@sjcrh/proteinpaint-client 2.200.0 → 2.201.0

package/dist/chunk-HQAJVJCQ.js

@@ -0,0 +1,195 @@
+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-VBSWS5N7.js"),
+  "../plots/barchart.events.js": () => import("./barchart.events-GZTY4IC3.js"),
+  "../plots/barchart.js": () => import("./barchart-OGCLBPQ2.js"),
+  "../plots/bars.renderer.js": () => import("./bars.renderer-54UCFLJS.js"),
+  "../plots/bars.settings.js": () => import("./bars.settings-SDU7PZOS.js"),
+  "../plots/brainImaging.js": () => import("./brainImaging-VIMLETC5.js"),
+  "../plots/controls.btns.js": () => import("./controls.btns-AP67YWKW.js"),
+  "../plots/controls.config.js": () => import("./controls.config-3OO3JK6E.js"),
+  "../plots/controls.js": () => import("./controls-QYHARIEY.js"),
+  "../plots/cuminc.js": () => import("./cuminc-L7OJTYXC.js"),
+  "../plots/dataDownload.js": () => import("./dataDownload-NPSWNOAG.js"),
+  "../plots/dictionary.js": () => import("./dictionary-GD67R72W.js"),
+  "../plots/dziviewer/plot.dzi.js": () => import("./plot.dzi-W66SBKTH.js"),
+  "../plots/facet.js": () => import("./facet-74LKIPTA.js"),
+  "../plots/gb/test/genomeBrowser.spec.js": () => import("./genomeBrowser.spec-25ZO5S2X.js"),
+  "../plots/geneExpression.js": () => import("./geneExpression-GATKMJJ5.js"),
+  "../plots/geneORA.js": () => import("./geneORA-LJRIR4VV.js"),
+  "../plots/geneset.js": () => import("./geneset-JXEJFEK2.js"),
+  "../plots/hierCluster.js": () => import("./hierCluster-SDH3TJQY.js"),
+  "../plots/importPlot.js": () => import("./importPlot-R2WRZGZU.js"),
+  "../plots/matrix.js": () => import("./matrix-5QWDN6SI.js"),
+  "../plots/matrix/hierCluster.config.js": () => import("./hierCluster.config-DO67TCXI.js"),
+  "../plots/matrix/hierCluster.interactivity.js": () => import("./hierCluster.interactivity-LGEAFT5T.js"),
+  "../plots/matrix/hierCluster.js": () => import("./hierCluster-OBBPQH24.js"),
+  "../plots/matrix/hierCluster.renderers.js": () => import("./hierCluster.renderers-FXDCU3PN.js"),
+  "../plots/matrix/matrix.cells.js": () => import("./matrix.cells-CFSI2NWU.js"),
+  "../plots/matrix/matrix.cluster.js": () => import("./matrix.cluster-NU5CYRUT.js"),
+  "../plots/matrix/matrix.config.js": () => import("./matrix.config-HE64MAL4.js"),
+  "../plots/matrix/matrix.data.js": () => import("./matrix.data-HTUZXQAM.js"),
+  "../plots/matrix/matrix.dom.js": () => import("./matrix.dom-F7AN3QGE.js"),
+  "../plots/matrix/matrix.groups.js": () => import("./matrix.groups-ZFKWVNMX.js"),
+  "../plots/matrix/matrix.interactivity.js": () => import("./matrix.interactivity-YB5G5W5T.js"),
+  "../plots/matrix/matrix.js": () => import("./matrix-SKPVVDVR.js"),
+  "../plots/matrix/matrix.layout.js": () => import("./matrix.layout-MFG65V7K.js"),
+  "../plots/matrix/matrix.legend.js": () => import("./matrix.legend-7MIZZJVB.js"),
+  "../plots/matrix/matrix.renderers.js": () => import("./matrix.renderers-PCZFHDDZ.js"),
+  "../plots/matrix/matrix.serieses.js": () => import("./matrix.serieses-7KYX3KAY.js"),
+  "../plots/matrix/matrix.sort.js": () => import("./matrix.sort-CR3J45MQ.js"),
+  "../plots/matrix/matrix.sorterUi.js": () => import("./matrix.sorterUi-YSKIX6B6.js"),
+  "../plots/matrix/test/hierCluster.integration.spec.js": () => import("./hierCluster.integration.spec-EB24C4VZ.js"),
+  "../plots/matrix/test/matrix.integration.spec.js": () => import("./matrix.integration.spec-YKJ4LZFY.js"),
+  "../plots/matrix/test/matrix.sort.unit.spec.js": () => import("./matrix.sort.unit.spec-GEAM5DSU.js"),
+  "../plots/matrix/test/matrix.sorterUi.unit.spec.js": () => import("./matrix.sorterUi.unit.spec-2MW64QS5.js"),
+  "../plots/matrix/test/oncomatrix.spec.js": () => import("./oncomatrix.spec-F43Y7CWN.js"),
+  "../plots/plot.brainImaging.js": () => import("./plot.brainImaging-M4HPNXZH.js"),
