@sjcrh/proteinpaint-client 2.181.0 → 2.182.0

package/dist/DE-2J2SK5UT.js

@@ -0,0 +1,93 @@
+import {
+  appInit
+} from "./chunk-OUKDZKSZ.js";
+import "./chunk-KVG7FTTK.js";
+import "./chunk-SKMFMGCD.js";
+import "./chunk-AZYDW5T7.js";
+import "./chunk-GW7DHJYH.js";
+import "./chunk-MXI3NXRB.js";
+import "./chunk-2OSEZCWZ.js";
+import "./chunk-UBGTQMOO.js";
+import "./chunk-TN5GSG34.js";
+import "./chunk-LUTT3MBZ.js";
+import "./chunk-HZETQJGD.js";
+import "./chunk-PRZWSBMA.js";
+import "./chunk-7FEHI46K.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-XD6BFNMR.js";
+import "./chunk-2SRMRC6L.js";
+import "./chunk-TCPU43TU.js";
+import "./chunk-XDI4UFCZ.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-5EF5U7MX.js";
+import "./chunk-IQIXGTQV.js";
+import "./chunk-UCLS2SVB.js";
+import "./chunk-MVTCBVSX.js";
+import "./chunk-F6V4AYWP.js";
+import "./chunk-5OHXYXLD.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-DVDDXOWT.js";
+import "./chunk-6MSCYO7K.js";
+import "./chunk-22NJUYET.js";
+import "./chunk-MDL2HG3N.js";
+import "./chunk-IGEQI6MR.js";
+import "./chunk-BEWDIM6H.js";
+import "./chunk-IH7ILDJS.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-TOU7EVFQ.js";
+import "./chunk-OAWQ6LOO.js";
+import "./chunk-SEEYV6P2.js";
+import "./chunk-NDWTN4U5.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-2J2SK5UT.js.map

package/dist/DE-2J2SK5UT.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../gdc/DE.ts"],
+  "sourcesContent": ["import { appInit } from '#mass/app'\n\n/*\nlaunches submission UI for differental gene expression\n*/\n\ninterface InitArg {\n\tdebugmode?: true\n\tgenome?: string\n\tdslabel?: string\n\tfilter0?: object\n\tstate?: {\n\t\tplots?: Array<{ chartType: string; [key: string]: any }>\n\t}\n\topts?: {\n\t\tapp?: Record<string, any>\n\t}\n}\n\ninterface UpdateArg {\n\tfilter0?: object\n\t[key: string]: any\n}\n\nexport async function init(\n\targ: InitArg,\n\tholder: HTMLElement,\n\tgenomes: any\n): Promise<{ update: (updateArg: UpdateArg) => Promise<void> }> {\n\tconst useGenome = arg.genome || 'hg38'\n\tconst useDslabel = arg.dslabel || 'GDC'\n\tconst genome = genomes[useGenome]\n\tconst massApi = await appInit({\n\t\t//debug: arg.debugmode, // is debug accepted?\n\t\tgenome,\n\t\tholder,\n\t\tstate: {\n\t\t\tgenome: useGenome,\n\t\t\tdslabel: useDslabel,\n\t\t\ttermfilter: { filter0: arg.filter0 },\n\t\t\tnav: { activeTab: 1, header_mode: 'hidden' },\n\t\t\tplots: [{ chartType: 'DEinput' }]\n\t\t},\n\t\topts: Object.assign(\n\t\t\t{\n\t\t\t\t// todo additional customizations\n\t\t\t\t// dictionary:{header:'Select a variable to build Correlation Plot'}\n\t\t\t\t// some way to make gene exp violin/boxplot to use log scale by default, but numeric dict term should not\n\t\t\t},\n\t\t\targ.opts || {}\n\t\t),\n\t\tapp: arg.opts?.app || {}\n\t})\n\tconst api = {\n\t\tupdate: async (updateArg: