@sjcrh/proteinpaint-client 2.198.0 → 2.200.0

package/dist/DifferentialAnalysis-SETJAZEN.js

@@ -0,0 +1,243 @@
+import {
+  getDefaultGseaSettings
+} from "./chunk-KTKZSYIH.js";
+import {
+  DATermTypes,
+  PlotBase,
+  Tabs,
+  enabledTermTypes,
+  getDefaultVolcanoSettings,
+  validateVolcanoSettings
+} from "./chunk-TKW5TW4Z.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-LSEFWW72.js";
+import {
+  importPlot
+} from "./chunk-3SHZTAGF.js";
+import {
+  Menu
+} from "./chunk-HYOEWQ5P.js";
+import "./chunk-6QCYT6G2.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-IIT367QZ.js";
+import "./chunk-RZGEKL77.js";
+import "./chunk-OTTMHVYH.js";
+import "./chunk-GNS6CQMA.js";
+import "./chunk-JVPWIVDT.js";
+import "./chunk-4WF3XDQP.js";
+import {
+  termType2label
+} from "./chunk-7JRDJNLR.js";
+import {
+  copyMerge,
+  getCompInit
+} from "./chunk-M3J4MINX.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-MPSLUEI4.js";
+import {
+  PROTEOME_DAP
+} from "./chunk-6PNPHACF.js";
+import "./chunk-WPHUM5S5.js";
+import "./chunk-JNITUVXP.js";
+import "./chunk-2KXLYFAO.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-VQZ2Z5YU.js";
+import "./chunk-UJELJXJG.js";
+import "./chunk-BZTWTH4Y.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-HFNDKYVF.js";
+
+// plots/diffAnalysis/view/DiffAnalysisView.ts
+var DiffAnalysisView = class {
+  constructor(app, config, dom) {
+    this.app = app;
+    this.config = config;
+    this.dom = dom;
+    setRenderers(this);
+    this.tabsData = this.getTabsOptions(this);
+    this.tabs = new Tabs({ holder: this.dom.tabsDiv, tabs: this.tabsData });
+    this.tabs.main();
+  }
+  update(plotConfig) {
+    const activeTabIndex = this.tabsData.findIndex((tab) => tab.id == plotConfig.childType);
+    this.tabs.update(activeTabIndex);
+  }
+};
+function setRenderers(self) {
+  self.getTabsOptions = (self2) => {
+    const tabs = [
+      {
+        active: self2.config.childType === "volcano",
+        id: "volcano",
+        label: "Volcano",
+        isVisible: () => true,
+        // isVisible: () => self.config.termType === TermTypes.GENE_EXPRESSION,
+        getPlotConfig: () => {
+          return {
+            childType: "volcano"
+          };
+        },
+        callback: self2.tabCallback
+      },
+      {
+        active: self2.config.childType === "gsea",
+        id: "gsea",
+        label: "Gene Set Enrichment Analysis",
+        isVisible: () => self2.config.termType !== PROTEOME_DAP,
+        // isVisible: () => self.config.termType === TermTypes.GENE_EXPRESSION,
+        getPlotConfig: () => {
+          return {
+            childType: "gsea"
+          };
+        },
+        callback: self2.tabCallback
+      }
+    ];
+    return tabs;
+  };
+  self.tabCallback = async (event, tab) => {
+    if (!event || !tab || !tab.id) return;
+    const plotConfig = tab.getPlotConfig();
+    await self.app.dispatch({
+      type: "plot_edit",
+      id: self.config.id,
+      config: plotConfig
+    });
+  };
+}
+
+// plots/diffAnalysis/DifferentialAnalysis.ts
+var { SINGLECELL_CELLTYPE } = DATermTypes;
+var DifferentialAnalysis = class extends PlotBase {
+  constructor(opts, api) {
+    super(opts, api);
+    this.type = "differentialAnalysis";
+    this.components = {
+      plots: {}
+    };
+    this.termType = opts.termType;
+    const holder = opts.holder.classed("sjpp-diff-analysis-main", true);
