@sjcrh/proteinpaint-client 2.166.0 → 2.167.1

package/dist/chunk-BAJ74DKS.js

@@ -0,0 +1,419 @@
+import {
+  getDefaultViolinSettings
+} from "./chunk-CV6ID6T7.js";
+import {
+  getDefaultScatterSettings
+} from "./chunk-5AMBV2JE.js";
+import {
+  getDefaultBarSettings
+} from "./chunk-2OVIUIIL.js";
+import {
+  getDefaultBoxplotSettings
+} from "./chunk-46T54RUY.js";
+import {
+  recoverInit
+} from "./chunk-SEL5UNRC.js";
+import {
+  importPlot
+} from "./chunk-J7IU77CA.js";
+import {
+  PlotBase,
+  defaultUiLabels
+} from "./chunk-GLSDMBHR.js";
+import {
+  term0_term2_defaultQ
+} from "./chunk-RQ7CE7SK.js";
+import {
+  Tabs,
+  fillTermWrapper,
+  filterRxCompInit
+} from "./chunk-W5EG334J.js";
+import {
+  isNumericTerm
+} from "./chunk-DKI7YOTJ.js";
+import {
+  Menu
+} from "./chunk-TGZA4ETW.js";
+import {
+  copyMerge,
+  getCompInit
+} from "./chunk-DDOM4XYV.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";
+  }
+  getDom(opts) {
+    const holder = opts.holder;
+    holder.header.style("padding", 0);
+    const paneTitleDiv = holder.header.append("div").style("display", "inline-block").style("color", "#999").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").style("display", "none").style("padding", "5px").style("background-color", "rgba(255,100,100,0.2)"),
+      // 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")
+    };
+  }
+  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 = this.config?.term;
+          const term2 = this.config?.term2;
+          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.recover = await recoverInit({
+      app: this.app,
+      holder: this.dom.localRecoverDiv,
+      getState: (appState2) => this.getState(appState2),
+      reactsTo: (action) => action.id == this.id && action.type == "plot_edit" && action._scope_ != "none",
+      plot_id: this.id,
+      maxHistoryLen: 10,
+      margin: "5px 10px"
+      //Prevents a gap appearing between the tabs and sandbox content
+    });
+    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='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`;
+    }
+    return {
+      termfilter: appState.termfilter,
+      config,
+      // quick fix to skip history tracking as needed
+      _scope_: appState._scope_
+    };
+  }
+  async main() {
+    this.dom.errdiv.style("display", "none").style("background-color", "rgba(255,100,100,0.2)").html("");
+    this.config = await this.getMutableConfig();
+    this.maySetSandboxHeader();
+    if (!this.components.plots[this.config.childType]) {
+      await this.setComponent(this.config);
+    }
+    this.render();
+    const activeTabIndex = this.tabsData.findIndex((tab) => tab.childType == this.config.childType);
+    this.chartToggles.update(activeTabIndex);
+    const numVisTabs = this.tabsData.filter((d) => d.isVisible()).length;
+    if (numVisTabs > 1) this.dom.chartToggles.style("display", "inline-block");
+    else this.dom.chartToggles.style("display", "none");
+  }
+  maySetSandboxHeader() {
+    const { term, term2 } = this.config;
+    const mainTerm = term.getTitleText?.() || term.term.name;
+    if (term2?.type) {
+      this.dom.paneTitleText.html(`${term2.getTitleText?.() || term2.term.name} vs ${mainTerm}`);
+    } else {
+      this.dom.paneTitleText.html(mainTerm);
+    }
+  }
+  async setComponent(config) {
+    const _ = await importPlot(config.childType, `unsupported childType='${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;
+    const config = await tab.getConfig();
+    if (config)
+      this.app.dispatch({
+        type: "plot_edit",
+        id: this.id,
+        config
+      });
+  }
+  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 `${e} [summary getPlotConfig()]`;
