@sjcrh/proteinpaint-client 2.225.0 → 2.227.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/2dmaf-B34EJADN.js +1362 -0
- package/dist/AggMatrixInput-USCXGZT2.js +402 -0
- package/dist/AggregateMatrix-VLCSBD65.js +37 -0
- package/dist/AppHeader-KE7QVEW5.js +826 -0
- package/dist/BoxPlot-3H5QKYRD.js +1247 -0
- package/dist/CorrelationVolcano-ACEJOJS6.js +613 -0
- package/dist/CorrelationVolcano-ACEJOJS6.js.map +7 -0
- package/dist/Cuminc-6LPS4LR7.js +1217 -0
- package/dist/DE-TTKEQYC7.js +85 -0
- package/dist/DEinput-W7WEO2NO.js +483 -0
- package/dist/DEinput-W7WEO2NO.js.map +7 -0
- package/dist/DM-2TUF6Q3C.js +86 -0
- package/dist/DifferentialAnalysis-3LP4RAWF.js +236 -0
- package/dist/Disco-UP5C7UWX.js +3445 -0
- package/dist/Disco.UI-V4I4LOMF.js +239 -0
- package/dist/DmrPlot-TZR2NGIH.js +366 -0
- package/dist/GB-4NRY4YMF.js +1388 -0
- package/dist/GB-4NRY4YMF.js.map +7 -0
- package/dist/GSEA-YGKBRJJO.js +870 -0
- package/dist/GeneExpInput-L3J2ECVQ.js +38 -0
- package/dist/Geomap-4MHU6F57.js +80 -0
- package/dist/HicApp-27VGP5F6.js +2240 -0
- package/dist/IDCViewer-37GJPPUY.js +10810 -0
- package/dist/NumBinaryEditor-SEC2NDGG.js +274 -0
- package/dist/NumBinaryEditor.unit.spec-UDYSUC4S.js +308 -0
- package/dist/NumContEditor-YPSYWU2A.js +100 -0
- package/dist/NumContEditor.unit.spec-NHFBMHQ5.js +160 -0
- package/dist/NumCustomBinEditor-N7US5Q64.js +29 -0
- package/dist/NumCustomBinEditor.unit.spec-2BMMUBYU.js +393 -0
- package/dist/NumDiscreteEditor-BLQ5DEB7.js +165 -0
- package/dist/NumDiscreteEditor.unit.spec-JOFPUFU5.js +229 -0
- package/dist/NumRegularBinEditor-7BFPBUW2.js +29 -0
- package/dist/NumRegularBinEditor.unit.spec-6GZMNRHA.js +274 -0
- package/dist/NumSplineEditor-LO3ZR3T3.js +205 -0
- package/dist/NumSplineEditor.unit.spec-MRA3DQSB.js +220 -0
- package/dist/NumericDensity-NUCVJZ74.js +29 -0
- package/dist/NumericDensity.unit.spec-TZLKWH4U.js +414 -0
- package/dist/NumericHandler-NH533VBN.js +30 -0
- package/dist/NumericHandler.unit.spec-V7MNEHML.js +225 -0
- package/dist/ProteomeInput-FEXWZOA2.js +610 -0
- package/dist/Regression-NJAPUGT7.js +1412 -0
- package/dist/RunChart2-QIJ6NUWY.js +744 -0
- package/dist/SC-5NWBVOEE.js +1290 -0
- package/dist/Violin-TMACI43Q.js +1105 -0
- package/dist/Volcano-BMLHQEXU.js +2745 -0
- package/dist/Volcano-BMLHQEXU.js.map +7 -0
- package/dist/Wsi-5TWAOBFG.js +650 -0
- package/dist/Wsi-5TWAOBFG.js.map +7 -0
- package/dist/aboutSunburst-53YAWTV5.js +93 -0
- package/dist/adSandbox-7VHXEI7W.js +29 -0
- package/dist/animatedBubbleChart-CTFGJIRR.js +542 -0
- package/dist/app-AQAQAPUN.js +38 -0
- package/dist/app-SZDIV5U4.js +28 -0
- package/dist/app.js +12 -12
- package/dist/bam-3U5R2KNC.js +872 -0
- package/dist/barchart-ZL5VSR7P.js +38 -0
- package/dist/barchart2-YELP2HI7.js +305 -0
- package/dist/block-AGX6Z4BR.js +6208 -0
- package/dist/block-AGX6Z4BR.js.map +7 -0
- package/dist/block.init-IBITFICI.js +29 -0
- package/dist/block.mds.expressionrank-4L76ILD4.js +350 -0
- package/dist/block.mds.geneboxplot-XA7DFHPV.js +819 -0