+    const controls = opts.controls ? holder : holder.append("div");
+    const div = holder.append("div").style("padding", "5px").style("display", "inline-block").style("vertical-align", "top");
+    const tabsDiv = div.append("div").attr("id", "sjpp-diff-analysis-tabs").style("display", "inline-block");
+    const plots = div.append("div").attr("id", "sjpp-diff-analysis-tabs-content");
+    this.dom = {
+      controls: controls.style("display", "inline-block"),
+      div,
+      tabsDiv,
+      plots,
+      tip: new Menu({ padding: "" })
+    };
+    this.plotsControlsDiv = {};
+    this.plotsDiv = {};
+    if (opts.parentId) this.parentId = opts.parentId;
+    if (opts.header) {
+      this.dom.header = {
+        title: opts.header.append("span").style("margin-right", "5px").style("color", "darkslategray"),
+        plot: opts.header.append("span").style("font-size", "0.7em").style("opacity", 0.6)
+      };
+    }
+  }
+  static {
+    this.type = "differentialAnalysis";
+  }
+  getState(appState) {
+    const config = appState.plots.find((p) => p.id === this.id);
+    if (!config) {
+      throw new Error(
+        `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`
+      );
+    }
+    return {
+      config
+    };
+  }
+  reactsTo(action) {
+    if (action.type.includes("cache_termq")) return true;
+    if (action.type.startsWith("plot_")) {
+      return action.id === this.id || action.id == this.parentId;
+    }
+    if (action.type.startsWith("filter")) return true;
+    if (action.type.startsWith("cohort")) return true;
+    if (action.type == "app_refresh") return true;
+  }
+  async init(appState) {
+    const state = this.getState(appState);
+    const config = structuredClone(state.config);
+    this.plotTabs = new DiffAnalysisView(this.app, config, this.dom);
+  }
+  async setComponent(config) {
+    this.plotsControlsDiv[config.childType] = this.dom.controls.append("div");
+    this.plotsDiv[config.childType] = this.dom.plots.append("div");
+    const opts = {
+      app: this.app,
+      holder: this.plotsDiv[config.childType],
+      id: this.id,
+      parent: this.api,
+      controls: this.plotsControlsDiv[config.childType],
+      termType: config.termType
+    };
+    const _ = await importPlot(config.childType, `unsupported childType='${config.childType}'`);
+    this.components.plots[config.childType] = await _.componentInit(opts);
+  }
+  async main() {
+    const config = structuredClone(this.state.config);
+    if (config.chartType != this.type) return;
+    if (!this.components.plots[config.childType]) await this.setComponent(config);
+    for (const childType in this.components.plots) {
+      const chart = this.components.plots[childType];
+      if (chart.type != config.childType) {
+        this.plotsDiv[chart.type].style("display", "none");
+        this.plotsControlsDiv[chart.type].style("display", "none");
+      }
+    }
+    this.plotsDiv[config.childType].style("display", "");
+    this.plotsControlsDiv[config.childType].style("display", "");
+    if (this.dom.header) {
+      if (config.tw) this.dom.header.title.text(config.tw.term.name);
+      if (config.headerText) this.dom.header.title.text(config.headerText);
+      const typeStr = termType2label(config.termType).toUpperCase();
+      this.dom.header.plot.text(` DIFFERENTIAL ${typeStr} ANALYSIS`);
+    }
+    if (this.plotTabs) this.plotTabs.update(config);