+  }
+  const config = {
+    chartType: "summary",
+    childType: "barchart",
+    //id: opts.term.term.id,
+    term: opts.term,
+    groups: [],
+    controlLabels: Object.assign({}, defaultUiLabels, app.vocabApi.termdbConfig.uiLabels || {}),
+    settings: {
+      controls: {
+        isOpen: false
+      },
+      common: {
+        use_logscale: false,
+        // flag for y-axis scale type, 0=linear, 1=log
+        use_percentage: false
+        // Move to barchart settings
+        // barheight: 300, // maximum bar length
+        // barwidth: 20, // bar thickness
+        // barspace: 2 // space between two bars
+      },
+      barchart: getDefaultBarSettings(app),
+      violin: getDefaultViolinSettings(app),
+      boxplot: getDefaultBoxplotSettings(app),
+      sampleScatter: getDefaultScatterSettings()
+    },
+    mayAdjustConfig(config2, edits = {}) {
+      if (edits.childType) {
+        if (config2.childType != edits.childType)
+          throw `action.config.childType was not applied in mass store.plot_edit()`;
+        return;
+      }
+      if (config2.term?.q?.mode == "continuous" && config2.term2?.q?.mode == "continuous") {
+        config2.childType = "sampleScatter";
+      } else if (config2.term?.q?.mode == "continuous" || config2.term2?.q?.mode == "continuous") {
+        if (!discreteByContinuousPlots.has(config2.childType)) {
+          if (opts.childType && !discreteByContinuousPlots.has(opts.childType)) {
+            console.warn(
+              `ignoring summary opts.childType='${opts.childType}' since it does not support plotting discrete by continuous tw's`
+            );
+            config2.childType = "violin";
+          } else {
+            config2.childType = opts.childType || "violin";
+          }
+        }
+      } else {
+        config2.childType = "barchart";
+      }
+    }
+  };
+  if (config.term.term.type == "geneVariant") config.settings.barchart.colorBars = true;
+  return copyMerge(config, opts);
+}
+var discreteByContinuousPlots = /* @__PURE__ */ new Set(["violin", "boxplot"]);
+
+export {
+  summaryInit,
+  componentInit,
+  getPlotConfig
+};
+//# sourceMappingURL=chunk-BAJ74DKS.js.map

package/dist/chunk-BAJ74DKS.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/summary.ts"],
+  "sourcesContent": ["import { getCompInit, copyMerge, type ComponentApi, type RxComponent } from '#rx'\nimport { PlotBase, defaultUiLabels } from './PlotBase.ts'\nimport { Menu } from '#dom/menu'\nimport { fillTermWrapper } from '#termsetting'\nimport { recoverInit } from '../rx/src/recover'\n// import { select } from 'd3-selection'\nimport { getDefaultViolinSettings } from './violin.js'\nimport { getDefaultBarSettings } from './barchart.js'\nimport { getDefaultBoxplotSettings } from './boxplot/BoxPlot.ts'\nimport { getDefaultScatterSettings } from './scatter/scatter.js'\nimport { Tabs } from '../dom/toggleButtons'\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\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\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', '#999')\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\n\t\t\t\t.append('div')\n\t\t\t\t.style('display', 'none')\n\t\t\t\t.style('padding', '5px')\n\t\t\t\t.style('background-color', 'rgba(255,100,100,0.2)'),\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')\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 = this.config?.term\n\t\t\t\t\tconst term2 = this.config?.term2\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\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\tthis.