+  "../plots/plot.disco.js": () => import("./plot.disco-HIT6GR44.js"),
+  "../plots/plot.ssgq.js": () => import("./plot.ssgq-MI2OMCUY.js"),
+  "../plots/regression.inputs.js": () => import("./regression.inputs-ZEFDNSVT.js"),
+  "../plots/regression.inputs.term.js": () => import("./regression.inputs.term-O2FQBX7L.js"),
+  "../plots/regression.inputs.values.table.js": () => import("./regression.inputs.values.table-63BQKSZP.js"),
+  "../plots/regression.js": () => import("./regression-GZ2YNX6Y.js"),
+  "../plots/regression.results.js": () => import("./regression.results-5J3QM4RX.js"),
+  "../plots/sampleView.js": () => import("./sampleView-QYTLYJEW.js"),
+  "../plots/singleCellPlot.js": () => import("./singleCellPlot-JS74VUGC.js"),
+  "../plots/stattable.js": () => import("./stattable-MDABSW3F.js"),
+  "../plots/survival/test/survival.integration.spec.js": () => import("./survival.integration.spec-HHWP3R4H.js"),
+  "../plots/table.js": () => import("./table-LTWQ3TLQ.js"),
+  "../plots/test/barchart.integration.spec.js": () => import("./barchart.integration.spec-Z6ECNFSM.js"),
+  "../plots/test/cuminc.integration.spec.js": () => import("./cuminc.integration.spec-LSWV3KOF.js"),
+  "../plots/test/dataDownload.integration.spec.js": () => import("./dataDownload.integration.spec-J6FRFLBK.js"),
+  "../plots/test/expclust.gdc.spec.js": () => import("./expclust.gdc.spec-ZSILLYNI.js"),
+  "../plots/test/regression.integration.spec.js": () => import("./regression.integration.spec-KDHC3KDU.js"),
+  "../plots/test/regression.spec.js": () => import("./regression.spec-WZAZTDDA.js"),
+  "../plots/test/summary.integration.spec.js": () => import("./summary.integration.spec-AVGSW5MF.js"),
+  "../plots/test/violin.integration.spec.js": () => import("./violin.integration.spec-PVEF77HB.js"),
+  "../plots/violin.interactivity.js": () => import("./violin.interactivity-FYU4TCFO.js"),
+  "../plots/violin.js": () => import("./violin-ZQ3DEYGR.js"),
+  "../plots/violin.renderer.js": () => import("./violin.renderer-XAERGBMV.js"),
+  "../plots/volcano/test/testData.js": () => import("./testData-LEJ53F2K.js"),
+  "../plots/wsiviewer/plot.wsi.js": () => import("./plot.wsi-7M5KTNFC.js")
+});
+
+// plots/importPlot.js
+async function importPlot(chartType, notFoundMessage = "") {
+  switch (chartType) {
+    case "aggregateMatrix":
+      return await import("./AggregateMatrix-YH2SN6VN.js");
+    case "AIProjectAdmin":
+      return await import("./AIProjectAdmin-W36NGUX2.js");
+    case "barchart":
+      return await import("./barchart-OGCLBPQ2.js");
+    case "boxplot":
+      return await import("./BoxPlot-4SXDAOBP.js");
+    case "correlationVolcano":
+      return await import("./CorrelationVolcano-NAWMGG4Q.js");
+    case "DEinput":
+      return await import("./DEinput-TKERM2YD.js");
+    case "dictionary":
+      return await import("./dictionary-GD67R72W.js");
+    case "differentialAnalysis":
+      return await import("./DifferentialAnalysis-Y4SU4BVP.js");
+    case "Disco":
+      return await import("./Disco-DLK3BYPV.js");
+    case "dmr":
+      return await import("./DmrPlot-JWBZJFS6.js");
+    case "DziViewer":
+      return await import("./DziViewer-6737GC22.js");
+    case "GeneExpInput":
+      return await import("./GeneExpInput-KX5I63YV.js");
+    case "genomeBrowser":
+      return await import("./GB-3UZSSIBW.js");
+    case "geomap":
+      return await import("./Geomap-QTUHM4VH.js");
+    case "grin2":
+      return await import("./grin2-EI5BVP4E.js");
+    case "gsea":
+      return await import("./GSEA-YLHBZY55.js");
+    case "imagePlot":
+      return await import("./imagePlot-LGLFG2QZ.js");
+    case "report":
+      return await import("./report-M5TYHH2W.js");
+    case "runChart2":