+  }
+};
+var DiffAnalysisInit = getCompInit(DifferentialAnalysis);
+var componentInit = DiffAnalysisInit;
+function getPlotConfig(opts) {
+  if (!opts.termType) throw new Error(".termType is required");
+  if (!enabledTermTypes.has(opts.termType))
+    throw new Error(`termType = '${opts.termType}' not supported by Differential Analysis`);
+  const config = {
+    chartType: "differentialAnalysis",
+    childType: "volcano",
+    termType: opts.termType,
+    settings: {},
+    highlightedData: opts.highlightedData || [],
+    hidePlotFilter: true
+    //TODO: Support filtering and reactivity in child plots
+  };
+  if (opts?.tw?.term?.name && opts.headerText)
+    throw new Error("Cannot provide both tw.term.name and headerText. Please choose one to use as the plot title.");
+  if (opts.termType == SINGLECELL_CELLTYPE) {
+    Object.assign(config, {
+      categoryName: opts.categoryName || "",
+      termId: opts.termId || "",
+      sample: opts.sample || { sID: "", eID: "" }
+    });
+  }
+  config.settings.volcano = getDefaultVolcanoSettings(opts.overrides, opts);
+  config.settings.gsea = getDefaultGseaSettings(opts.overrides, opts);
+  validateVolcanoSettings(config, opts);
+  return copyMerge(config, opts);
+}
+export {
+  DiffAnalysisInit,
+  componentInit,
+  getPlotConfig
+};
+//# sourceMappingURL=DifferentialAnalysis-SETJAZEN.js.map

package/dist/DifferentialAnalysis-SETJAZEN.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/diffAnalysis/view/DiffAnalysisView.ts", "../plots/diffAnalysis/DifferentialAnalysis.ts"],
+  "sourcesContent": ["import type { MassAppApi } from '#mass/types/mass'\nimport { Tabs, type RenderedTab } from '#dom'\nimport type { DiffAnalysisDom, DiffAnalysisPlotConfig } from '../DiffAnalysisTypes'\nimport { PROTEOME_DAP } from '#types'\n\nexport class DiffAnalysisView {\n\tapp: MassAppApi\n\tconfig: DiffAnalysisPlotConfig\n\tdom: DiffAnalysisDom\n\ttabs: Tabs\n\ttabsData: RenderedTab[]\n\tgetTabsOptions: any\n\tconstructor(app: MassAppApi, config: DiffAnalysisPlotConfig, dom: DiffAnalysisDom) {\n\t\tthis.app = app\n\t\tthis.config = config\n\t\tthis.dom = dom\n\t\tsetRenderers(this)\n\t\tthis.tabsData = this.getTabsOptions(this)\n\t\tthis.tabs = new Tabs({ holder: this.dom.tabsDiv, tabs: this.tabsData })\n\t\tthis.tabs.main()\n\t}\n\n\tupdate(plotConfig) {\n\t\tconst activeTabIndex = this.tabsData.findIndex(tab => tab.id == plotConfig.childType)\n\t\tthis.tabs.update(activeTabIndex)\n\t}\n}\n\nfunction setRenderers(self) {\n\tself.getTabsOptions = self => {\n\t\tconst tabs = [\n\t\t\t{\n\t\t\t\tactive: self.config.childType === 'volcano',\n\t\t\t\tid: 'volcano',\n\t\t\t\tlabel: 'Volcano',\n\t\t\t\tisVisible: () => true,\n\t\t\t\t// isVisible: () => self.config.termType === TermTypes.GENE_EXPRESSION,\n\t\t\t\tgetPlotConfig: () => {\n\t\t\t\t\treturn {\n\t\t\t\t\t\tchildType: 'volcano'\n\t\t\t\t\t}\n\t\t\t\t},\n\t\t\t\tcallback: self.tabCallback\n\t\t\t},\n\t\t\t{\n\t\t\t\tactive: self.config.childType === 'gsea',\n\t\t\t\tid: 'gsea',\n\t\t\t\tlabel: 'Gene Set Enrichment Analysis',\n\t\t\t\tisVisible: () => self.config.termType !== PROTEOME_DAP,\n\t\t\t\t// isVisible: () => self.config.termType === TermTypes.GENE_EXPRESSION,\n\t\t\t\tgetPlotConfig: () => {\n\t\t\t\t\treturn {\n\t\t\t\t\t\tchildType: 'gsea'\n\t\t\t\t\t}\n\t\t\t\t},\n\t\t\t\tcallback: self.tabCallback\n\t\t\t}\n\t\t]\n\t\treturn tabs\n\t}\n\n\tself.tabCallback = async (event, tab) => {\n\t\t/** When loading a mass session file, the callback for the\n\t\t * tab will trigger before the plot component is initialized.