@sjcrh/proteinpaint-client 2.184.0 → 2.185.0

package/dist/DE-NLGMZ44O.js

@@ -0,0 +1,93 @@
+import {
+  appInit
+} from "./chunk-QEWMCAJW.js";
+import "./chunk-JMJW3ERE.js";
+import "./chunk-SKMFMGCD.js";
+import "./chunk-3T2PCWII.js";
+import "./chunk-YQVEBFGT.js";
+import "./chunk-3JAC5CHL.js";
+import "./chunk-EBGX226R.js";
+import "./chunk-UVPAZM3G.js";
+import "./chunk-MHCTLVGE.js";
+import "./chunk-ZT3PB4XX.js";
+import "./chunk-HZETQJGD.js";
+import "./chunk-PRZWSBMA.js";
+import "./chunk-YWUVCXFS.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-3QBZ2Y77.js";
+import "./chunk-HYOEWQ5P.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-G6O3URDN.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-KWM6B3NL.js";
+import "./chunk-UCLS2SVB.js";
+import "./chunk-6ZCHECOT.js";
+import "./chunk-MVTCBVSX.js";
+import "./chunk-2K5DSRBJ.js";
+import "./chunk-X4NI4JLQ.js";
+import "./chunk-L4QG7XZE.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-UWYCEYML.js";
+import "./chunk-7UHUOC6F.js";
+import "./chunk-ZYY54HBU.js";
+import "./chunk-EGWVYY7K.js";
+import "./chunk-AMYSEKPF.js";
+import "./chunk-TV74I3Y5.js";
+import "./chunk-KSGA62R2.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-TOU7EVFQ.js";
+import "./chunk-OAWQ6LOO.js";
+import "./chunk-KYBIQBXE.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-HFNDKYVF.js";
+
+// gdc/DE.ts
+async function init(arg, holder, genomes) {
+  const useGenome = arg.genome || "hg38";
+  const useDslabel = arg.dslabel || "GDC";
+  const genome = genomes[useGenome];
+  const massApi = await appInit({
+    //debug: arg.debugmode, // is debug accepted?
+    genome,
+    holder,
+    state: {
+      genome: useGenome,
+      dslabel: useDslabel,
+      termfilter: { filter0: arg.filter0 },
+      nav: { activeTab: 1, header_mode: "hidden" },
+      plots: [{ chartType: "DEinput" }]
+    },
+    opts: Object.assign(
+      {
+        // todo additional customizations
+        // dictionary:{header:'Select a variable to build Correlation Plot'}
+        // some way to make gene exp violin/boxplot to use log scale by default, but numeric dict term should not
+      },
+      arg.opts || {}
+    ),
+    app: arg.opts?.app || {}
+  });
+  const api = {
+    update: async (updateArg) => {
+      if (!massApi) return;
+      if ("filter0" in updateArg) {
+        massApi.dispatch({
+          type: "app_refresh",
+          subactions: [
+            {
+              type: "filter_replace",
+              filter0: updateArg.filter0
+            }
+          ]
+        });
+      }
+    },
+    triggerAbort: (reason = "") => massApi.triggerAbort(reason)
+  };
+  return api;
+}
+export {
+  init
+};
+//# sourceMappingURL=DE-NLGMZ44O.js.map

