@sjcrh/proteinpaint-client 2.198.0 → 2.200.0

package/dist/chunk-3SHZTAGF.js

@@ -0,0 +1,193 @@
+import {
+  __glob
+} from "./chunk-HFNDKYVF.js";
+
+// import("../plots/**/*.js") in plots/importPlot.js
+var globImport_plots_js = __glob({
+  "../plots/barchart.data.js": () => import("./barchart.data-LSK2P2PR.js"),
+  "../plots/barchart.events.js": () => import("./barchart.events-Y4H2GADS.js"),
+  "../plots/barchart.js": () => import("./barchart-UHCTYRMJ.js"),
+  "../plots/bars.renderer.js": () => import("./bars.renderer-54UCFLJS.js"),
+  "../plots/bars.settings.js": () => import("./bars.settings-SDU7PZOS.js"),
+  "../plots/brainImaging.js": () => import("./brainImaging-D43CQQN6.js"),
+  "../plots/controls.btns.js": () => import("./controls.btns-AP67YWKW.js"),
+  "../plots/controls.config.js": () => import("./controls.config-3AJKR4ZZ.js"),
+  "../plots/controls.js": () => import("./controls-2S5QVWUC.js"),
+  "../plots/cuminc.js": () => import("./cuminc-WQB6FHVS.js"),
+  "../plots/dataDownload.js": () => import("./dataDownload-HM4UYOBO.js"),
+  "../plots/dictionary.js": () => import("./dictionary-EEPTFDYD.js"),
+  "../plots/dziviewer/plot.dzi.js": () => import("./plot.dzi-YAZA6RQS.js"),
+  "../plots/facet.js": () => import("./facet-5YYY3MUN.js"),
+  "../plots/gb/test/genomeBrowser.spec.js": () => import("./genomeBrowser.spec-42OTTMGO.js"),
+  "../plots/geneExpression.js": () => import("./geneExpression-5NWQXMJ3.js"),
+  "../plots/geneORA.js": () => import("./geneORA-3VWFWDYI.js"),
+  "../plots/geneset.js": () => import("./geneset-RJAULSKC.js"),
+  "../plots/hierCluster.js": () => import("./hierCluster-HMJF3PBE.js"),
+  "../plots/importPlot.js": () => import("./importPlot-VMYXDP66.js"),
+  "../plots/matrix.js": () => import("./matrix-W72XRUZD.js"),
+  "../plots/matrix/hierCluster.config.js": () => import("./hierCluster.config-TAS7XKTU.js"),
+  "../plots/matrix/hierCluster.interactivity.js": () => import("./hierCluster.interactivity-IKTAJ6CU.js"),
+  "../plots/matrix/hierCluster.js": () => import("./hierCluster-GJPPMFNR.js"),
+  "../plots/matrix/hierCluster.renderers.js": () => import("./hierCluster.renderers-I6WFZRNW.js"),
+  "../plots/matrix/matrix.cells.js": () => import("./matrix.cells-DEEUWC74.js"),
+  "../plots/matrix/matrix.cluster.js": () => import("./matrix.cluster-NU5CYRUT.js"),
+  "../plots/matrix/matrix.config.js": () => import("./matrix.config-JYXQOXDT.js"),
+  "../plots/matrix/matrix.data.js": () => import("./matrix.data-ENXNM6RP.js"),
+  "../plots/matrix/matrix.dom.js": () => import("./matrix.dom-F7AN3QGE.js"),
+  "../plots/matrix/matrix.groups.js": () => import("./matrix.groups-EXSNNESB.js"),
+  "../plots/matrix/matrix.interactivity.js": () => import("./matrix.interactivity-G6AL566T.js"),
+  "../plots/matrix/matrix.js": () => import("./matrix-ALBCAZP5.js"),
+  "../plots/matrix/matrix.layout.js": () => import("./matrix.layout-UBUPIJ3R.js"),
+  "../plots/matrix/matrix.legend.js": () => import("./matrix.legend-S3P4F2DG.js"),
+  "../plots/matrix/matrix.renderers.js": () => import("./matrix.renderers-IXFGXHJQ.js"),
+  "../plots/matrix/matrix.serieses.js": () => import("./matrix.serieses-THHXUAPM.js"),
+  "../plots/matrix/matrix.sort.js": () => import("./matrix.sort-WJV6LIZI.js"),
+  "../plots/matrix/matrix.sorterUi.js": () => import("./matrix.sorterUi-VXVCOKEZ.js"),
+  "../plots/matrix/test/hierCluster.integration.spec.js": () => import("./hierCluster.integration.spec-RLHQKX65.js"),
+  "../plots/matrix/test/matrix.integration.spec.js": () => import("./matrix.integration.spec-BW6U6PIW.js"),
+  "../plots/matrix/test/matrix.sort.unit.spec.js": () => import("./matrix.sort.unit.spec-LGMIL2LR.js"),
+  "../plots/matrix/test/matrix.sorterUi.unit.spec.js": () => import("./matrix.sorterUi.unit.spec-CWSEJ62U.js"),
+  "../plots/matrix/test/oncomatrix.spec.js": () => import("./oncomatrix.spec-BME6CQWF.js"),
+  "../plots/plot.brainImaging.js": () => import("./plot.brainImaging-YBYMHCEG.js"),
+  "../plots/plot.disco.js": () => import("./plot.disco-CMDKRSOM.js"),
+  "../plots/plot.ssgq.js": () => import("./plot.ssgq-YKCOEXZP.js"),
+  "../plots/regression.inputs.js": () => import("./regression.inputs-SMC5CNPY.js"),
+  "../plots/regression.inputs.term.js": () => import("./regression.inputs.term-XS54IQC2.js"),
+  "../plots/regression.inputs.values.table.js": () => import("./regression.inputs.values.table-LNPM3MX5.js"),
+  "../plots/regression.js": () => import("./regression-CE54AQMY.js"),
+  "../plots/regression.results.js": () => import("./regression.results-25ZRRDEE.js"),