UpdateArg) => {\n\t\t\tif (!massApi) return\n\n\t\t\t// NOTE: changes inside the mass app (nav tabs, sandbox, etc) are handled internally\n\t\t\t// within the mass app instance; only embedder portal-dispatched changes, such as filter0,\n\t\t\t// should be handled below\n\n\t\t\tif ('filter0' in updateArg) {\n\t\t\t\tmassApi.dispatch({\n\t\t\t\t\ttype: 'app_refresh',\n\t\t\t\t\tsubactions: [\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\ttype: 'filter_replace',\n\t\t\t\t\t\t\tfilter0: updateArg.filter0\n\t\t\t\t\t\t}\n\t\t\t\t\t]\n\t\t\t\t})\n\t\t\t}\n\t\t},\n\t\ttriggerAbort: (reason = '') => massApi.triggerAbort(reason)\n\t}\n\n\treturn api\n}\n"],
+  "mappings": ";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAwBA,eAAsB,KACrB,KACA,QACA,SAC+D;AAC/D,QAAM,YAAY,IAAI,UAAU;AAChC,QAAM,aAAa,IAAI,WAAW;AAClC,QAAM,SAAS,QAAQ,SAAS;AAChC,QAAM,UAAU,MAAM,QAAQ;AAAA;AAAA,IAE7B;AAAA,IACA;AAAA,IACA,OAAO;AAAA,MACN,QAAQ;AAAA,MACR,SAAS;AAAA,MACT,YAAY,EAAE,SAAS,IAAI,QAAQ;AAAA,MACnC,KAAK,EAAE,WAAW,GAAG,aAAa,SAAS;AAAA,MAC3C,OAAO,CAAC,EAAE,WAAW,UAAU,CAAC;AAAA,IACjC;AAAA,IACA,MAAM,OAAO;AAAA,MACZ;AAAA;AAAA;AAAA;AAAA,MAIA;AAAA,MACA,IAAI,QAAQ,CAAC;AAAA,IACd;AAAA,IACA,KAAK,IAAI,MAAM,OAAO,CAAC;AAAA,EACxB,CAAC;AACD,QAAM,MAAM;AAAA,IACX,QAAQ,OAAO,cAAyB;AACvC,UAAI,CAAC,QAAS;AAMd,UAAI,aAAa,WAAW;AAC3B,gBAAQ,SAAS;AAAA,UAChB,MAAM;AAAA,UACN,YAAY;AAAA,YACX;AAAA,cACC,MAAM;AAAA,cACN,SAAS,UAAU;AAAA,YACpB;AAAA,UACD;AAAA,QACD,CAAC;AAAA,MACF;AAAA,IACD;AAAA,IACA,cAAc,CAAC,SAAS,OAAO,QAAQ,aAAa,MAAM;AAAA,EAC3D;AAEA,SAAO;AACR;",
+  "names": []
+}

package/dist/DEinput-QM3GOQHM.js

@@ -0,0 +1,297 @@
+import {
+  PlotBase,
+  excludeFilterByTag,
+  filterInit,
+  filterJoin,
+  filterPromptInit,
+  getNormalRoot,
+  negateFilter,
+  renderPreAnalysisData,
+  renderTable
+} from "./chunk-7FEHI46K.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-XD6BFNMR.js";
+import "./chunk-2SRMRC6L.js";
+import {
+  dofetch3
+} from "./chunk-TCPU43TU.js";
+import "./chunk-XDI4UFCZ.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-5EF5U7MX.js";
+import "./chunk-IQIXGTQV.js";
+import "./chunk-UCLS2SVB.js";
+import {
+  copyMerge,
+  getCompInit
+} from "./chunk-MVTCBVSX.js";
+import "./chunk-F6V4AYWP.js";
+import "./chunk-5OHXYXLD.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-DVDDXOWT.js";
+import "./chunk-6MSCYO7K.js";
+import "./chunk-22NJUYET.js";
+import "./chunk-MDL2HG3N.js";
+import {
+  getColors
+} from "./chunk-IGEQI6MR.js";
+import "./chunk-BEWDIM6H.js";
+import "./chunk-IH7ILDJS.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-TOU7EVFQ.js";
+import "./chunk-OAWQ6LOO.js";
+import "./chunk-SEEYV6P2.js";
+import "./chunk-NDWTN4U5.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");
+    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-QM3GOQHM.js.map

package/dist/DEinput-QM3GOQHM.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/DEinput.ts"],