+    //See frequencyChart
+    case "frequencyChart":
+      return await import("./RunChart2-2L6T3ITZ.js");
+    case "profileBarchart2":
+      return await import("./barchart2-DT42I747.js");
+    case "profileForms":
+      return await import("./profileForms-DFPCNJW2.js");
+    case "profilePlot":
+      return await import("./profilePlot-ECTPPVB2.js");
+    case "profilePolar2":
+      return await import("./polar2-7VSWGT4U.js");
+    case "profileRadar2":
+      return await import("./radar2-4QQER64E.js");
+    case "profileRadarFacility2":
+      return await import("./radarFacility2-MZKORRDY.js");
+    case "proteinView":
+      return await import("./proteinView-6ELOLOIU.js");
+    case "numericDictTermCluster":
+      return await import("./numericDictTermCluster-3HXLMURH.js");
+    case "proteomeAbundance":
+      return await import("./proteomeAbundance-NQ4635NL.js");
+    case "animatedBubbleChart":
+      return await import("./animatedBubbleChart-XKW6TCZP.js");
+    case "bubbleHeatmap":
+      return await import("./bubbleHeatmap-Y4SGMVJY.js");
+    case "cellTypeBubbleHeatmap":
+      return await import("./cellTypeBubbleHeatmap-QW37ZT5W.js");
+    case "brainRegions":
+      return await import("./brainRegions-DRYZT5K5.js");
+    case "studyCatalog":
+      return await import("./studyCatalog-EU33KE5H.js");
+    case "proteomeCohortCompare":
+      return await import("./proteomeCohortCompare-V2FMWI62.js");
+    case "geneRanking":
+      return await import("./geneRanking-TWLBKQZG.js");
+    case "ProteomeInput":
+      return await import("./ProteomeInput-MM373EL3.js");
+    case "sampleScatter":
+      return await import("./scatter-UOPJYXL3.js");
+    case "sc":
+      return await import("./SC-JKD3Z2X5.js");
+    case "summarizeCnvGeneexp":
+      return await import("./summarizeCnvGeneexp-QL25OQNB.js");
+    case "summarizeGeneexpSurvival":
+      return await import("./summarizeGeneexpSurvival-B7HTCH7L.js");
+    case "summarizeMutationDiagnosis":
+      return await import("./summarizeMutationDiagnosis-HCSDSVII.js");
+    case "summarizeMutationSurvival":
+      return await import("./summarizeMutationSurvival-6WEASSA2.js");
+    case "summarizeMutationCnv":
+      return await import("./summarizeMutationCnv-DFAPX2JE.js");
+    case "summaryInput":
+      return await import("./summaryInput-MOQ6HUCX.js");
+    case "summary":
+      return await import("./summary-BWYXE77G.js");
+    case "survival":
+      return await import("./survival-5TFMM7NP.js");
+    case "table":
+      return await import("./table-LTWQ3TLQ.js");
+    case "violin":
+      return await import("./violin-ZQ3DEYGR.js");
+    case "volcano":
+      return await import("./Volcano-STGBS7IJ.js");
+    case "WSISamplesPlot":
+      return await import("./WsiSamplesPlot-D3L3AILR.js");
+    case "WSIViewer":
+      return await import("./WSIViewer-LOBVUTOD.js");
+    default:
+      if (notFoundMessage) throw notFoundMessage;
+      return await globImport_plots_js(`../plots/${chartType}.js`);
+  }
+}
+
+export {
+  importPlot
+};
+//# sourceMappingURL=chunk-HQAJVJCQ.js.map

package/dist/chunk-HQAJVJCQ.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 'aggregateMatrix':\n\t\t\treturn await import('./aggregateMatrix/AggregateMatrix.ts')\n\t\t\t\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"],