+  "../plots/sampleView.js": () => import("./sampleView-QAAJ26KT.js"),
+  "../plots/singleCellPlot.js": () => import("./singleCellPlot-JDSARDRV.js"),
+  "../plots/stattable.js": () => import("./stattable-MDABSW3F.js"),
+  "../plots/survival/test/survival.integration.spec.js": () => import("./survival.integration.spec-7ZYBBZKT.js"),
+  "../plots/table.js": () => import("./table-XSJJ3UZV.js"),
+  "../plots/test/barchart.integration.spec.js": () => import("./barchart.integration.spec-BFGZFECA.js"),
+  "../plots/test/cuminc.integration.spec.js": () => import("./cuminc.integration.spec-WAYRLHUH.js"),
+  "../plots/test/dataDownload.integration.spec.js": () => import("./dataDownload.integration.spec-F5CO4BWA.js"),
+  "../plots/test/expclust.gdc.spec.js": () => import("./expclust.gdc.spec-FR26VSUA.js"),
+  "../plots/test/regression.integration.spec.js": () => import("./regression.integration.spec-6QSMYPWJ.js"),
+  "../plots/test/regression.spec.js": () => import("./regression.spec-EDWHFRPY.js"),
+  "../plots/test/summary.integration.spec.js": () => import("./summary.integration.spec-KPKROD6L.js"),
+  "../plots/test/violin.integration.spec.js": () => import("./violin.integration.spec-JVODKUCL.js"),
+  "../plots/violin.interactivity.js": () => import("./violin.interactivity-STOCZMVN.js"),
+  "../plots/violin.js": () => import("./violin-2IAVZGFF.js"),
+  "../plots/violin.renderer.js": () => import("./violin.renderer-MKDTJ3EX.js"),
+  "../plots/volcano/test/testData.js": () => import("./testData-LEJ53F2K.js"),
+  "../plots/wsiviewer/plot.wsi.js": () => import("./plot.wsi-7ADVYTQS.js")
+});
+
+// plots/importPlot.js
+async function importPlot(chartType, notFoundMessage = "") {
+  switch (chartType) {
+    case "AIProjectAdmin":
+      return await import("./AIProjectAdmin-DKLEFCGX.js");
+    case "barchart":
+      return await import("./barchart-UHCTYRMJ.js");
+    case "boxplot":
+      return await import("./BoxPlot-5JQCYENZ.js");
+    case "correlationVolcano":
+      return await import("./CorrelationVolcano-HR6IP2SZ.js");
+    case "DEinput":
+      return await import("./DEinput-XCR4VMR3.js");
+    case "dictionary":
+      return await import("./dictionary-EEPTFDYD.js");
+    case "differentialAnalysis":
+      return await import("./DifferentialAnalysis-SETJAZEN.js");
+    case "Disco":
+      return await import("./Disco-QEBEVQS2.js");
+    case "dmr":
+      return await import("./DmrPlot-CWBQDZL7.js");
+    case "DziViewer":
+      return await import("./DziViewer-6737GC22.js");
+    case "GeneExpInput":
+      return await import("./GeneExpInput-2N62XM7Z.js");
+    case "genomeBrowser":
+      return await import("./GB-5PYCR4SV.js");
+    case "geomap":
+      return await import("./Geomap-ANMR32HE.js");
+    case "grin2":
+      return await import("./grin2-FT5BQJMB.js");
+    case "gsea":
+      return await import("./GSEA-6UKMI6GY.js");
+    case "imagePlot":
+      return await import("./imagePlot-N4OXNMVA.js");
+    case "report":
+      return await import("./report-U6L3KBYG.js");
+    case "runChart2":
+    //See frequencyChart
+    case "frequencyChart":
+      return await import("./RunChart2-N4JPWNVV.js");
+    case "profileBarchart2":
+      return await import("./barchart2-VIZKZRMP.js");
+    case "profileForms":
+      return await import("./profileForms-RLB6SMPQ.js");
+    case "profilePlot":
+      return await import("./profilePlot-AP52VLLO.js");
+    case "profilePolar2":
+      return await import("./polar2-O5SHVLP4.js");
+    case "profileRadar2":
+      return await import("./radar2-ELVGQFZE.js");
+    case "profileRadarFacility2":
+      return await import("./radarFacility2-SDAZHGNG.js");
+    case "proteinView":
+      return await import("./proteinView-S7WDBMQU.js");
+    case "numericDictTermCluster":
+      return await import("./numericDictTermCluster-H4JSPW22.js");
+    case "proteomeAbundance":
+      return await import("./proteomeAbundance-NQ4635NL.js");
+    case "animatedBubbleChart":
+      return await import("./animatedBubbleChart-N6MBJ4X3.js");
+    case "bubbleHeatmap":
+      return await import("./bubbleHeatmap-IL44M4QZ.js");
+    case "cellTypeBubbleHeatmap":
+      return await import("./cellTypeBubbleHeatmap-NQP7RCZO.js");
+    case "brainRegions":
+      return await import("./brainRegions-HJ2VGL3L.js");
+    case "studyCatalog":
+      return await import("./studyCatalog-O3VGIKDM.js");
+    case "proteomeCohortCompare":
+      return await import("./proteomeCohortCompare-ERVUM7RO.js");
+    case "geneRanking":
+      return await import("./geneRanking-PKDVD5OD.js");
+    case "ProteomeInput":
