\n\t\tdelete this.error\n\t\tthis.dom.errdiv.style('display', 'none').html('')\n\t\tthis.dom.loading.style('display', '')\n\n\t\tthis.config = await this.getMutableConfig()\n\t\tthis.maySetSandboxHeader()\n\n\t\tif (!this.components.plots[this.config.childType]) {\n\t\t\tawait this.setComponent(this.config)\n\t\t}\n\n\t\tthis.dom.loading.style('display', 'none')\n\t\tthis.render()\n\n\t\tconst activeTabIndex = this.tabsData.findIndex(tab => tab.childType == this.config.childType)\n\t\tthis.chartToggles.update(activeTabIndex)\n\n\t\t//Only show tabs when more than one are present\n\t\tconst numVisTabs = this.tabsData.filter(d => d.isVisible()).length\n\t\tif (numVisTabs > 1) this.dom.chartToggles.style('display', 'inline-block')\n\t\telse this.dom.chartToggles.style('display', 'none')\n\t}\n\n\tmaySetSandboxHeader() {\n\t\tconst { term, term2, headerText, assayCohortTitle } = this.config\n\t\tconst mainTerm = term.getTitleText?.() || term.term.name\n\t\tconst _headerPretext = headerText ? `${headerText} ` : ''\n\t\t//TODO: Should change .assayCohortTitle to headerSuffix, something more generic\n\t\tconst _headerSuffix = assayCohortTitle ? ` (${assayCohortTitle})` : ''\n\t\tconst titleBase = mainTerm + _headerSuffix\n\t\tif (term2?.type) {\n\t\t\tthis.dom.paneTitleText.html(`${_headerPretext}${term2.getTitleText?.() || term2.term.name} vs ${titleBase}`)\n\t\t} else {\n\t\t\tthis.dom.paneTitleText.html(`${_headerPretext}${titleBase}`)\n\t\t}\n\t}\n\n\tasync setComponent(config) {\n\t\t// !!! quick fix for rollup to bundle,\n\t\t// will eventually need to move to a subnested folder structure\n\t\tconst _ = await importPlot(config.childType, `unsupported childType='${config.childType}'`)\n\t\tthis.dom.plotDivs[config.childType] = this.dom.viz.append('div')\n\n\t\t// assumes only 1 chart per chartType would be rendered in the summary sandbox\n\t\tthis.components.plots[config.childType] = await _.componentInit({\n\t\t\tapp: this.app,\n\t\t\tholder: this.dom.plotDivs[config.childType],\n\t\t\tid: this.id,\n\t\t\tparent: this.api\n\t\t})\n\t}\n\n\tdestroy() {\n\t\t// the dom.holder itself is not a d3-selection,\n\t\t// so need to specify a destroy function here\n\t\t// since the default rx.componentApi.destroy()\n\t\t// does not work when dom.holder is not a d3-selection\n\t\tthis.dom.holder.app_div.selectAll('*').remove()\n\t\tthis.dom.holder.app_div.remove()\n\t\tfor (const key in this.dom) {\n\t\t\tdelete this.dom[key]\n\t\t}\n\t}\n\n\tinitUi(opts, config) {\n\t\tthis.dom.paneTitleText.html(config.term.term.name)\n\t\tthis.chartToggles.main()\n\t}\n\n\tasync tabClickCallback(event, tab) {\n\t\tif (!tab || !tab.getConfig) return\n\t\tlet config\n\t\ttry {\n\t\t\tthis.dom.viz.style('display', 'none')\n\t\t\tthis.dom.loading.style('display', '')\n\t\t\tconfig = await tab.getConfig()\n\t\t\tthis.dom.loading.style('display', 'none')\n\t\t\tthis.dom.viz.style('display', '')\n\t\t\tif (config)\n\t\t\t\tthis.app.dispatch({\n\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\tid: this.id,\n\t\t\t\t\tconfig: config\n\t\t\t\t})\n\t\t} catch (e: any) {\n\t\t\tthis.dom.loading.style('display', 'none')\n\t\t\tthis.error = e\n\t\t\tthis.dom.errdiv.style('display', '').html(`Error: ${e.message || e.error || e}`)\n\t\t}\n\t}\n\n\tasync getWrappedTermCopy(term, mode) {\n\t\tif (!term) return\n\t\tconst tw = structuredClone(term)\n\t\t// TODO: this is not type safe, assumes any q{} can be set to any