package/dist/DEinput-OJ7P4UMP.js

@@ -0,0 +1,297 @@
+import {
+  PlotBase,
+  excludeFilterByTag,
+  filterInit,
+  filterJoin,
+  filterPromptInit,
+  getNormalRoot,
+  negateFilter,
+  renderPreAnalysisData,
+  renderTable
+} from "./chunk-YWUVCXFS.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-3QBZ2Y77.js";
+import "./chunk-HYOEWQ5P.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-G6O3URDN.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-KWM6B3NL.js";
+import "./chunk-UCLS2SVB.js";
+import {
+  dofetch3
+} from "./chunk-6ZCHECOT.js";
+import {
+  copyMerge,
+  getCompInit
+} from "./chunk-MVTCBVSX.js";
+import "./chunk-2K5DSRBJ.js";
+import "./chunk-X4NI4JLQ.js";
+import "./chunk-L4QG7XZE.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-UWYCEYML.js";
+import "./chunk-7UHUOC6F.js";
+import "./chunk-ZYY54HBU.js";
+import "./chunk-EGWVYY7K.js";
+import {
+  getColors
+} from "./chunk-AMYSEKPF.js";
+import "./chunk-TV74I3Y5.js";
+import "./chunk-KSGA62R2.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-TOU7EVFQ.js";
+import "./chunk-OAWQ6LOO.js";
+import "./chunk-KYBIQBXE.js";
+import "./chunk-I6Y4O3RR.js";
+import {
+  rgb
+} from "./chunk-OMR2DT66.js";
+import "./chunk-HFNDKYVF.js";
+
+// plots/DEinput.ts
+var colorScale = getColors(5);
+var DEinputPlot = class _DEinputPlot extends PlotBase {
+  constructor(opts, api) {
+    super(opts, api);
+    this.components = {};
+    this.type = _DEinputPlot.type;
+    this.opts = opts;
+    this.dom = this.getDom();
+    this.groups = [];
+  }
+  static {
+    this.type = "DEinput";
+  }
+  getDom() {
+    const header = this.opts?.header?.html("Differential Gene Expression") || void 0;
+    const holder = this.opts.holder.append("div").style("margin", "10px");
+    const table = holder.append("div");
+    const btns = holder.append("div").style("margin-top", "5px");
+    const addGroup = btns.append("div").style("display", "inline-block");
+    const submit = btns.append("div").style("display", "none").style("margin-left", "15px").attr("class", "sja_new_filter_btn sja_menuoption");
+    const loading = holder.append("div").style("display", "none").style("margin", "20px 10px").text("Loading...");
+    const preAnalysis = holder.append("div").style("display", "none").style("margin-top", "20px").style("margin-left", "5px");
+    const dom = { header, table, addGroup, submit, loading, preAnalysis };
+    return dom;
+  }
+  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 init() {
+  }
+  // TODO: handle errors
+  async main() {
+    this.dom.preAnalysis.selectAll("*").remove();
+    this.makeGroupsUI();
+    this.mayRenderSubmit();
+  }
+  async makeGroupsUI() {
+    if (!this.filterPrompt) {
+      this.filterPrompt = await filterPromptInit({
+        holder: this.dom.addGroup,
+        vocabApi: this.app.vocabApi,
+        emptyLabel: "Add group",
+        header_mode: "hide_search",
+        callback: async (f) => {
+          const filter2 = getNormalRoot(f);
+          this.addNewGroup(filter2, this.groups);
+          await this.main();
+        },
+        debug: this.opts.debug
+      });
+    }
+    const filter = structuredClone(this.state.termfilter.filter);
+    this.filterPrompt.main(excludeFilterByTag(filter, "cohortFilter"));
+    if (!this.groups.length) {
+      this.dom.table.style("display", "none");
+      return;
+    }
+    this.dom.table.style("display", "block").selectAll("*").remove();
+    const tableArg = {
+      div: this.dom.table,
+      columns: [
+        {},
+        // blank column to add delete buttons
+        {
+          label: "NAME",
+          editCallback: async (i, cell) => {
+            const newName = cell.value;
+            const index = this.groups.findIndex((group) => group.name == newName);
+            if (index != -1) {
+              alert(`Group named ${newName} already exists`);
+              await this.main();
+            } else {
+              this.groups[i].name = newName;
+              await this.main();
+            }
+          }
+        },
+        {
+          label: "COLOR",
+          editCallback: async (i, cell) => {
+            this.groups[i].color = cell.color;
+            this.main();
+          }
+        },
+        //{ label: '#SAMPLE' }, // will re-enable when filtered sample count can be supported for gdc
+        { label: "FILTER" }
+      ],
+      rows: [],
+      striped: false,
+      // no alternating row bg color so delete button appears more visible
+      showLines: false
+    };
+    for (const g of this.groups) {
+      tableArg.rows.push([
+        {},
+        // blank cell to add delete button