+      return await import("./ProteomeInput-GBVCLNS7.js");
+    case "sampleScatter":
+      return await import("./scatter-BSGDMOC2.js");
+    case "sc":
+      return await import("./SC-RCZT5BRP.js");
+    case "summarizeCnvGeneexp":
+      return await import("./summarizeCnvGeneexp-55DNXHXA.js");
+    case "summarizeGeneexpSurvival":
+      return await import("./summarizeGeneexpSurvival-VLO4DC5M.js");
+    case "summarizeMutationDiagnosis":
+      return await import("./summarizeMutationDiagnosis-MHFM7RX6.js");
+    case "summarizeMutationSurvival":
+      return await import("./summarizeMutationSurvival-G4KHSUBN.js");
+    case "summarizeMutationCnv":
+      return await import("./summarizeMutationCnv-QX7BADYL.js");
+    case "summaryInput":
+      return await import("./summaryInput-TOAL53EP.js");
+    case "summary":
+      return await import("./summary-PJYRCQNY.js");
+    case "survival":
+      return await import("./survival-RKV5BPDK.js");
+    case "table":
+      return await import("./table-XSJJ3UZV.js");
+    case "violin":
+      return await import("./violin-2IAVZGFF.js");
+    case "volcano":
+      return await import("./Volcano-2BQ6SYHO.js");
+    case "WSISamplesPlot":
+      return await import("./WsiSamplesPlot-DYSFMD22.js");
+    case "WSIViewer":
+      return await import("./WSIViewer-UDA4WIRT.js");
+    default:
+      if (notFoundMessage) throw notFoundMessage;
+      return await globImport_plots_js(`../plots/${chartType}.js`);
+  }
+}
+
+export {
+  importPlot
+};
+//# sourceMappingURL=chunk-3SHZTAGF.js.map

package/dist/chunk-3SHZTAGF.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/importPlot.js"],
+  "sourcesContent": ["export async function importPlot(chartType, notFoundMessage = '') {\n\t// TODO: move to dynamic import of exact plot names here, instead of string-pattern,\n\t// so that the bundler does not have to guess code file extension, directory names and letter casing\n\tswitch (chartType) {\n\t\tcase 'AIProjectAdmin':\n\t\t\treturn await import('./aiProjectAdmin/AIProjectAdmin.ts')\n\n\t\tcase 'barchart':\n\t\t\treturn await import(`./barchart.js`)\n\n\t\tcase 'boxplot':\n\t\t\treturn await import(`./boxplot/BoxPlot.ts`)\n\n\t\tcase 'correlationVolcano':\n\t\t\treturn await import(`./corrVolcano/CorrelationVolcano.ts`)\n\n\t\tcase 'DEinput':\n\t\t\treturn await import(`./DEinput.ts`)\n\n\t\tcase 'dictionary':\n\t\t\treturn await import(`./dictionary.js`)\n\n\t\tcase 'differentialAnalysis':\n\t\t\treturn await import(`./diffAnalysis/DifferentialAnalysis.ts`)\n\n\t\tcase 'Disco':\n\t\t\treturn await import('./disco/Disco.ts')\n\n\t\tcase 'dmr':\n\t\t\treturn await import('./dmr/DmrPlot.ts')\n\n\t\tcase 'DziViewer':\n\t\t\treturn await import(`./dziviewer/DziViewer.ts`)\n\n\t\tcase 'GeneExpInput':\n\t\t\treturn await import(`./GeneExpInput.ts`)\n\n\t\tcase 'genomeBrowser':\n\t\t\treturn await import('./gb/GB.ts')\n\n\t\tcase 'geomap':\n\t\t\treturn await import('./geomap/Geomap.ts')\n\n\t\tcase 'grin2':\n\t\t\treturn await import('./grin2/grin2')\n\n\t\tcase 'gsea':\n\t\t\treturn await import(`./gsea/GSEA.ts`)\n\n\t\tcase 'imagePlot':\n\t\t\treturn await import('./imagePlot.ts')\n\n\t\tcase 'report':\n\t\t\treturn await import(`./report/report.ts`)\n\n\t\tcase 'runChart2': //See frequencyChart\n\t\tcase 'frequencyChart':\n\t\t\treturn await import(`./runChart2/RunChart2.ts`)\n\n\t\tcase 'profileBarchart2':\n\t\t\treturn await import('./profile/barchart2.ts')\n\n\t\tcase 'profileForms':\n\t\t\treturn await import('./profile/profileForms.ts')\n\n\t\tcase 'profilePlot':\n\t\t\treturn await import('./profile/profilePlot.ts')\n\n\t\tcase 'profilePolar2':\n\t\t\treturn await import('./profile/polar2.ts')\n\n\t\tcase 'profileRadar2':\n\t\t\treturn await import('./profile/radar2.ts')\n\n\t\tcase 'profileRadarFacility2':\n\t\t\treturn await import('./profile/radarFacility2.ts')\n\n\t\tcase 'proteinView':\n\t\t\treturn await import(`./proteinView.ts`)\n\n\t\tcase 'numericDictTermCluster':\n\t\t\treturn await import(`./numericDictTermCluster.ts`)\n\n\t\tcase 'proteomeAbundance':\n\t\t\treturn await import(`./proteomeAbundance.ts`)\n\n\t\tcase 'animatedBubbleChart':\n\t\t\treturn await import(`./animatedBubbleChart.ts`)\n\n\t\tcase 'bubbleHeatmap':\n\t\t\treturn await import('./bubbleHeatmap.ts')\n\n\t\tcase 'cellTypeBubbleHeatmap':\n\t\t\treturn await import('./cellTypeBubbleHeatmap.ts')\n\n\t\tcase 'brainRegions':\n\t\t\treturn await import('./brainRegions.ts')\n\n\t\tcase 'studyCatalog':\n\t\t\treturn await import('./studyCatalog.ts')\n\n\t\tcase 