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='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`\n\t\t}\n\t\treturn {\n\t\t\ttermfilter: appState.termfilter,\n\t\t\tconfig,\n\t\t\t// quick fix to skip history tracking as needed\n\t\t\t_scope_: appState._scope_\n\t\t}\n\t}\n\n\tasync main() {\n\t\tthis.dom.errdiv.style('display', 'none').style('background-color', 'rgba(255,100,100,0.2)').html('')\n\t\tthis.config = await this.getMutableConfig()\n\t\tthis.maySetSandboxHeader()\n\n\t\tif (!this.components.plots[this.config.childType]) {\n\t\t\tawait this.setComponent(this.config)\n\t\t}\n\n\t\tthis.render()\n\n\t\tconst activeTabIndex = this.tabsData.findIndex(tab => tab.childType == this.config.childType)\n\t\tthis.chartToggles.update(activeTabIndex)\n\n\t\t//Only show tabs when more than one are present\n\t\tconst numVisTabs = this.tabsData.filter(d => d.isVisible()).length\n\t\tif (numVisTabs > 1) this.dom.chartToggles.style('display', 'inline-block')\n\t\telse this.dom.chartToggles.style('display', 'none')\n\t}\n\n\tmaySetSandboxHeader() {\n\t\tconst { term, term2 } = this.config\n\t\tconst mainTerm = term.getTitleText?.() || term.term.name\n\t\tif (term2?.type) {\n\t\t\tthis.dom.paneTitleText.html(`${term2.getTitleText?.() || term2.term.name} vs ${mainTerm}`)\n\t\t} else {\n\t\t\tthis.dom.paneTitleText.html(mainTerm)\n\t\t}\n\t}\n\n\tasync setComponent(config) {\n\t\t// !!! quick fix for rollup to bundle,\n\t\t// will eventually need to move to a subnested folder structure\n\t\tconst _ = await importPlot(config.childType, `unsupported childType='${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\tconst config = await tab.getConfig()\n\t\tif (config)\n\t\t\tthis.app.dispatch({\n\t\t\t\ttype: 'plot_edit',\n\t\t\t\tid: this.id,\n\t\t\t\tconfig: config\n\t\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\t//id: opts.term.term.id,\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()\n\t\t},\n\t\tmayAdjustConfig(config, edits: { childType?: string } = {}) {\n\t\t\t/*\n\t\t\t\twhen recovering from state rehydration:\n\t\t\t\t- Mass store must call mayAdjustConfig(), if available, since the recovered state\n\t\t\t\tmay be partial such as from an example url. Even a previously saved \"full\" state\n\t\t\t\tmay still need to be filled or reshaped with new state config/settings.\n\t\t\t*/\n\n\t\t\tif (edits.childType) {\n\t\t\t\t// no need to set config.childType if a value is already specified\n\t\t\t\t// in an edits object (optional second argument), as processed by mass store\n\t\t\t\tif (config.childType != edits.childType)\n\t\t\t\t\tthrow `action.config.childType was not applied in mass store.plot_edit()`\n\t\t\t\treturn\n\t\t\t}\n\n\t\t\t// config.childType may be stale, OR edits.childType may not be available,\n\t\t\t// when the summary plot_edit is triggered by replacing a term, such as replacing\n\t\t\t// categorical overlay with numeric, in which case the dispatched action might not\n\t\t\t// know in advance what the chiltType should be. It is much more reliable and consistent\n\t\t\t// to determine the default plots here, depending on the processed config.\n\t\t\tif (config.term?.q?.mode == 'continuous' && config.term2?.q?.mode == 'continuous') {\n\t\t\t\t// TODO: may need more logic later if more than one summary childType,\n\t\t\t\t// besides scatter, can support 2 continuous terms\n\t\t\t\tconfig.childType = 'sampleScatter'\n\t\t\t} else if (config.term?.q?.mode == 'continuous' || config.term2?.q?.mode == 'continuous') {\n\t\t\t\tif (!discreteByContinuousPlots.has(config.childType)) {\n\t\t\t\t\t// only change config.childType if the current value is not supported by discrete + continuous tw\n\t\t\t\t\tif (opts.childType && !discreteByContinuousPlots.has(opts.childType)) {\n\t\t\t\t\t\tconsole.warn(\n\t\t\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\t\t)\n\t\t\t\t\t\tconfig.childType = 'violin'\n\t\t\t\t\t} else {\n\t\t\t\t\t\tconfig.childType = opts.childType || 'violin'\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\t// TODO: may need more logic later if more than one summary childType,\n\t\t\t\t// besides barchart, can support discrete tw only\n\t\t\t\tconfig.childType = 'barchart'\n\t\t\t}\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\treturn copyMerge(config, opts)\n}\n\nconst discreteByContinuousPlots = new Set(['violin', 'boxplot'])\n"],
+  "mappings": 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+  "names": ["appState", "config"]
+}

package/dist/chunk-BTYCW3D5.js

@@ -0,0 +1,85 @@
+import {
+  TermTypes
+} from "./chunk-DKI7YOTJ.js";
+import {
+  roundValue
+} from "./chunk-5OHXYXLD.js";
+
+// plots/volcano/settings/defaults.ts
+var maxSampleCutoff = 4e3;
+var maxGESampleCutoff = 3e3;
+function getDefaultVolcanoSettings(overrides = {}, opts) {
+  const defaults = {
+    defaultSignColor: "red",
+    defaultNonSignColor: "black",
+    defaultHighlightColor: "#ffa200",
+    // orange-yellow
+    foldChangeCutoff: 0.3,
+    height: 400,
+    pValue: roundValue(-Math.log10(0.05), 2),
+    pValueType: "adjusted",
+    //Only declare this value in one place
+    sampleNumCutoff: opts.termType == TermTypes.GENE_EXPRESSION ? maxGESampleCutoff : maxSampleCutoff,
+    width: 400
+  };
+  addGEDefaults(opts.termType, defaults);
+  addSCCTDefaults(opts.termType);
+  return Object.assign(defaults, overrides);
+}
+function addGEDefaults(termType, defaults) {
+  if (termType != TermTypes.GENE_EXPRESSION) return;
+  const features = JSON.parse(sessionStorage.getItem("optionalFeatures"));
+  const method = features?.runDE_methods?.includes("Wilcoxon") ? "wilcoxon" : "edgeR";
+  defaults.cpmCutoff = 1;
+  defaults.method = method;
+  defaults.minCount = 10;
+  defaults.minTotalCount = 15;
+  defaults.rankBy = "abs(foldChange)";
+}
+function addSCCTDefaults(termType) {
+  if (termType != TermTypes.SINGLECELL_CELLTYPE) return;
+}
+function validateVolcanoSettings(config, opts) {
+  if (config.termType == TermTypes.SINGLECELL_CELLTYPE) return;
+  if (!config.settings.volcano) return;
+  const settings = config.settings.volcano;
+  const sampleNum = getSampleNum(opts);
+  if (sampleNum > maxSampleCutoff) {
+    throw new Error(
+      `Sample size ${sampleNum} exceeds max sample size of ${maxSampleCutoff}. Please reduce sample size.`
+    );
+  }
+  validateGESettings(config.termType, settings, sampleNum, opts);
+  validateSCCTSettings(config.termType);
+}
+function getSampleNum(config) {
+  if (config.termType == TermTypes.GENE_EXPRESSION) {
+    return config.samplelst.groups.reduce((sum, g) => sum + g.values.length, 0);
+  }
+  if (config.termType == TermTypes.SINGLECELL_CELLTYPE) {
+    return maxSampleCutoff;
+  }
+}
+function validateGESettings(termType, settings, sampleNum, opts) {
+  if (termType != TermTypes.GENE_EXPRESSION) return;
+  const largeNum = sampleNum > settings.sampleNumCutoff;
+  if (!opts.overrides && largeNum) {
+    settings.method = "wilcoxon";
+  } else if (largeNum && settings.method != "wilcoxon") {
+    throw new Error(
+      `${settings.method} is not supported for ${sampleNum} samples when termtype = ${termType}. Please use Wilcoxon.`
+    );
+  }
+}
+function validateSCCTSettings(termType) {
+  if (termType != TermTypes.SINGLECELL_CELLTYPE) return;
+}
+
+export {
+  maxSampleCutoff,
+  maxGESampleCutoff,
+  getDefaultVolcanoSettings,
+  validateVolcanoSettings,
+  getSampleNum
+};
+//# sourceMappingURL=chunk-BTYCW3D5.js.map