+  "sourcesContent": ["import { PlotBase } from './PlotBase.ts'\nimport { getCompInit, copyMerge, type ComponentApi, type RxComponent } from '#rx'\nimport {\n\tfilterInit,\n\tfilterPromptInit,\n\tgetNormalRoot,\n\texcludeFilterByTag,\n\tfilterJoin,\n\tnegateFilter\n} from '#filter/filter'\nimport { getColors } from '#shared/common.js'\nimport { rgb } from 'd3-color'\nimport { renderTable } from '#dom'\nimport { dofetch3 } from '#common/dofetch'\nimport { renderPreAnalysisData } from '#mass/groups'\n\nconst colorScale = getColors(5)\n\n// TODO: need to also consider filter0 whenever pp filter is considered\nclass DEinputPlot extends PlotBase implements RxComponent {\n\tstatic type = 'DEinput'\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\t// expected class-specific props\n\tconfig: any\n\tgroups: any[]\n\tfilterPrompt: any\n\n\tconstructor(opts, api) {\n\t\tsuper(opts, api)\n\t\tthis.type = DEinputPlot.type\n\t\tthis.opts = opts\n\t\tthis.dom = this.getDom()\n\t\tthis.groups = []\n\t}\n\n\tgetDom() {\n\t\tconst header = this.opts.header.html('Differential Gene Expression')\n\t\tconst holder = this.opts.holder.append('div').style('margin', '10px')\n\t\tconst table = holder.append('div')\n\t\tconst btns = holder.append('div').style('margin-top', '5px')\n\t\tconst addGroup = btns.append('div').style('display', 'inline-block')\n\t\tconst submit = btns\n\t\t\t.append('div')\n\t\t\t.style('display', 'none')\n\t\t\t.style('margin-left', '15px')\n\t\t\t.attr('class', 'sja_new_filter_btn sja_menuoption')\n\t\tconst loading = holder.append('div').style('display', 'none').style('margin', '20px 10px').text('Loading...')\n\t\tconst preAnalysis = holder\n\t\t\t.append('div')\n\t\t\t.style('display', 'none')\n\t\t\t.style('margin-top', '20px')\n\t\t\t.style('margin-left', '5px')\n\t\tconst dom = { header, table, addGroup, submit, loading, preAnalysis }\n\t\treturn dom\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 init() {}\n\n\t// TODO: handle errors\n\tasync main() {\n\t\tthis.dom.preAnalysis.selectAll('*').remove()\n\t\tthis.makeGroupsUI()\n\t\tthis.mayRenderSubmit()\n\t}\n\n\tasync makeGroupsUI() {\n\t\t// filter prompt\n\t\tif (!this.filterPrompt) {\n\t\t\tthis.filterPrompt = await filterPromptInit({\n\t\t\t\tholder: this.dom.addGroup,\n\t\t\t\tvocabApi: this.app.vocabApi,\n\t\t\t\temptyLabel: 'Add group',\n\t\t\t\theader_mode: 'hide_search',\n\t\t\t\tcallback: async f => {\n\t\t\t\t\tconst filter = getNormalRoot(f)\n\t\t\t\t\tthis.addNewGroup(filter, this.groups)\n\t\t\t\t\tawait this.main()\n\t\t\t\t},\n\t\t\t\tdebug: this.opts.debug\n\t\t\t})\n\t\t}\n\n\t\t// TODO: need to also consider filter0\n\t\t// filterPrompt.main() always empties the filterUiRoot data\n\t\tconst filter = structuredClone(this.state.termfilter.filter)\n\t\tthis.filterPrompt.main(excludeFilterByTag(filter, 'cohortFilter')) // provide