'proteomeCohortCompare':\n\t\t\treturn await import('./proteomeCohortCompare.ts')\n\n\t\tcase 'geneRanking':\n\t\t\treturn await import(`./geneRanking.ts`)\n\n\t\tcase 'ProteomeInput':\n\t\t\treturn await import('./ProteomeInput.ts')\n\n\t\tcase 'sampleScatter':\n\t\t\treturn await import(`./scatter/scatter.js`)\n\n\t\tcase 'sc':\n\t\t\treturn await import('./sc/SC.ts')\n\n\t\tcase 'summarizeCnvGeneexp':\n\t\t\treturn await import(`./summarizeCnvGeneexp.ts`)\n\n\t\tcase 'summarizeGeneexpSurvival':\n\t\t\treturn await import(`./summarizeGeneexpSurvival.ts`)\n\n\t\tcase 'summarizeMutationDiagnosis':\n\t\t\treturn await import(`./summarizeMutationDiagnosis.ts`)\n\n\t\tcase 'summarizeMutationSurvival':\n\t\t\treturn await import(`./summarizeMutationSurvival.ts`)\n\n\t\tcase 'summarizeMutationCnv':\n\t\t\treturn await import(`./summarizeMutationCnv.ts`)\n\n\t\tcase 'summaryInput':\n\t\t\treturn await import(`./summaryInput.ts`)\n\n\t\tcase 'summary':\n\t\t\treturn await import(`./summary.ts`)\n\n\t\tcase 'survival':\n\t\t\treturn await import(`./survival/survival.js`)\n\n\t\tcase 'table':\n\t\t\treturn await import(`./table.js`)\n\n\t\tcase 'violin':\n\t\t\treturn await import(`./violin.js`)\n\n\t\tcase 'volcano':\n\t\t\treturn await import(`./volcano/Volcano.ts`)\n\n\t\tcase 'WSISamplesPlot':\n\t\t\treturn await import('./wsisamples/WsiSamplesPlot.ts')\n\n\t\tcase 'WSIViewer':\n\t\t\treturn await import('./wsiviewer/WSIViewer.ts')\n\n\t\tdefault:\n\t\t\t// temporary option to force an error, to bypass the default filename matching\n\t\t\tif (notFoundMessage) throw notFoundMessage\n\n\t\t\t// TODO: should always throw here once all chart types are handled separately as cases;\n\t\t\t// the pattern matching below is problematic because:\n\t\t\t// - it matches non-plot code file names\n\t\t\t// - it assumes a non-typescript, .js file extension\n\t\t\t// - it doesn't handle plot code that are organized under its own subdirectory\n\t\t\treturn await import(`../plots/${chartType}.js`)\n\t}\n}\n"],
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+  "names": []
+}

package/dist/chunk-46X6AQ7Z.js

@@ -0,0 +1,123 @@
+import {
+  pickCollectionFraction,
+  renderTable
+} from "./chunk-TKW5TW4Z.js";
+
+// termdb/handlers/termCollection.ts
+var SearchHandler = class {
+  async init(opts) {
+    this.callback = opts.callback;
+    this.app = opts.app;
+    opts.holder.style("display", "");
+    const termlst = opts.details.termlst ?? [];
+    const memberType = opts.details.memberType || opts.details.type;
+    if (opts.termCollectionSelectionMode === "fraction" && memberType === "numeric") {
+      pickCollectionFraction({
+        holder: opts.holder,
+        term: makeTerm(opts.details, termlst, opts.usecase),
+        callback: (tw) => opts.callback(tw)
+      });
+      return;
+    }
+    const tableDiv = opts.holder.append("div");
+    renderTable({
+      columns: [{ label: "VARIABLES" }],
+      rows: termlst.map((t) => {
+        return [{ value: t.name }];
+      }),
+      div: tableDiv,
+      maxWidth: "30vw",
+      maxHeight: "40vh",
+      // the button is disabled while the selection cannot be submitted
+      noButtonCallback: () => updateSelectBtn(),
+      striped: false,
+      showHeader: true,
+      //false,
+      selectAll: true,
+      columnButtons: void 0,
+      //Leave until table.js is typed
+      buttons: void 0
+    });
+    let categoryTable;
+    let ckSource = [];
+    if (opts.details.categoryKeys) {
+      ckSource = opts.details.categoryKeys;
+      const categoryDiv = opts.holder.append("div").style("margin-top", "15px");
+      const values = opts.details.termlst[0].values || {};
+      categoryTable = categoryDiv.append("div");
+      renderTable({
+        columns: [{ label: "CATEGORIES" }],
+        rows: ckSource.map((ck) => {
+          return [{ value: values[ck.key]?.label ?? ck.key, checked: ck.shown }];
+        }),
+        div: categoryTable,
+        maxWidth: "30vw",
+        maxHeight: "40vh",
+        noButtonCallback: () => updateSelectBtn(),
+        striped: false,
+        showHeader: true,
+        //false,
+        selectAll: true,
+        columnButtons: void 0,
+        //Leave until table.js is typed
+        buttons: void 0
+      });
+    }
+    function getRowChecks(div) {
+      const trs = div.select("table").select("tbody").node().querySelectorAll("tr");
+      return [...trs].map((tr) => tr.querySelectorAll("td")[1]?.querySelector("input")?.checked === true);
+    }
+    function getSelectedTermlst() {
+      const checked = getRowChecks(tableDiv);