mode\n\t\ttw.q.mode = mode // {mode, isAtomic: true}\n\t\t// If tw.q is empty/undefined, the default q\n\t\t// will be assigned by fillTw by term type\n\t\tawait fillTermWrapper(tw, this.app.vocabApi)\n\t\treturn tw\n\t}\n\n\trender() {\n\t\tfor (const childType of Object.keys(this.components.plots)) {\n\t\t\tconst chart = this.components.plots[childType]\n\t\t\t// hide non-active charts first, so not to momentarily have two visible charts\n\t\t\tif (chart.type != this.config.childType) {\n\t\t\t\tthis.dom.plotDivs[chart.type].style('display', 'none')\n\t\t\t}\n\t\t}\n\n\t\tthis.dom.plotDivs[this.config.childType].style('display', '')\n\t}\n\n\tgetChartImages() {\n\t\tconst chart = this.components.plots[this.config.childType]\n\t\tif (chart?.getChartImages) {\n\t\t\treturn chart.getChartImages()\n\t\t}\n\t\treturn null\n\t}\n}\n\nexport const summaryInit = getCompInit(SummaryPlot)\nexport const componentInit = summaryInit\n\nexport async function getPlotConfig(opts, app) {\n\tif (!opts.term) throw 'summary getPlotConfig: opts.term{} missing'\n\ttry {\n\t\topts.term = await fillTermWrapper(\n\t\t\topts.term,\n\t\t\tapp.vocabApi,\n\t\t\topts.term.q || { geneVariant: { type: 'predefined-groupset' } }\n\t\t)\n\t\t// supply term0_term2_defaultQ if opts.term0/2.bins/q is undefined\n\t\t// e.g. for scatterplot, opts.term2.q.mode='continuous' so will not\n\t\t// want to override with q.mode from term0_term2_defaultQ\n\t\tif (opts.term2)\n\t\t\topts.term2 = await fillTermWrapper(\n\t\t\t\topts.term2,\n\t\t\t\tapp.vocabApi,\n\t\t\t\topts.term2.bins || opts.term2.q ? undefined : term0_term2_defaultQ\n\t\t\t)\n\t\tif (opts.term0)\n\t\t\topts.term0 = await fillTermWrapper(\n\t\t\t\topts.term0,\n\t\t\t\tapp.vocabApi,\n\t\t\t\topts.term0.bins || opts.term0.q ? undefined : term0_term2_defaultQ\n\t\t\t)\n\t\t// dynamic scatterplot is a child type of summary and following args are possible; if present, initialize them\n\t\tif (opts.colorTW) opts.colorTW = await fillTermWrapper(opts.colorTW, app.vocabApi)\n\t\tif (opts.shapeTW) opts.shapeTW = await fillTermWrapper(opts.shapeTW, app.vocabApi)\n\t\tif (opts.scaleDotTW) opts.scaleDotTW = await fillTermWrapper(opts.scaleDotTW, app.vocabApi)\n\t} catch (e: any) {\n\t\tif (e.stack) console.log(e.stack)\n\t\tthrow `${e} [summary getPlotConfig()]`\n\t}\n\n\tconst config = {\n\t\tchartType: 'summary',\n\t\tchildType: 'barchart',\n\t\tterm: opts.term,\n\t\tgroups: [],\n\t\tcontrolLabels: Object.assign({}, defaultUiLabels, app.vocabApi.termdbConfig.uiLabels || {}),\n\t\tsettings: {\n\t\t\tcontrols: {\n\t\t\t\tisOpen: false\n\t\t\t},\n\t\t\tcommon: {\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\t// Move to barchart settings\n\t\t\t\t// barheight: 300, // maximum bar length\n\t\t\t\t// barwidth: 20, // bar thickness\n\t\t\t\t// barspace: 2 // space between two bars\n\t\t\t},\n\n\t\t\tbarchart: getDefaultBarSettings(app),\n\n\t\t\tviolin: getDefaultViolinSettings(app),\n\n\t\t\tboxplot: getDefaultBoxplotSettings(app),\n\n\t\t\tsampleScatter: getDefaultScatterSettings(opts)\n\t\t},\n\t\tmayAdjustConfig(config, edits: { childType?: string } = {}) {\n\t\t\treturn mayAdjustConfig(config, opts, edits)\n\t\t}\n\t}\n\t//config.mayAdjustConfig(config)\n\n\t// TODO: may do similar thing for custom term\n\tif (config.term.term.type == 'geneVariant') config.settings.barchart.colorBars = true\n\n\t// may apply term-specific changes to the default object\n\tcopyMerge(config, opts)\n\t// always use the dataset-configured control/ui labels\n\t// to override ui labels from recovered session state\n\tObject.assign(config.controlLabels, app.vocabApi.termdbConfig.uiLabels || {})\n\treturn config\n}\n\nconst discreteByContinuousPlots = new Set(['violin', 'boxplot'])\n\n/**\n * Adjusts the childType of a summary plot config based on the term types and modes.