+  "mappings": ";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,eAAsB,WAAW,WAAW,kBAAkB,IAAI;AAGjE,UAAQ,WAAW;AAAA,IAClB,KAAK;AACJ,aAAO,MAAM,OAAO,+BAAsC;AAAA,IAE3D,KAAK;AACJ,aAAO,MAAM,OAAO,8BAAoC;AAAA,IAEzD,KAAK;AACJ,aAAO,MAAM,OAAO,wBAAe;AAAA,IAEpC,KAAK;AACJ,aAAO,MAAM,OAAO,uBAAsB;AAAA,IAE3C,KAAK;AACJ,aAAO,MAAM,OAAO,kCAAqC;AAAA,IAE1D,KAAK;AACJ,aAAO,MAAM,OAAO,uBAAc;AAAA,IAEnC,KAAK;AACJ,aAAO,MAAM,OAAO,0BAAiB;AAAA,IAEtC,KAAK;AACJ,aAAO,MAAM,OAAO,oCAAwC;AAAA,IAE7D,KAAK;AACJ,aAAO,MAAM,OAAO,qBAAkB;AAAA,IAEvC,KAAK;AACJ,aAAO,MAAM,OAAO,uBAAkB;AAAA,IAEvC,KAAK;AACJ,aAAO,MAAM,OAAO,yBAA0B;AAAA,IAE/C,KAAK;AACJ,aAAO,MAAM,OAAO,4BAAmB;AAAA,IAExC,KAAK;AACJ,aAAO,MAAM,OAAO,kBAAY;AAAA,IAEjC,KAAK;AACJ,aAAO,MAAM,OAAO,sBAAoB;AAAA,IAEzC,KAAK;AACJ,aAAO,MAAM,OAAO,qBAAe;AAAA,IAEpC,KAAK;AACJ,aAAO,MAAM,OAAO,oBAAgB;AAAA,IAErC,KAAK;AACJ,aAAO,MAAM,OAAO,yBAAgB;AAAA,IAErC,KAAK;AACJ,aAAO,MAAM,OAAO,sBAAoB;AAAA,IAEzC,KAAK;AAAA;AAAA,IACL,KAAK;AACJ,aAAO,MAAM,OAAO,yBAA0B;AAAA,IAE/C,KAAK;AACJ,aAAO,MAAM,OAAO,yBAAwB;AAAA,IAE7C,KAAK;AACJ,aAAO,MAAM,OAAO,4BAA2B;AAAA,IAEhD,KAAK;AACJ,aAAO,MAAM,OAAO,2BAA0B;AAAA,IAE/C,KAAK;AACJ,aAAO,MAAM,OAAO,sBAAqB;AAAA,IAE1C,KAAK;AACJ,aAAO,MAAM,OAAO,sBAAqB;AAAA,IAE1C,KAAK;AACJ,aAAO,MAAM,OAAO,8BAA6B;AAAA,IAElD,KAAK;AACJ,aAAO,MAAM,OAAO,2BAAkB;AAAA,IAEvC,KAAK;AACJ,aAAO,MAAM,OAAO,sCAA6B;AAAA,IAElD,KAAK;AACJ,aAAO,MAAM,OAAO,iCAAwB;AAAA,IAE7C,KAAK;AACJ,aAAO,MAAM,OAAO,mCAA0B;AAAA,IAE/C,KAAK;AACJ,aAAO,MAAM,OAAO,6BAAoB;AAAA,IAEzC,KAAK;AACJ,aAAO,MAAM,OAAO,qCAA4B;AAAA,IAEjD,KAAK;AACJ,aAAO,MAAM,OAAO,4BAAmB;AAAA,IAExC,KAAK;AACJ,aAAO,MAAM,OAAO,4BAAmB;AAAA,IAExC,KAAK;AACJ,aAAO,MAAM,OAAO,qCAA4B;AAAA,IAEjD,KAAK;AACJ,aAAO,MAAM,OAAO,2BAAkB;AAAA,IAEvC,KAAK;AACJ,aAAO,MAAM,OAAO,6BAAoB;AAAA,IAEzC,KAAK;AACJ,aAAO,MAAM,OAAO,uBAAsB;AAAA,IAE3C,KAAK;AACJ,aAAO,MAAM,OAAO,kBAAY;AAAA,IAEjC,KAAK;AACJ,aAAO,MAAM,OAAO,mCAA0B;AAAA,IAE/C,KAAK;AACJ,aAAO,MAAM,OAAO,wCAA+B;AAAA,IAEpD,KAAK;AACJ,aAAO,MAAM,OAAO,0CAAiC;AAAA,IAEtD,KAAK;AACJ,aAAO,MAAM,OAAO,yCAAgC;AAAA,IAErD,KAAK;AACJ,aAAO,MAAM,OAAO,oCAA2B;AAAA,IAEhD,KAAK;AACJ,aAAO,MAAM,OAAO,4BAAmB;AAAA,IAExC,KAAK;AACJ,aAAO,MAAM,OAAO,uBAAc;AAAA,IAEnC,KAAK;AACJ,aAAO,MAAM,OAAO,wBAAwB;AAAA,IAE7C,KAAK;AACJ,aAAO,MAAM,OAAO,qBAAY;AAAA,IAEjC,KAAK;AACJ,aAAO,MAAM,OAAO,sBAAa;AAAA,IAElC,KAAK;AACJ,aAAO,MAAM,OAAO,uBAAsB;AAAA,IAE3C,KAAK;AACJ,aAAO,MAAM,OAAO,8BAAgC;AAAA,IAErD,KAAK;AACJ,aAAO,MAAM,OAAO,yBAA0B;AAAA,IAE/C;AAEC,UAAI,gBAAiB,OAAM;AAO3B,aAAO,MAAa,gCAAY,SAAS;AAAA,EAC3C;AACD;",
+  "names": []
+}

package/dist/chunk-IQVBMLFI.js

@@ -0,0 +1,446 @@
+import {
+  schemeCategory20
+} from "./chunk-V2OJLJSK.js";
+import {
+  isNumericTerm
+} from "./chunk-X6VTVZY7.js";
+import {
+  dtcnv,
+  dtsnvindel
+} from "./chunk-GEQUQ3GG.js";
+import {
+  category10_default
+} from "./chunk-2KXLYFAO.js";
+import {
+  linear,
+  ordinal
+} from "./chunk-UJELJXJG.js";
+import {
+  __export
+} from "./chunk-HFNDKYVF.js";
+
+// plots/matrix/matrix.legend.js
+var matrix_legend_exports = {};
+__export(matrix_legend_exports, {
+  CNVkey2order: () => CNVkey2order,
+  getLegendData: () => getLegendData,
+  getLegendItemText: () => getLegendItemText
+});
+function getLegendData(legendGroups, refs, self) {
+  const s = this.settings.matrix;
+  const legendData = [];
+  const dvt = this.config.divideBy || {};
+  const dvtId = dvt && "id" in dvt ? dvt.id : dvt.name;
+  for (const $id in legendGroups) {
+    const legend = legendGroups[$id];
+    if ($id == "Consequences") {
+      for (const f of this.config.legendValueFilter.lst) {
+        if (f.tvs.term.type !== "geneVariant") continue;
+        if (f.legendGrpName != $id) continue;
+        if (f.tvs.legendFilterType == "geneVariant_soft" && f.filteredOutCats.length == 0) {
+          continue;
+        }
+        for (const v of f.tvs.values) {
+          for (const key of v.mclasslst) {
+            const legendk = v.origin ? v.origin + key : key;
+            legend.values[legendk] = {
+              key,
+              dt: v.dt,
+              origin: v.origin,
+              label: v.label || self.mclass[key].label,
+              fill: v.color || self.mclass[key]?.color,
+              order: CNVkey2order(key),
+              crossedOut: f.tvs.legendFilterType == "geneVariant_hard" ? true : false,