+      return termlst.filter((term, i) => checked[i]);
+    }
+    function getCategoryKeys() {
+      if (!categoryTable) return void 0;
+      const checked = getRowChecks(categoryTable);
+      return ckSource.map((ck, i) => ({ key: ck.key, shown: checked[i] }));
+    }
+    function getSelectionError() {
+      if (getSelectedTermlst().length < 2) return "Select at least two variables.";
+      if (getCategoryKeys()?.every((ck) => !ck.shown)) return "Select at least one category.";
+      return void 0;
+    }
+    function updateSelectBtn() {
+      if (!selectBtn) return;
+      const error = getSelectionError();
+      selectBtn.property("disabled", Boolean(error)).attr("title", error || null);
+    }
+    const selectBtn = opts.holder.append("div").style("float", "right").style("padding", "6px 20px").append("button").attr("data-testid", "sjpp-term-collection-select").text("Select").on("click", () => {
+      opts.callback({
+        // makeTerm() extracts propsByTermId (color, etc) for the selected terms
+        ...makeTerm(opts.details, getSelectedTermlst(), opts.usecase),
+        categoryKeys: getCategoryKeys()
+      });
+    });
+    updateSelectBtn();
+  }
+};
+function makeTerm(details, termlst, usecase) {
+  const propsByTermId = {};
+  if (details.propsByTermId) {
+    for (const term of termlst) {
+      if (details.propsByTermId[term.id]) propsByTermId[term.id] = details.propsByTermId[term.id];
+    }
+  }
+  return {
+    type: "termCollection",
+    termIds: termlst.map((term) => term.id),
+    termlst,
+    name: details.name,
+    valueTransform: details.valueTransformByPlots?.[usecase?.target],
+    // memberType = ds.cohort.termdb.termCollections[].type for client code
+    memberType: details.memberType || details.type,
+    categoryKeys: details.categoryKeys,
+    isleaf: true,
+    propsByTermId
+  };
+}
+
+export {
+  SearchHandler
+};
+//# sourceMappingURL=chunk-46X6AQ7Z.js.map

package/dist/chunk-46X6AQ7Z.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../termdb/handlers/termCollection.ts"],
+  "sourcesContent": ["import { renderTable } from '#dom'\nimport type { CategoryKey } from '#types'\nimport { pickCollectionFraction } from './termCollectionFractionSelection.ts'\n\nexport class SearchHandler {\n\tcallback: any\n\tapp: any\n\n\tasync init(opts) {\n\t\t// opts.details is the term object for term collection\n\t\tthis.callback = opts.callback\n\t\tthis.app = opts.app\n\n\t\topts.holder.style('display', '')\n\n\t\tconst termlst = opts.details.termlst ?? []\n\t\tconst memberType = opts.details.memberType || opts.details.type\n\t\tif (opts.termCollectionSelectionMode === 'fraction' && memberType === 'numeric') {\n\t\t\tpickCollectionFraction({\n\t\t\t\tholder: opts.holder,\n\t\t\t\tterm: makeTerm(opts.details, termlst, opts.usecase),\n\t\t\t\tcallback: tw => opts.callback(tw)\n\t\t\t})\n\t\t\treturn\n\t\t}\n\n\t\tconst tableDiv = opts.holder.append('div')\n\t\trenderTable({\n\t\t\tcolumns: [{ label: 'VARIABLES' }],\n\t\t\trows: termlst.map(t => {\n\t\t\t\treturn [{ value: t.name }]\n\t\t\t}),\n\t\t\tdiv: tableDiv,\n\t\t\tmaxWidth: '30vw',\n\t\t\tmaxHeight: '40vh',\n\t\t\t// the button is disabled while the selection cannot be submitted\n\t\t\tnoButtonCallback: () => updateSelectBtn(),\n\t\t\tstriped: false,\n\t\t\tshowHeader: true, //false,\n\t\t\tselectAll: true,\n\t\t\tcolumnButtons: undefined, //Leave until table.js is typed\n\t\t\tbuttons: undefined\n\t\t})\n\n\t\tlet categoryTable\n\t\tlet ckSource: CategoryKey[] = []\n\t\tif (opts.details.categoryKeys) {\n\t\t\t// later, if there's just one category, simply show a disabled checked box for this category and no longer uncheckable\n\t\t\tckSource = opts.details.categoryKeys as CategoryKey[]\n\t\t\tconst categoryDiv = opts.holder.append('div').style('margin-top', '15px')\n\t\t\tconst values = opts.details.termlst[0].values || {}\n\t\t\tcategoryTable = categoryDiv.append('div')\n\t\t\trenderTable({\n\t\t\t\tcolumns: [{ label: 'CATEGORIES' }],\n\t\t\t\trows: ckSource.map((ck: CategoryKey) => {\n\t\t\t\t\treturn [{ value: values[ck.key]?.label ?? ck.key, checked: ck.shown }]\n\t\t\t\t}),\n\t\t\t\tdiv: categoryTable,\n\t\t\t\tmaxWidth: '30vw',\n\t\t\t\tmaxHeight: '40vh',\n\t\t\t\tnoButtonCallback: () => updateSelectBtn(),\n\t\t\t\tstriped: false,\n\t\t\t\tshowHeader: true, //false,\n\t\t\t\tselectAll: true,\n\t\t\t\tcolumnButtons: undefined, //Leave until table.js is typed\n\t\t\t\tbuttons: undefined\n\t\t\t})\n\t\t}\n\n\t\t/** true for each checked row of a rendered table, in row order */\n\t\tfunction