mass filter to limit the term tree\n\n\t\tif (!this.groups.length) {\n\t\t\t// no groups, hide table\n\t\t\tthis.dom.table.style('display', 'none')\n\t\t\treturn\n\t\t}\n\n\t\t// clear table and populate rows\n\t\tthis.dom.table.style('display', 'block').selectAll('*').remove()\n\t\tconst tableArg: any = {\n\t\t\tdiv: this.dom.table,\n\t\t\tcolumns: [\n\t\t\t\t{}, // blank column to add delete buttons\n\t\t\t\t{\n\t\t\t\t\tlabel: 'NAME',\n\t\t\t\t\teditCallback: async (i, cell) => {\n\t\t\t\t\t\tconst newName = cell.value\n\t\t\t\t\t\tconst index = this.groups.findIndex(group => group.name == newName)\n\t\t\t\t\t\tif (index != -1) {\n\t\t\t\t\t\t\talert(`Group named ${newName} already exists`)\n\t\t\t\t\t\t\tawait this.main()\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\tthis.groups[i].name = newName\n\t\t\t\t\t\t\tawait this.main()\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\tlabel: 'COLOR',\n\t\t\t\t\teditCallback: async (i, cell) => {\n\t\t\t\t\t\tthis.groups[i].color = cell.color\n\t\t\t\t\t\tthis.main()\n\t\t\t\t\t}\n\t\t\t\t},\n\t\t\t\t//{ label: '#SAMPLE' }, // will re-enable when filtered sample count can be supported for gdc\n\t\t\t\t{ label: 'FILTER' }\n\t\t\t],\n\t\t\trows: [],\n\t\t\tstriped: false, // no alternating row bg color so delete button appears more visible\n\t\t\tshowLines: false\n\t\t}\n\n\t\tfor (const g of this.groups) {\n\t\t\ttableArg.rows.push([\n\t\t\t\t{}, // blank cell to add delete button\n\t\t\t\t{ value: g.name }, // to allow click to show <input>\n\t\t\t\t{ color: g.color },\n\t\t\t\t// { value: 'n=' + (await self.vocabApi.getFilteredSampleCount(g.filter)) }, // will re-enable when filtered sample count can be supported for gdc\n\t\t\t\t{} // blank cell to show filter ui\n\t\t\t])\n\t\t}\n\n\t\trenderTable(tableArg)\n\n\t\t// after rendering table, iterate over rows again to fill cells with control elements\n\t\tfor (const [i, row] of tableArg.rows.entries()) {\n\t\t\t// add delete button in 1st cell\n\t\t\trow[0].__td\n\t\t\t\t.append('div')\n\t\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t\t.style('padding', '1px 6px')\n\t\t\t\t.html('&times;')\n\t\t\t\t.on('click', () => {\n\t\t\t\t\tthis.groups.splice(i, 1)\n\t\t\t\t\tthis.main()\n\t\t\t\t})\n\n\t\t\t// create filter ui in its cell\n\t\t\tconst group = this.groups[i]\n\t\t\tfilterInit({\n\t\t\t\tholder: row[3].__td,\n\t\t\t\tvocabApi: this.app.vocabApi,\n\t\t\t\theader_mode: 'hide_search',\n\t\t\t\tcallback: f => {\n\t\t\t\t\tif (!f || f.lst.length == 0) {\n\t\t\t\t\t\t// blank filter (user removed last tvs from this filter), delete this element from groups[]\n\t\t\t\t\t\tconst i = this.groups.findIndex(g => g.name == group.name)\n\t\t\t\t\t\tthis.groups.splice(i, 1)\n\t\t\t\t\t} else {\n\t\t\t\t\t\t// update filter\n\t\t\t\t\t\tgroup.filter = f\n\t\t\t\t\t}\n\t\t\t\t\tthis.main()\n\t\t\t\t}\n\t\t\t}).main(group.filter)\n\t\t}\n\n\t\tthis.dom.addGroup.select('.sja_new_filter_btn').style('pointer-events', 'auto').style('opacity', 1)\n\t}\n\n\taddNewGroup(filter, groups, name?: string) {\n\t\tif (!groups) throw 'groups is missing'\n\t\tif (!name) {\n\t\t\tconst base = 'New group'\n\t\t\tname = base\n\t\t\tfor (let i = 0; ; i++) {\n\t\t\t\tname = base + (i === 0 ? '' : ' ' + i)\n\t\t\t\tif (!groups.find(g => g.name === name)) break\n\t\t\t}\n\t\t}\n\t\tconst newGroup = {\n\t\t\tname,\n\t\t\tfilter,\n\t\t\tcolor: rgb(colorScale(groups.length)).formatHex()\n\t\t}\n\t\tgroups.push(newGroup)\n\t}\n\n\tmayRenderSubmit() {\n\t\tif (!this.groups.length) {\n\t\t\tthis.dom.submit.style('display', 'none')\n\t\t\treturn\n\t\t}\n\t\tthis.dom.submit.style('display', 'inline-block')\n\t\tif (this.groups.length == 1) {\n\t\t\t// single group of samples, compare with all other samples\n\t\t\tthis.dom.submit.text(`Submit (${this.groups[0].name} vs others)`)\n\t\t\tthis.dom.submit.on('click', async () => {\n\t\t\t\tconst groups = [this.groups[0]]\n\t\t\t\tconst otherGroup = {\n\t\t\t\t\tname: 'Not in ' + groups[0].name,\n\t\t\t\t\tcolor: '#ccc',\n\t\t\t\t\tfilter: negateFilter(groups[0].filter)\n\t\t\t\t}\n\t\t\t\tgroups.push(otherGroup)\n\t\t\t\tawait this.clickSubmit(groups)\n\t\t\t})\n\t\t} else if (this.groups.length == 2) {\n\t\t\t// two groups of samples, compare these groups\n\t\t\tthis.dom.addGroup.select('.sja_new_filter_btn').style('pointer-events', 'none').style('opacity', 0.5)\n\t\t\tthis.dom.submit.text(`Submit (${this.groups[0].name} vs ${this.groups[1].name})`)\n\t\t\tthis.dom.submit.on('click', async () => {\n\t\t\t\tawait this.clickSubmit(this.groups)\n\t\t\t})\n\t\t} else {\n\t\t\tthrow new Error('cannot exceed 2 groups')\n\t\t}\n\t}\n\n\tasync clickSubmit(groups) {\n\t\tthis.dom.loading.style('display', 'block')\n\t\tconst samplelstTW: any = {\n\t\t\tq: { groups: [] },\n\t\t\tterm: {\n\t\t\t\tname: groups.map(g => g.name).join(' vs '),\n\t\t\t\ttype: 'samplelst',\n\t\t\t\tvalues: {}\n\t\t\t}\n\t\t}\n\t\tfor (const g of groups) {\n\t\t\tconst samples = await this.app.vocabApi.getFilteredSampleList(\n\t\t\t\tfilterJoin([g.filter, this.state.termfilter.filter])\n\t\t\t)\n\t\t\tconst sampleIds = samples.map(s => {\n\t\t\t\treturn { sampleId: s }\n\t\t\t})\n\t\t\tsamplelstTW.q.groups.push({\n\t\t\t\tname: g.name,\n\t\t\t\tin: true,\n\t\t\t\tvalues: sampleIds\n\t\t\t})\n\t\t\tsamplelstTW.term.values[g.name] = {\n\t\t\t\tcolor: g.color,\n\t\t\t\tkey: g.name,\n\t\t\t\tlabel: g.name,\n\t\t\t\tlist: sampleIds\n\t\t\t}\n\t\t}\n\n\t\t// get actual numbers of samples with rnaseq count\n\t\tconst body = {\n\t\t\tgenome: this.app.vocabApi.vocab.genome,\n\t\t\tdslabel: this.app.vocabApi.vocab.dslabel,\n\t\t\tsamplelst: { groups: samplelstTW.q.groups },\n\t\t\tfilter: this.state.termfilter.filter,\n\t\t\tfilter0: this.state.termfilter.filter0,\n\t\t\tpreAnalysis: true\n\t\t}\n\t\tconst preAnalysisData = await dofetch3('termdb/DE', { body })\n\n\t\tthis.dom.loading.style('display', 'none')\n\n\t\t// render sample counts\n\t\tthis.dom.preAnalysis.style('display', 'block')\n\t\tthis.dom.preAnalysis.append('div').style('font-weight', 'bold').text('Samples with gene expression data:')\n\n\t\trenderPreAnalysisData({\n\t\t\tpreAnalysisData,\n\t\t\tsamplelstTW,\n\t\t\tgroups: samplelstTW.q.groups,\n\t\t\tholder: this.dom.preAnalysis,\n\t\t\tself: this\n\t\t})\n\t}\n}\n\nexport const DEinputInit = getCompInit(DEinputPlot)\nexport const componentInit = DEinputInit\n\nexport async function getPlotConfig(opts) {\n\tconst config = {\n\t\tchartType: 'DEinput',\n\t\tsettings: {}\n\t}\n\n\t// may apply term-specific changes to the default object\n\treturn copyMerge(config, opts)\n}\n"],
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+  "names": ["filter", "i"]
+}

package/dist/DifferentialAnalysis-DS7CQOT6.js

@@ -0,0 +1,238 @@
+import {
+  getDefaultGseaSettings
+} from "./chunk-G6ELKVBG.js";
+import "./chunk-DHZL3FBC.js";
+import {
+  PlotBase,
+  Tabs,
+  getDefaultVolcanoSettings,
+  validateVolcanoSettings
+} from "./chunk-7FEHI46K.js";
+import "./chunk-HJ6L54YS.js";
+import {
+  importPlot
+} from "./chunk-XD6BFNMR.js";
+import {
+  Menu
+} from "./chunk-2SRMRC6L.js";
+import "./chunk-TCPU43TU.js";
+import "./chunk-XDI4UFCZ.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-5EF5U7MX.js";
+import "./chunk-IQIXGTQV.js";
+import "./chunk-UCLS2SVB.js";
+import {
+  copyMerge,
+  getCompInit
+} from "./chunk-MVTCBVSX.js";
+import "./chunk-F6V4AYWP.js";
+import "./chunk-5OHXYXLD.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-DVDDXOWT.js";
+import "./chunk-6MSCYO7K.js";
+import "./chunk-22NJUYET.js";
+import {
+  DNA_METHYLATION,
+  GENE_EXPRESSION,
+  SINGLECELL_CELLTYPE,
+  termType2label
+} from "./chunk-MDL2HG3N.js";
+import "./chunk-IGEQI6MR.js";
+import "./chunk-BEWDIM6H.js";
+import "./chunk-IH7ILDJS.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-TOU7EVFQ.js";
+import "./chunk-OAWQ6LOO.js";
+import "./chunk-SEEYV6P2.js";
+import "./chunk-NDWTN4U5.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 = {
+        terms: opts.header.append("span"),
+        title: opts.header.append("span").style("font-size", "0.8em").style("opacity", 0.7)
+      };
+    }
+  }
+  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.terms.text(config.tw.term.name);
+      const typeStr = termType2label(config.termType).toUpperCase();
+      this.dom.header.title.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.termType == SINGLECELL_CELLTYPE) {
+    Object.assign(config, {
+      categoryName: opts.categoryName || "",
+      termId: opts.termId || "",
+      sample: opts.sample || ""
+    });
+  }
+  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-DS7CQOT6.js.map