+              greyedOut: f.tvs.legendFilterType == "geneVariant_soft" ? true : false
+            };
+          }
+        }
+      }
+      const keys2 = Object.keys(legend.values);
+      if (!keys2.length) continue;
+      legendData.unshift({
+        name: "Consequences",
+        order: legend.order,
+        $id: legend.$id,
+        dt: legend.dt,
+        origin: legend.origin,
+        items: keys2.map((key, i) => {
+          const item = legend.values[key];
+          const count = item.samples?.size;
+          return {
+            termid: "Consequences",
+            key: item.key,
+            text: this.getLegendItemText(item, count, {}, s),
+            color: item.fill,
+            order: i,
+            border: "1px solid #ccc",
+            count,
+            isLegendItem: true,
+            dt: item.dt,
+            crossedOut: item.crossedOut,
+            greyedOut: item.greyedOut,
+            origin: item.origin
+          };
+        })
+      });
+      legendData[0].items.sort((a, b) => a.text < b.text ? -1 : 1);
+      continue;
+    }
+    const t = $id == dvtId ? { tw: dvt } : this.termOrder.find((t2) => t2.tw.$id == $id || t2.tw.legend?.group == $id) || {
+      tw: { term: { id: $id, name: $id, type: $id === "CNV" ? "geneVariant" : "" } }
+    };
+    for (const f of this.config.legendValueFilter.lst) {
+      const name = t.tw.legend?.group || t.tw.label || t.tw.term.name;
+      if (f.legendGrpName != $id && f.legendGrpName != name && f.tvs.term.name != name) continue;
+      if (f.tvs.term.type == "geneVariant") {
+        for (const v of f.tvs.values) {
+          if (legend.dt && !legend.dt.includes(v.dt)) legend.dt.push(v.dt);
+          if (f.tvs.legendFilterType == "geneVariant_soft" && f.filteredOutCats.length == 0) {
+            continue;
+          }
+          for (const key of v.mclasslst) {
+            const legendk = v.origin ? v.origin + key : key;
+            legend.values[legendk] = {
+              key,
+              dt: v.dt,
+              origin: v.origin,
+              label: v.label || self.mclass[key]?.label || "Gain and loss",
+              fill: v.color || self.mclass[key]?.color,
+              order: CNVkey2order(key),
+              crossedOut: f.tvs.legendFilterType == "geneVariant_hard" ? true : false,
+              greyedOut: f.tvs.legendFilterType == "geneVariant_soft" ? true : false
+            };
+          }
+        }
+      } else {
+        if (isNumericTerm(f.tvs.term)) {
+          if (t.ref?.bins) {
+            for (const v of f.tvs.ranges) {
+              const termValues = t.ref.bins;
+              legend.values[v.name] = {
+                key: v.name,
+                label: termValues?.find((vl) => vl.name == v.name)?.name || v.name,
+                fill: termValues?.find((vl) => vl.name == v.name)?.color,
+                crossedOut: true
+              };
+            }
+          }
+        } else if (f.tvs.term.type == "survival") {
+          for (const v of f.tvs.values) {
+            const termValues = t.tw.term.values;
+            legend.values[v.key] = {
+              key: v.key,
+              label: termValues?.[v.key]?.label || "Exit code: " + v.key,
+              fill: v.key == 1 ? "#ff7f0e" : "#1f77b4",
+              crossedOut: true
+            };
+          }
+        } else {
+          for (const v of f.tvs.values) {
+            const termValues = t.tw.term.values;
+            legend.values[v.key] = {
+              key: v.key,
+              label: termValues?.[v.key]?.label || v.key,
+              fill: termValues?.[v.key]?.color,
+              crossedOut: true
+            };
+          }
+        }
+      }
+    }
+    const keys = Object.keys(legend.values).sort();
+    const hasScale = Object.values(legend.values).find((v) => v.scale);