getRowChecks(div: any): boolean[] {\n\t\t\tconst trs = div.select('table').select('tbody').node().querySelectorAll('tr')\n\t\t\treturn [...trs].map((tr: any) => tr.querySelectorAll('td')[1]?.querySelector('input')?.checked === true)\n\t\t}\n\t\tfunction getSelectedTermlst() {\n\t\t\tconst checked = getRowChecks(tableDiv)\n\t\t\treturn termlst.filter((term, i) => checked[i])\n\t\t}\n\t\tfunction getCategoryKeys(): CategoryKey[] | undefined {\n\t\t\tif (!categoryTable) return undefined\n\t\t\tconst checked = getRowChecks(categoryTable)\n\t\t\treturn ckSource.map((ck: CategoryKey, i: number) => ({ key: ck.key, shown: checked[i] }))\n\t\t}\n\t\t/** The reason the current selection cannot be submitted, or undefined when it can be */\n\t\tfunction getSelectionError(): string | undefined {\n\t\t\t// a lone member is not a collection, e.g. nothing to sum for a fraction or stack in a bar\n\t\t\tif (getSelectedTermlst().length < 2) return 'Select at least two variables.'\n\t\t\tif (getCategoryKeys()?.every(ck => !ck.shown)) return 'Select at least one category.'\n\t\t\treturn undefined\n\t\t}\n\t\tfunction updateSelectBtn() {\n\t\t\tif (!selectBtn) return\n\t\t\tconst error = getSelectionError()\n\t\t\t// a vanilla button is greyed out by the browser when disabled, no styling needed here\n\t\t\tselectBtn.property('disabled', Boolean(error)).attr('title', error || null)\n\t\t}\n\n\t\tconst selectBtn = opts.holder\n\t\t\t.append('div')\n\t\t\t.style('float', 'right')\n\t\t\t.style('padding', '6px 20px')\n\t\t\t.append('button')\n\t\t\t.attr('data-testid', 'sjpp-term-collection-select')\n\t\t\t.text('Select')\n\t\t\t.on('click', () => {\n\t\t\t\topts.callback({\n\t\t\t\t\t// makeTerm() extracts propsByTermId (color, etc) for the selected terms\n\t\t\t\t\t...makeTerm(opts.details, getSelectedTermlst(), opts.usecase),\n\t\t\t\t\tcategoryKeys: getCategoryKeys()\n\t\t\t\t})\n\t\t\t})\n\t\tupdateSelectBtn()\n\t}\n}\n\nfunction makeTerm(details: any, termlst: any[], usecase: any) {\n\tconst propsByTermId = {}\n\tif (details.propsByTermId) {\n\t\tfor (const term of termlst) {\n\t\t\tif (details.propsByTermId[term.id]) propsByTermId[term.id] = details.propsByTermId[term.id]\n\t\t}\n\t}\n\treturn {\n\t\ttype: 'termCollection',\n\t\ttermIds: termlst.map(term => term.id),\n\t\ttermlst,\n\t\tname: details.name,\n\t\tvalueTransform: details.valueTransformByPlots?.[usecase?.target],\n\t\t// memberType = ds.cohort.termdb.termCollections[].type for client code\n\t\tmemberType: details.memberType || details.type,\n\t\tcategoryKeys: details.categoryKeys,\n\t\tisleaf: true,\n\t\tpropsByTermId\n\t}\n}\n"],
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+  "names": []
+}

package/dist/chunk-4FQYRDZS.js

@@ -0,0 +1,276 @@
+import {
+  Menu
+} from "./chunk-HYOEWQ5P.js";
+import {
+  pointer_default,
+  select_default
+} from "./chunk-I6Y4O3RR.js";
+
+// dom/svgSeriesTips.js
+function getSeriesTip(line, rect, _tip = null) {
+  const tip = _tip || new Menu({ padding: "5px" });
+  line.style("display", "none");
+  const rectNode = rect.style("fill", "transparent").node();
+  function mouseOver(event) {
+    const m = pointer_default(event, rectNode);
+    const mx = m[0];
+    const xVal = +opts.xScale.invert(mx).toFixed(opts.decimals);
+    const x = opts.xScale(xVal);
+    line.style("display", "").attr("stroke", "#aaa").attr("stroke-dasharray", 4).attr("x1", x).attr("x2", x);
+    const seriesHtmls = [];
+    for (const series of opts.serieses) {
+      const data = series.data;
+      const data_x = data.map((d) => d.x);
+      if (xVal >= Math.min(...data_x) && xVal <= Math.max(...data_x)) {
+        const max = Math.max(...data_x.filter((x2) => x2 <= xVal));
+        const timepoint = data.find((d) => d.x == max);
+        if (timepoint) seriesHtmls.push(timepoint.html);
+      }
+    }
+    if (seriesHtmls.length) {
+      tip.show(event.clientX, event.clientY).d.html(`<span>${opts.xTitleLabel}: ${xVal}</span><br>` + seriesHtmls.map((d) => d).join(opts.separator));
+    } else {
+      tip.hide();
+    }
+  }
+  rect.on("mouseover", mouseOver).on("mousemove", mouseOver).on("mouseout", () => {
+    line.style("display", "none");
+    tip.hide();
+  });
+  const opts = {
+    separator: "<br>",
+    decimals: 1
+  };
+  return {
+    /*
+    			Will update the length of the vertical line
+    			and reassign optional data values
+    
+    			!!! MUST call api.update() before the expected mouseover event,
+    			so that the line will have the proper length and the mouse
+    			position could be computed with .xScale !!! 