\n\t\t * check for the event before triggering an app.dispatch.*/\n\t\tif (!event || !tab || !tab.id) return\n\t\tconst plotConfig = tab.getPlotConfig()\n\t\tawait self.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: self.config.id,\n\t\t\tconfig: plotConfig\n\t\t})\n\t}\n}\n", "import type { BasePlotConfig, MassState } from '#mass/types/mass'\nimport type { Div } from '../../types/d3'\nimport { getCompInit, copyMerge, type RxComponent } from '#rx'\nimport { PlotBase } from '../PlotBase'\nimport { importPlot } from '../importPlot.js'\nimport { Menu } from '#dom'\nimport { termType2label } from '#shared/terms.js'\nimport type { DiffAnalysisDom, /*DiffAnalysisOpts,*/ DiffAnalysisPlotConfig } from './DiffAnalysisTypes'\nimport { DiffAnalysisView } from './view/DiffAnalysisView'\nimport { getDefaultVolcanoSettings, validateVolcanoSettings } from '../volcano/settings/defaults.ts'\nimport { getDefaultGseaSettings } from '#plots/gsea/settings/defaults.ts'\nimport { DATermTypes, enabledTermTypes } from './enabledTermTypes'\n\nconst { SINGLECELL_CELLTYPE } = DATermTypes\n\nclass DifferentialAnalysis extends PlotBase implements RxComponent {\n\tstatic type = 'differentialAnalysis'\n\treadonly type = 'differentialAnalysis'\n\tcomponents: {\n\t\tplots: { [key: string]: any }\n\t}\n\tdom: DiffAnalysisDom\n\tparentId?: string\n\tplotTabs?: DiffAnalysisView\n\tplotsDiv: { [key: string]: Div }\n\tplotsControlsDiv: { [key: string]: Div }\n\ttermType: string\n\n\tconstructor(opts: any, api) {\n\t\tsuper(opts, api)\n\t\tthis.components = {\n\t\t\tplots: {}\n\t\t}\n\t\tthis.termType = opts.termType\n\t\tconst holder = opts.holder.classed('sjpp-diff-analysis-main', true)\n\t\tconst controls = opts.controls ? holder : holder.append('div')\n\t\tconst div = holder\n\t\t\t.append('div')\n\t\t\t.style('padding', '5px')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('vertical-align', 'top')\n\t\tconst tabsDiv = div.append('div').attr('id', 'sjpp-diff-analysis-tabs').style('display', 'inline-block')\n\t\tconst plots = div.append('div').attr('id', 'sjpp-diff-analysis-tabs-content')\n\t\tthis.dom = {\n\t\t\tcontrols: controls.style('display', 'inline-block'),\n\t\t\tdiv,\n\t\t\ttabsDiv,\n\t\t\tplots: plots,\n\t\t\ttip: new Menu({ padding: '' })\n\t\t}\n\t\tthis.plotsControlsDiv = {}\n\t\tthis.plotsDiv = {}\n\n\t\tif (opts.parentId) this.parentId = opts.parentId\n\n\t\tif (opts.header) {\n\t\t\tthis.dom.header = {\n\t\t\t\ttitle: opts.header.append('span').style('margin-right', '5px').style('color', 'darkslategray'),\n\t\t\t\tplot: opts.header.append('span').style('font-size', '0.7em').style('opacity', 0.6)\n\t\t\t}\n\t\t}\n\t}\n\n\tgetState(appState: MassState) {\n\t\tconst config = appState.plots.find((p: BasePlotConfig) => p.id === this.id)\n\t\tif (!config) {\n\t\t\tthrow new Error(\n\t\t\t\t`No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`\n\t\t\t)\n\t\t}\n\t\treturn {\n\t\t\tconfig\n\t\t}\n\t}\n\n\treactsTo(action) {\n\t\tif (action.type.includes('cache_termq')) return true\n\t\tif (action.type.startsWith('plot_')) {\n\t\t\treturn action.id === this.id || action.id == this.parentId\n\t\t}\n\t\tif (action.type.startsWith('filter')) return true\n\t\tif (action.type.startsWith('cohort')) return