+    if (hasScale) {
+      if (legend === legendGroups?.CNV) {
+        const gain = legend.values["CNV_amp"];
+        const loss = legend.values["CNV_loss"];
+        if (gain?.scale && loss?.scale) {
+          const colors = loss.scales?.legend.range;
+          const domain = loss.scales?.legend.domain;
+          const setLegendAttr = (item) => {
+            return {
+              $id,
+              domain: item.scales.legend.domain,
+              key: item.key,
+              isLegendItem: true,
+              minLabel: domain[0],
+              //item.minLoss, // item.maxLabel,
+              maxLabel: domain.slice(-1)[0],
+              //item.maxGain, // item.maxLabel,
+              scale: item.scale,
+              termid: "CNV"
+            };
+          };
+          const numericInputs = {
+            cutoffMode: s.cnvValues.cutoffMode,
+            defaultPercentile: s.cnvValues.defaultPercentile,
+            percentile: s.cnvValues.percentile,
+            callback: async (obj) => {
+              const cValues = self.config.settings.matrix.cnvValues;
+              if (obj.cutoffMode == "fixed") {
+                if (cValues.min == null) cValues.min = domain[0];
+                if (cValues.max == null) cValues.max = domain[domain.length - 1];
+                if (obj.min != cValues.min) obj.max = Math.abs(obj.min);
+                else obj.min = -obj.max;
+              }
+              self.config.settings.matrix.cnvValues = {
+                defaultPercentile: self.config.settings.matrix.cnvValues.defaultPercentile,
+                cutoffMode: obj.cutoffMode,
+                min: obj.min,
+                max: obj.max,
+                percentile: obj.percentile
+              };
+              await self.app.dispatch({
+                type: "plot_edit",
+                id: self.opts.id,
+                config: self.config
+              });
+            }
+          };
+          legend.values.CNV_gain_loss = {
+            key: $id,
+            label: "Gain and Loss",
+            dt: dtcnv,
+            order: -1,
+            domain,
+            name: "CNV gain/loss",
+            scale: linear().domain(domain).range(colors),
+            scales: loss.scales,
+            //Prevent the colors and domain recalculating below
+            minLabel: domain[0],
+            //loss.maxLabel,
+            maxLabel: domain.slice(-1)[0],
+            labels: { left: "Loss", right: "Gain" },
+            parents: [Object.assign(setLegendAttr(loss), loss), Object.assign(setLegendAttr(gain), gain)],
+            samples: /* @__PURE__ */ new Set([...gain.samples, ...loss.samples]),
+            numericInputs
+          };
+          delete legend.values[gain.key];
+          delete legend.values[loss.key];
+          keys.splice(keys.indexOf(gain.key), 1);
+          keys.splice(keys.indexOf(loss.key), 1);
+          keys.push("CNV_gain_loss");
+        }
+      }
+      const legendGrpLabelMaxChars = s.legendGrpLabelMaxChars || 26;
+      legendData.push({
+        name: $id.length < legendGrpLabelMaxChars ? $id : $id.slice(0, legendGrpLabelMaxChars) + "...",
+        //name:$id,
+        order: legend.order,
+        $id: legend.$id,
+        dt: legend.dt,
+        origin: legend.origin,
+        hasScale,
+        items: keys.map((key, i) => {
+          const item = legend.values[key];
+          const count = item.samples?.size;
+          if (item.scale) {
+            const colors = item.scales?.legend?.range || getColors(item);
+            const domain = item.scales?.legend?.domain || setColorScaleDomain(item.minLabel, item.maxLabel, item.domain, colors);
+            const opts = {
+              termid: $id,
+              key: item.key,