+    
+    			_opts{}
+    			.xScale					required
+    										the d3-scale object that was used for the rect dimensions
+    										
+    			.xTitleLabel			required
+    										title of x-axis
+    										will be used as label of x-value in tooltip
+    
+    			.serieses[{data}] 		required
+    										array of series objects, assumed to be visibly rendered
+    							
+    				.data[{x, html}]	required
+    										array of data objects
+    										the series data that is currently rendered in the chart
+    					
+    					.x 				required, float
+    										the datapoint's actual, unscaled x value
+    					
+    					.html   		required, string
+    										the HTML to display in the tooltip if this datapoint's 
+    										x value matched the vertical line's position
+    
+    			.separator				optional, string
+    										the html to be used to join the series html strings when displayed in the tooltip
+    
+    			.decimals				optional, number
+    										number of decimal places of the datapoint's x-value
+    										will control the precision of the vertical line
+    		*/
+    update(_opts = {}) {
+      Object.assign(opts, _opts);
+      const x = rect.attr("x");
+      const y = rect.attr("y");
+      line.attr("x1", x).attr("x2", x).attr("y1", y).attr("y2", rect.attr("height") - y);
+    },
+    /*
+    	detroy to help minimize memory leaks
+    	from elements and event handlers not being garbage collected
+    	because of non-deactivated references
+    */
+    destroy() {
+      rect.on("mouseover", null).on("mousemove", null).on("mouseout", null);
+    }
+  };
+}
+
+// dom/renderAtRisk.js
+function renderAtRiskG({ g, s, chart, order, term2toColor, onSerieClick }) {
+  const atRiskGroups = [];
+  const xTickValues = chart.xTickValues.filter((xTick) => xTick >= chart.xMin);
+  for (const series of chart.visibleSerieses) {
+    const counts = [];
+    let i = 0, d = series.data[0], prev = d, nCensored = 0;
+    for (const time of xTickValues) {
+      while (d && d.x < time) {
+        nCensored += d.ncensor;
+        prev = d;
+        i++;
+        d = series.data[i];
+      }
+      if (d && d.x === time) {
+        counts.push([time, d.nrisk, nCensored]);
+      } else {
+        counts.push([time, prev.nrisk - prev.nevent - prev.ncensor, nCensored]);
+      }
+    }
+    const { seriesId, seriesLabel } = series;
+    atRiskGroups.push({ seriesId, seriesLabel, counts });
+  }
+  const y = s.svgh - s.svgPadding.top - s.svgPadding.bottom + 60;
+  const seriesOrder = order || chart.serieses.map((s2) => s2.seriesId);
+  g.selectAll(".sjpp-atrisk-title").remove();
+  if (s.atRiskVisible) {
+    atRiskGroups.sort((a, b) => seriesOrder.indexOf(a.seriesId) - seriesOrder.indexOf(b.seriesId));
+    const addYoffset = chart.serieses.length == 1 && !chart.serieses[0].seriesId;
+    const titleg = g.append("text").attr("class", "sjpp-atrisk-title").attr("transform", `translate(${s.atRiskLabelOffset}, ${addYoffset ? 2 * s.axisTitleFontSize : 0})`).attr("text-anchor", "end").attr("font-size", `${s.axisTitleFontSize - 4}px`).attr("cursor", chart.serieses.length == 1 ? "pointer" : "default").text("Number at risk").on("click", chart.serieses.length == 1 ? (e) => onSerieClick({ seriesId: "" }, e.clientX, e.clientY) : null);
+    if (term2toColor[""]) titleg.style("fill", s.defaultColor);
+    titleg.append("tspan").attr("x", 0).attr("y", s.axisTitleFontSize - 4).text("(# censored)");
+  } else {
+    atRiskGroups.length = 0;
+  }
+  const sg = g.attr("transform", `translate(0,${y})`).selectAll(":scope > g").data(atRiskGroups, (s2) => s2.seriesLabel || s2.seriesId);
+  sg.exit().remove();
+  sg.each(function(atRiskGroup, i) {
+    const { seriesId, seriesLabel, counts } = atRiskGroup;
+    const y2 = (i + 1) * (2 * s.axisTitleFontSize);
+    const g2 = select_default(this).attr("transform", `translate(0,${y2})`).attr("fill", term2toColor[""] ? s.defaultColor : term2toColor[seriesId].adjusted);
+    let legendText = g2.select(":scope>text");
+    if (!legendText.size()) legendText = g2.append("text");
+    legendText.text(seriesId && seriesId !== "*" ? seriesLabel || seriesId : "");
+    let ticksG = g2.select(":scope>g");
+    if (!ticksG.size()) ticksG = g2.append("g");
+    renderAtRiskTick(ticksG, chart, xTickValues, s, atRiskGroup);
+  });
+  sg.enter().append("g").each(function(atRiskGroup, i) {
+    const { seriesId, seriesLabel, counts } = atRiskGroup;
+    const y2 = (i + 1) * (2 * s.axisTitleFontSize);
+    const g2 = select_default(this).attr("transform", `translate(0,${y2})`).attr("fill", term2toColor[""] ? s.defaultColor : term2toColor[seriesId].adjusted).on("click", (e) => onSerieClick({ seriesId }, e.clientX, e.clientY));
+    g2.append("text").attr("data-testid", "sjpp-atrisk-seriesId").attr("transform", `translate(${s.atRiskLabelOffset}, 0)`).attr("text-anchor", "end").attr("font-size", `${s.axisTitleFontSize - 4}px`).attr("cursor", "pointer").datum({ seriesId }).text(seriesId && seriesId !== "*" ? seriesLabel || seriesId : "");
+    renderAtRiskTick(g2.append("g"), chart, xTickValues, s, atRiskGroup);
+  });
+}
+function renderAtRiskTick(g, chart, xTickValues, s, atRiskGroup) {
+  const { seriesId, counts } = atRiskGroup;
+  const reversed = counts.slice().reverse();
+  const data = xTickValues.map((tickVal) => {
+    if (tickVal === 0) return { seriesId, tickVal, atRisk: counts[0][1], nCensored: counts[0][2] };
+    const d = reversed.find((d2) => d2[0] <= tickVal);
+    return { seriesId, tickVal, atRisk: d[1], nCensored: d[2] };
+  });
+  const text = g.selectAll("text").data(data);
+  text.exit().remove();