+        { value: g.name },
+        // to allow click to show <input>
+        { color: g.color },
+        // { value: 'n=' + (await self.vocabApi.getFilteredSampleCount(g.filter)) }, // will re-enable when filtered sample count can be supported for gdc
+        {}
+        // blank cell to show filter ui
+      ]);
+    }
+    renderTable(tableArg);
+    for (const [i, row] of tableArg.rows.entries()) {
+      row[0].__td.append("div").attr("class", "sja_menuoption").style("padding", "1px 6px").html("&times;").on("click", () => {
+        this.groups.splice(i, 1);
+        this.main();
+      });
+      const group = this.groups[i];
+      filterInit({
+        holder: row[3].__td,
+        vocabApi: this.app.vocabApi,
+        header_mode: "hide_search",
+        callback: (f) => {
+          if (!f || f.lst.length == 0) {
+            const i2 = this.groups.findIndex((g) => g.name == group.name);
+            this.groups.splice(i2, 1);
+          } else {
+            group.filter = f;
+          }
+          this.main();
+        }
+      }).main(group.filter);
+    }
+    this.dom.addGroup.select(".sja_new_filter_btn").style("pointer-events", "auto").style("opacity", 1);
+  }
+  addNewGroup(filter, groups, name) {
+    if (!groups) throw "groups is missing";
+    if (!name) {
+      const base = "New group";
+      name = base;
+      for (let i = 0; ; i++) {
+        name = base + (i === 0 ? "" : " " + i);
+        if (!groups.find((g) => g.name === name)) break;
+      }
+    }
+    const newGroup = {
+      name,
+      filter,
+      color: rgb(colorScale(groups.length)).formatHex()
+    };
+    groups.push(newGroup);
+  }
+  mayRenderSubmit() {
+    if (!this.groups.length) {
+      this.dom.submit.style("display", "none");
+      return;
+    }
+    this.dom.submit.style("display", "inline-block");
+    if (this.groups.length == 1) {
+      this.dom.submit.text(`Submit (${this.groups[0].name} vs others)`);
+      this.dom.submit.on("click", async () => {
+        const groups = [this.groups[0]];
+        const otherGroup = {
+          name: "Not in " + groups[0].name,
+          color: "#ccc",
+          filter: negateFilter(groups[0].filter)
+        };
+        groups.push(otherGroup);
+        await this.clickSubmit(groups);
+      });
+    } else if (this.groups.length == 2) {
+      this.dom.addGroup.select(".sja_new_filter_btn").style("pointer-events", "none").style("opacity", 0.5);
+      this.dom.submit.text(`Submit (${this.groups[0].name} vs ${this.groups[1].name})`);
+      this.dom.submit.on("click", async () => {
+        await this.clickSubmit(this.groups);
+      });
+    } else {
+      throw new Error("cannot exceed 2 groups");
+    }
+  }
+  async clickSubmit(groups) {
+    this.dom.loading.style("display", "block");
+    const samplelstTW = {
+      q: { groups: [] },
+      term: {
+        name: groups.map((g) => g.name).join(" vs "),
+        type: "samplelst",
+        values: {}
+      }
+    };
+    for (const g of groups) {
+      const samples = await this.app.vocabApi.getFilteredSampleList(
+        filterJoin([g.filter, this.state.termfilter.filter])
+      );
+      const sampleIds = samples.map((s) => {
+        return { sampleId: s };
+      });
+      samplelstTW.q.groups.push({
+        name: g.name,
+        in: true,
+        values: sampleIds
+      });
+      samplelstTW.term.values[g.name] = {
+        color: g.color,
+        key: g.name,
+        label: g.name,
+        list: sampleIds
+      };
+    }
+    const body = {
+      genome: this.app.vocabApi.vocab.genome,
+      dslabel: this.app.vocabApi.vocab.dslabel,
+      samplelst: { groups: samplelstTW.q.groups },
+      filter: this.state.termfilter.filter,
+      filter0: this.state.termfilter.filter0,
+      preAnalysis: true
+    };
+    const preAnalysisData = await dofetch3("termdb/DE", { body });
+    this.dom.loading.style("display", "none");
+    this.dom.preAnalysis.style("display", "block");
+    this.dom.preAnalysis.append("div").style("font-weight", "bold").text("Samples with gene expression data:");
+    renderPreAnalysisData({
+      preAnalysisData,
+      samplelstTW,
+      groups: samplelstTW.q.groups,
+      holder: this.dom.preAnalysis,
+      self: this
+    });
+  }
+};
+var DEinputInit = getCompInit(DEinputPlot);
+var componentInit = DEinputInit;
+async function getPlotConfig(opts) {
+  const config = {
+    chartType: "DEinput",
+    settings: {}
+  };
+  return copyMerge(config, opts);
+}
+export {
+  DEinputInit,
+  componentInit,
+  getPlotConfig
+};
+//# sourceMappingURL=DEinput-OJ7P4UMP.js.map