+              text: this.getLegendItemText(item, count, t, s),
+              width: 100,
+              scale: item.scale,
+              colors,
+              domain,
+              order: "order" in item ? item.order : i,
+              count,
+              isLegendItem: true,
+              dt: item.dt,
+              crossedOut: item.crossedOut,
+              greyedOut: item.greyedOut,
+              origin: item.origin,
+              parents: item.parents,
+              labels: item.labels
+            };
+            if (item.numericInputs) {
+              opts.numericInputs = item.numericInputs;
+            }
+            return opts;
+          } else {
+            return {
+              termid: $id,
+              key: item.key,
+              text: this.getLegendItemText(item, count, t, s),
+              color: item.fill || this.colorScaleByTermId[$id](key),
+              order: "order" in item ? item.order : i,
+              count,
+              isLegendItem: true,
+              dt: item.dt,
+              crossedOut: item.crossedOut,
+              greyedOut: item.greyedOut,
+              origin: item.origin
+            };
+          }
+        })
+      });
+    } else {
+      const grp = $id;
+      const term = t.tw.term;
+      const ref = legend.ref;
+      if (ref.bins)
+        keys.sort((a, b) => ref.bins.findIndex((bin) => bin.name === a) - ref.bins.findIndex((bin) => bin.name === b));
+      else if (ref.keyOrder) keys.sort((a, b) => ref.keyOrder.indexOf(a) - ref.keyOrder.indexOf(b));
+      if (!this.colorScaleByTermId[grp])
+        this.colorScaleByTermId[grp] = keys.length < 11 ? ordinal(category10_default) : ordinal(schemeCategory20);
+      const name = t.tw.legend?.group || t.tw.label || term.name;
+      const legendGrpLabelMaxChars = s.legendGrpLabelMaxChars || 26;
+      legendData.push({
+        name: name.length < legendGrpLabelMaxChars ? name : name.slice(0, legendGrpLabelMaxChars) + "...",
+        order: legend.order,
+        $id: legend.$id,
+        dt: legend.dt,
+        origin: legend.origin,
+        items: keys.map((key, i) => {
+          const item = legend.values[key];
+          const count = item.samples?.size;
+          return {
+            $id,
+            termid: term.id || term.name,
+            key: item.key,
+            text: this.getLegendItemText(item, count, t, s),
+            color: t.scale || item.fill || this.colorScaleByTermId[grp](key),
+            order: "order" in item ? item.order : i,
+            count,
+            isExcluded: item.isExcluded,
+            //onClickCallback: this.handleLegendItemClick,
+            isLegendItem: true,
+            dt: item.dt,
+            crossedOut: item.crossedOut,
+            greyedOut: item.greyedOut,
+            origin: item.origin
+          };
+        })
+      });
+    }
+  }
+  for (const grpFilter of self.config.legendGrpFilter.lst) {
+    if (grpFilter.dt.length == 1 && grpFilter.dt[0] == 4 && !legendData.filter((l) => l.dt)?.find((l) => l.dt.length == 1 && l.dt[0] == 4)) {
+      legendData.push({
+        name: "CNV",
+        dt: grpFilter.dt,
+        origin: grpFilter.origin,
+        crossedOut: true,
+        items: grpFilter.filteredOutCats.map((fc) => {
+          return {
+            dt: 4,
+            termid: "CNV",
+            origin: grpFilter.origin,
+            key: fc,
+            text: self.mclass[fc].label,
+            color: self.mclass[fc]?.color,
+            isLegendItem: true
+          };
+        })
+      });
+    } else if (grpFilter.dt.includes(dtsnvindel)) {
+      const controlLabels = self.settings.matrix.controlLabels;
+      const groupName = grpFilter.origin ? `${grpFilter.origin[0].toUpperCase() + grpFilter.origin.slice(1)} ${controlLabels.Mutations}` : controlLabels.Mutations;