true\n\t\tif (action.type == 'app_refresh') return true\n\t}\n\n\tasync init(appState: MassState) {\n\t\tconst state = this.getState(appState)\n\t\tconst config = structuredClone(state.config) as DiffAnalysisPlotConfig\n\n\t\tthis.plotTabs = new DiffAnalysisView(this.app, config, this.dom)\n\t}\n\n\tasync setComponent(config: DiffAnalysisPlotConfig) {\n\t\tthis.plotsControlsDiv[config.childType] = this.dom.controls.append('div')\n\t\tthis.plotsDiv[config.childType] = this.dom.plots.append('div')\n\t\tconst opts = {\n\t\t\tapp: this.app,\n\t\t\tholder: this.plotsDiv[config.childType],\n\t\t\tid: this.id,\n\t\t\tparent: this.api,\n\t\t\tcontrols: this.plotsControlsDiv[config.childType],\n\t\t\ttermType: config.termType\n\t\t}\n\t\tconst _ = await importPlot(config.childType, `unsupported childType='${config.childType}'`)\n\t\tthis.components.plots[config.childType] = await _.componentInit(opts)\n\t}\n\n\tasync main() {\n\t\tconst config = structuredClone(this.state.config)\n\t\tif (config.chartType != this.type) return\n\n\t\t//TODO: Change to use parentId instead\n\t\tif (!this.components.plots[config.childType]) await this.setComponent(config)\n\n\t\tfor (const childType in this.components.plots) {\n\t\t\tconst chart = this.components.plots[childType]\n\t\t\tif (chart.type != config.childType) {\n\t\t\t\tthis.plotsDiv[chart.type].style('display', 'none')\n\t\t\t\tthis.plotsControlsDiv[chart.type].style('display', 'none')\n\t\t\t}\n\t\t}\n\t\tthis.plotsDiv[config.childType].style('display', '')\n\t\tthis.plotsControlsDiv[config.childType].style('display', '')\n\n\t\tif (this.dom.header) {\n\t\t\tif (config.tw) this.dom.header.title.text(config.tw.term.name)\n\t\t\tif (config.headerText) this.dom.header.title.text(config.headerText)\n\t\t\tconst typeStr = termType2label(config.termType).toUpperCase()\n\t\t\tthis.dom.header.plot.text(` DIFFERENTIAL ${typeStr} ANALYSIS`)\n\t\t}\n\n\t\tif (this.plotTabs) this.plotTabs.update(config)\n\t}\n}\n\nexport const DiffAnalysisInit = getCompInit(DifferentialAnalysis)\nexport const componentInit = DiffAnalysisInit\n\nexport function getPlotConfig(opts: any) {\n\tif (!opts.termType) throw new Error('.termType is required')\n\tif (!enabledTermTypes.has(opts.termType))\n\t\tthrow new Error(`termType = '${opts.termType}' not supported by Differential Analysis`)\n\n\tconst config = {\n\t\tchartType: 'differentialAnalysis',\n\t\tchildType: 'volcano',\n\t\ttermType: opts.termType,\n\t\tsettings: {},\n\t\thighlightedData: opts.highlightedData || [],\n\t\thidePlotFilter: true //TODO: Support filtering and reactivity in child plots\n\t} as any\n\n\tif (opts?.tw?.term?.name && opts.headerText)\n\t\tthrow new Error('Cannot provide both tw.term.name and headerText. Please choose one to use as the plot title.')\n\n\t/** TODO: Fix this config. This only applies to the\n\t * gdc and won't work long term for terms */\n\tif (opts.termType == SINGLECELL_CELLTYPE) {\n\t\tObject.assign(config, {\n\t\t\tcategoryName: opts.categoryName || '',\n\t\t\ttermId: opts.termId || '',\n\t\t\tsample: opts.sample || { sID: '', eID: '' }\n\t\t})\n\t}\n\t\n\tconfig.settings.volcano = getDefaultVolcanoSettings(opts.overrides, opts)\n\tconfig.settings.gsea = getDefaultGseaSettings(opts.overrides, opts)\n\n\tvalidateVolcanoSettings(config, opts)\n\n\treturn copyMerge(config, opts)\n}\n"],
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