+  text.attr("transform", (d) => `translate(${chart.xScale(d.tickVal)},0)`).attr("text-anchor", "middle").attr("font-size", `${s.axisTitleFontSize - 4}px`).attr("cursor", "pointer").each(renderAtRiskLabel);
+  text.enter().append("text").attr("transform", (d) => `translate(${chart.xScale(d.tickVal)},0)`).attr("text-anchor", "middle").attr("font-size", `${s.axisTitleFontSize - 4}px`).attr("cursor", "pointer").each(renderAtRiskLabel);
+  function renderAtRiskLabel(d) {
+    const tspans = select_default(this).selectAll("tspan").data([d.atRisk, `(${d.nCensored})`]);
+    tspans.exit().remove();
+    tspans.attr("y", (d2, i) => i === 0 ? 0 : i * (s.axisTitleFontSize - 4)).text((d2) => d2);
+    tspans.enter().append("tspan").attr("x", 0).attr("y", (d2, i) => i === 0 ? 0 : i * (s.axisTitleFontSize - 4)).text((d2) => d2);
+  }
+}
+
+// dom/renderPvalueTable.js
+function renderPvalues({
+  title,
+  titleTestid = void 0,
+  holder,
+  plot,
+  tests,
+  s,
+  bins,
+  tip,
+  setActiveMenu,
+  updateHiddenPvalues
+}) {
+  let fontSize;
+  if (s.axisTitleFontSize) {
+    fontSize = s.axisTitleFontSize - 2;
+  } else fontSize = 15;
+  const maxPvalsToShow = 10;
+  holder.selectAll("*").remove();
+  if (!plot) {
+    throw `plot type '${plot}' not recognized`;
+  }
+  holder.append("div").style("padding-bottom", "5px").style("font-size", fontSize + "px").style("font-weight", "bold").attr("data-testid", titleTestid || "sjpp-pvalueTable-title").text(title);
+  const tablediv = holder.append("div").style("border", "1px solid #ccc");
+  if (plot == "violin" && tests.pvalues.length > maxPvalsToShow || tests.length > maxPvalsToShow) {
+    tablediv.style("overflow", "auto").style("height", "220px");
+  }
+  const visibleTests = s.hiddenPvalues ? tests.filter((t) => !s.hiddenPvalues.find((p) => p.series1.id === t.series1.id && p.series2.id === t.series2.id)) : tests;
+  if (plot == "violin" ? visibleTests.pvalues.length : visibleTests.length) {
+    const binOrder = bins && bins.length > 0 ? bins.map((b) => b.label) : null;
+    if (binOrder) {
+      for (const test of visibleTests) {
+        const orderedSeries = [test.series1.id, test.series2.id].sort(
+          (a, b) => binOrder.indexOf(a) - binOrder.indexOf(b)
+        );
+        if (test.series2.id == orderedSeries[0]) {
+          test.series1_new = test.series2;
+          test.series2_new = test.series1;
+          test.series1 = test.series1_new;
+          test.series2 = test.series2_new;
+          delete test.series1_new;
+          delete test.series2_new;
+        }
+      }
+      visibleTests.sort(
+        (a, b) => binOrder.indexOf(a.series1.id) - binOrder.indexOf(b.series1.id) || binOrder.indexOf(a.series2.id) - binOrder.indexOf(b.series2.id)
+      );
+    }
+    const table = tablediv.append("table").style("width", "100%");
+    table.append("thead").append("tr").selectAll("td").data(["Group 1", "Group 2", "P-value"]).enter().append("td").style("padding", "1px 8px 1px 2px").style("color", "#555").style("position", "sticky").style("top", "0px").style("background", "white").style("font-size", fontSize + "px").text((column) => column);
+    const tbody = table.append("tbody");
+    const tr = tbody.selectAll("tr").data(plot == "violin" ? visibleTests.pvalues : visibleTests).enter().append("tr").attr("class", `pp-${plot}-chartLegends-pvalue`);
+    if (plot == "survival") {
+      tr.on("click", (event, t) => {
+        const hiddenPvalues = s.hiddenPvalues.slice();
+        hiddenPvalues.push(t);
+        updateHiddenPvalues(hiddenPvalues);
+      });
+    }
+    tr.selectAll("td").data((d) => [d.series1, d.series2, d.pvalue]).enter().append("td").attr("aria-label", plot ? "Click to hide a p-value" : "").style("color", plot == "violin" ? "black" : (d) => d.color).style("padding", "1px 8px 1px 2px").style("font-size", fontSize + "px").style("cursor", plot == "survival" ? "pointer" : "auto").text((d) => plot == "violin" ? d : d.text);
+    if (plot == "cuminc") {
+      if (visibleTests.find((test) => test.permutation)) {
+        holder.append("div").style("margin-top", "10px").style("font-size", fontSize - 2 + "px").text("*computed by permutation of Gray's test statistic");
+      }
+    }
+  }
+  if (plot == "survival") {
+    const hiddenTests = tests.filter(
+      (t) => s.hiddenPvalues.find((p) => p.series1.id === t.series1.id && p.series2.id === t.series2.id)
+    );
+    if (hiddenTests.length) {
+      holder.append("div").style("color", "#aaa").style("cursor", "pointer").html(`<span style='color:#aaa; font-weight:400'><span>Hidden tests (${hiddenTests.length})</span>`).on("click", (event) => {
+        tip.clear();
+        const divs = tip.d.append("div").selectAll("div").data(hiddenTests).enter().append("div").each(function(d) {
+          setActiveMenu(true);
+          const div = select_default(this);
+          div.append("input").attr("type", "checkbox").style("margin-right", "5px");
+          div.append("span").html(`${d.series1.id} vs ${d.series2.id}`);
+        });
+        tip.d.append("button").html("Show checked test(s)").on("click", () => {
+          const hiddenPvalues = [];
+          divs.filter(function() {
+            return !select_default(this.firstChild).property("checked");
+          }).each((d) => hiddenPvalues.push(d));
+          updateHiddenPvalues(hiddenPvalues);
+          tip.hide();
+        });
+        tip.show(event.clientX, event.clientY);
+      });
+    }
+    if (s.maxTimeToEvent && visibleTests.length) {
+      holder.append("div").style("margin-top", "10px").style("font-size", fontSize - 2 + "px").text((visibleTests.length > 1 ? "p-values are" : "p-value is") + " computed with all survival data");
+    }
+  }
+}
+
+export {
+  getSeriesTip,
+  renderAtRiskG,
+  renderPvalues
+};
+//# sourceMappingURL=chunk-4FQYRDZS.js.map