+      if (!legendData.filter((l) => l.dt)?.find((l) => l.dt.includes(dtsnvindel) && l.origin == grpFilter.origin)) {
+        legendData.push({
+          name: groupName,
+          dt: grpFilter.dt,
+          origin: grpFilter.origin,
+          crossedOut: true,
+          items: grpFilter.filteredOutCats.map((fc) => {
+            return {
+              dt: self.mclass[fc].dt,
+              origin: grpFilter.origin,
+              termid: groupName,
+              key: fc,
+              text: self.mclass[fc].label,
+              color: self.mclass[fc]?.color,
+              isLegendItem: true
+            };
+          })
+        });
+      }
+    } else if (grpFilter.dt.length == 1 && grpFilter.dt[0] == 2 && !legendData.filter((l) => l.dt)?.find((l) => l.dt.length == 1 && l.dt[0] == 2)) {
+      legendData.push({
+        name: "Fusion RNA",
+        dt: grpFilter.dt,
+        origin: grpFilter.origin,
+        crossedOut: true,
+        items: grpFilter.filteredOutCats.map((fc) => {
+          return {
+            dt: 2,
+            origin: grpFilter.origin,
+            termid: "Fusion RNA",
+            key: fc,
+            text: self.mclass[fc].label,
+            color: self.mclass[fc]?.color,
+            isLegendItem: true
+          };
+        })
+      });
+    } else if (grpFilter.dt.length == 1 && grpFilter.dt[0] == 5 && !legendData.filter((l) => l.dt)?.find((l) => l.dt.length == 1 && l.dt[0] == 5)) {
+      legendData.push({
+        name: "Structural Variation",
+        dt: grpFilter.dt,
+        origin: grpFilter.origin,
+        crossedOut: true,
+        items: grpFilter.filteredOutCats.map((fc) => {
+          return {
+            dt: 5,
+            origin: grpFilter.origin,
+            termid: "Structural Variation",
+            key: fc,
+            text: self.mclass[fc].label,
+            color: self.mclass[fc]?.color,
+            isLegendItem: true
+          };
+        })
+      });
+    }
+  }
+  for (const itemsGrp of legendData) {
+    itemsGrp.items.sort((a, b) => {
+      const getStatusOrder = (item) => {
+        if (!item.greyedOut && !item.crossedOut) return 0;
+        if (item.greyedOut && !item.crossedOut) return 1;
+        if (item.crossedOut) return 2;
+        return 3;
+      };
+      return getStatusOrder(a) - getStatusOrder(b);
+    });
+  }
+  return legendData.sort(
+    (a, b) => a.crossedOut && b.crossedOut ? 0 : a.crossedOut ? 1 : b.crossedOut ? -1 : a.order && b.order ? a.order - b.order : a.order ? -1 : b.order ? 1 : 0
+  );
+}
+function getLegendItemText(item, count, t, s) {
+  if (item.crossedOut || item.greyedOut) {
+    return item.label;
+  }
+  let text = item.label;
+  const notes = [count];
+  if (item.isExcluded) notes.push("hidden");
+  if (t?.tw?.term?.type == "geneVariant" && s.geneVariantCountSamplesSkipMclass.includes(item.key))
+    notes.push("not counted");
+  if (!notes.length) return text;
+  return text += ` (${notes.join(", ")})`;
+}
+function setColorScaleDomain(min, max, domain, colors) {
+  if (domain[0] === min && domain[domain.length - 1] === max) return domain;
+  const step = (max - min) / (colors.length - 1);
+  return colors.map((_, i) => {
+    if (i === (colors.length - 1) / 2 && min < 0 && max > 0) return 0;
+    return min + step * i;
+  });
+}
+function getColors(item) {
+  return item.domain?.map((c) => item.scale(c)) || item.scale.range();
+}
+function CNVkey2order(key) {
+  return key == "CNV_homozygous_deletion" ? -5 : key == "CNV_amplification" ? -4 : key == "CNV_loss" ? -3 : key == "CNV_amp" ? -2 : key == "CNV_loh" ? -1 : 0;
+}
+
+export {
+  getLegendData,
+  getLegendItemText,
+  CNVkey2order,
+  matrix_legend_exports
+};
+//# sourceMappingURL=chunk-IQVBMLFI.js.map