\n * This is exported so it can be tested directly.\n */\nexport function mayAdjustConfig(config, opts, edits: { childType?: string } = {}) {\n\t/*\n\t\twhen recovering from state rehydration:\n\t\t- Mass store must call mayAdjustConfig(), if available, since the recovered state\n\t\tmay be partial such as from an example url. Even a previously saved \"full\" state\n\t\tmay still need to be filled or reshaped with new state config/settings.\n\t*/\n\n\tif (edits.childType) {\n\t\t// no need to set config.childType if a value is already specified\n\t\t// in an edits object (optional second argument), as processed by mass store\n\t\tif (config.childType != edits.childType) throw `action.config.childType was not applied in mass store.plot_edit()`\n\t\treturn\n\t}\n\t// config.childType may be stale, OR edits.childType may not be available,\n\t// when the summary plot_edit is triggered by replacing a term, such as replacing\n\t// categorical overlay with numeric, in which case the dispatched action might not\n\t// know in advance what the chiltType should be. It is much more reliable and consistent\n\t// to determine the default plots here, depending on the processed config.\n\tif (config.term?.q?.mode == 'continuous' && config.term2?.q?.mode == 'continuous') {\n\t\t// TODO: may need more logic later if more than one summary childType,\n\t\t// besides scatter, can support 2 continuous terms\n\t\tconfig.childType = 'sampleScatter'\n\t} else if (config.term?.term?.type == 'termCollection') {\n\t\tif (config.term.term.memberType == 'categorical') {\n\t\t\tconfig.childType = 'barchart' // ok to overwrite as it can only be barchart\n\t\t} else if (config.term.term.memberType == 'numeric') {\n\t\t\tif (config.childType) {\n\t\t\t\t// already given.\n\t\t\t\tif (config.childType == 'barchart') {\n\t\t\t\t\t// wrong type, overwrite with default\n\t\t\t\t\tconfig.childType = 'violin'\n\t\t\t\t} else {\n\t\t\t\t\t// do not overwrite e.g. if value is boxplot. though this is not further validated\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\tconfig.childType = 'violin'\n\t\t\t}\n\t\t} else {\n\t\t\tthrow new Error('config.term.term.memberType not categorical or numeric')\n\t\t}\n\t} else if (config.term?.q?.mode == 'continuous' || config.term2?.q?.mode == 'continuous') {\n\t\tif (!discreteByContinuousPlots.has(config.childType)) {\n\t\t\t// only change config.childType if the current value is not supported by discrete + continuous tw\n\t\t\tif (opts.childType && !discreteByContinuousPlots.has(opts.childType)) {\n\t\t\t\tconsole.warn(\n\t\t\t\t\t`ignoring summary opts.childType='${opts.childType}' since it does not support plotting discrete by continuous tw's`\n\t\t\t\t)\n\t\t\t\tconfig.childType = 'violin'\n\t\t\t} else {\n\t\t\t\tconfig.childType = opts.childType || 'violin'\n\t\t\t}\n\t\t}\n\t} else {\n\t\t// TODO: may need more logic later if more than one summary childType,\n\t\t// besides barchart, can support discrete tw only\n\t\tconfig.childType = 'barchart'\n\t}\n}\n"],
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