package/dist/DifferentialAnalysis-G75VUHDI.js

@@ -0,0 +1,241 @@
+import {
+  getDefaultGseaSettings
+} from "./chunk-XVDWYTJ6.js";
+import "./chunk-3B7EWIVB.js";
+import {
+  PlotBase,
+  Tabs,
+  getDefaultVolcanoSettings,
+  validateVolcanoSettings
+} from "./chunk-YWUVCXFS.js";
+import "./chunk-HJ6L54YS.js";
+import {
+  importPlot
+} from "./chunk-3QBZ2Y77.js";
+import {
+  Menu
+} from "./chunk-HYOEWQ5P.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-G6O3URDN.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-KWM6B3NL.js";
+import "./chunk-UCLS2SVB.js";
+import "./chunk-6ZCHECOT.js";
+import {
+  copyMerge,
+  getCompInit
+} from "./chunk-MVTCBVSX.js";
+import "./chunk-2K5DSRBJ.js";
+import "./chunk-X4NI4JLQ.js";
+import "./chunk-L4QG7XZE.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-UWYCEYML.js";
+import "./chunk-7UHUOC6F.js";
+import "./chunk-ZYY54HBU.js";
+import {
+  DNA_METHYLATION,
+  GENE_EXPRESSION,
+  SINGLECELL_CELLTYPE,
+  termType2label
+} from "./chunk-EGWVYY7K.js";
+import "./chunk-AMYSEKPF.js";
+import "./chunk-TV74I3Y5.js";
+import "./chunk-KSGA62R2.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-TOU7EVFQ.js";
+import "./chunk-OAWQ6LOO.js";
+import "./chunk-KYBIQBXE.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-OMR2DT66.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: () => true,
+        // 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 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 ${typeStr} ANALYSIS`);
+    }
+    if (this.plotTabs) this.plotTabs.update(config);
+  }
+};
+var DiffAnalysisInit = getCompInit(DifferentialAnalysis);
+var componentInit = DiffAnalysisInit;
+var enabledTermTypes = [GENE_EXPRESSION, SINGLECELL_CELLTYPE, DNA_METHYLATION];
+function getPlotConfig(opts) {
+  if (!opts.termType) throw new Error(".termType is required");
+  if (!enabledTermTypes.includes(opts.termType))
+    throw new Error(`termType = '${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);
+  validateVolcanoSettings(config, opts);
+  return copyMerge(config, opts);
+}
+export {
+  DiffAnalysisInit,
+  componentInit,
+  getPlotConfig
+};
+//# sourceMappingURL=DifferentialAnalysis-G75VUHDI.js.map

package/dist/DifferentialAnalysis-G75VUHDI.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'\n// import { TermTypes } from '#shared/terms.js'\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: () => 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: '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 { GENE_EXPRESSION, termType2label, SINGLECELL_CELLTYPE, DNA_METHYLATION } 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.js'\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 ${typeStr} ANALYSIS`)\n\t\t}\n\n\t\tif (this.plotTabs) this.plotTabs.update(config)\n\t}\n}\n\nexport const DiffAnalysisInit = getCompInit(DifferentialAnalysis)\nexport const componentInit = DiffAnalysisInit\n\n//Use this as a sanity check.\nconst enabledTermTypes = [GENE_EXPRESSION, SINGLECELL_CELLTYPE, DNA_METHYLATION]\n\nexport function getPlotConfig(opts: any) {\n\tif (!opts.termType) throw new Error('.termType is required')\n\tif (!enabledTermTypes.includes(opts.termType))\n\t\tthrow new Error(`termType = '${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\n\tconfig.settings.volcano = getDefaultVolcanoSettings(opts.overrides, opts)\n\tconfig.settings.gsea = getDefaultGseaSettings(opts.overrides)\n\n\tvalidateVolcanoSettings(config, opts)\n\n\treturn copyMerge(config, opts)\n}\n"],
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