- package/dist/block.mds.junction-GTZD3HEN.js +1534 -0
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- package/dist/block.tk.aicheck-CV53ULEP.js +274 -0
- package/dist/block.tk.bam-KJYFNJCX.js +1906 -0
- package/dist/block.tk.bigwig.ui-A352D6PT.js +202 -0
- package/dist/block.tk.hicstraw-QAFTQESL.js +814 -0
- package/dist/block.tk.junction-XURB4RWZ.js +2353 -0
- package/dist/block.tk.junction.textmatrixui-RNRWWNGY.js +190 -0
- package/dist/block.tk.ld-GWJMVPX3.js +90 -0
- package/dist/block.tk.menu-BJZYFMQX.js +1050 -0
- package/dist/block.tk.pgv-7XNJTHEW.js +934 -0
- package/dist/brainImaging-37EDZLGN.js +550 -0
- package/dist/brainRegions-FEW52QUB.js +213 -0
- package/dist/bubbleHeatmap-YN34AA4H.js +374 -0
- package/dist/bubbleHeatmap-YN34AA4H.js.map +7 -0
- package/dist/cellTypeBubbleHeatmap-X4K63FOK.js +274 -0
- package/dist/cellTypeBubbleHeatmap-X4K63FOK.js.map +7 -0
- package/dist/chunk-24CVFDVW.js +1219 -0
- package/dist/chunk-24CVFDVW.js.map +7 -0
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- package/dist/chunk-JI632MAR.js.map +7 -0
- package/dist/chunk-JKPMBNRM.js +100 -0
- package/dist/chunk-JKPMBNRM.js.map +7 -0
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- package/dist/chunk-VPRP24DY.js.map +7 -0
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- package/dist/chunk-ZO7KUAIF.js +5258 -0
- package/dist/chunk-ZO7KUAIF.js.map +7 -0
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- package/dist/cohort-NKRTCX5Z.js +66 -0
- package/dist/cohortSunburst-DFJW6WXU.js +402 -0
- package/dist/condition-PYFOEVX5.js +323 -0
- package/dist/controls-RVNIN66W.js +30 -0
- package/dist/controls.config-XVEYYBI4.js +30 -0
- package/dist/correlation-MNL4DGSW.js +91 -0
- package/dist/customdata.inputui-WFIIJATQ.js +280 -0
- package/dist/dataDownload-CMSP5FA4.js +326 -0
- package/dist/databrowser.ui-FYZPXXEJ.js +424 -0
- package/dist/dictionary-76BXY6WU.js +109 -0
- package/dist/dnaMethylation-WTIJVNIU.js +29 -0
- package/dist/dnaMethylation.integration.spec-YXQEFLC5.js +194 -0
- package/dist/dnaMethylation.unit.spec-22FLJWVB.js +95 -0
- package/dist/dnaMethylation.unit.spec-22FLJWVB.js.map +7 -0
- package/dist/dofetch-XID2XEJT.js +49 -0
- package/dist/e2pca-DD6DA7X3.js +340 -0
- package/dist/ep-S4PI4AUJ.js +1247 -0
- package/dist/expclust.gdc.spec-BDV4RJO6.js +298 -0
- package/dist/facet-EOXEW2LN.js +556 -0
- package/dist/gb-AKE7RDPB.js +77 -0
- package/dist/geneExpClustering-73ED7HIN.js +240 -0
- package/dist/geneExpression-AEJILDKJ.js +29 -0
- package/dist/geneExpression-NXDXXKEA.js +309 -0
- package/dist/geneExpression.unit.spec-VUJWR4TA.js +150 -0
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- package/dist/geneORA-7KFQ4PW2.js +269 -0
- package/dist/geneRanking-RKJU4PM2.js +544 -0
- package/dist/geneVariant-2AGC3ECG.js +32 -0
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- package/dist/geneVariant.integration.spec-UJXGQEZG.js +672 -0
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- package/dist/geneset-BU6V3CB5.js +199 -0
- package/dist/genomeBrowser.spec-BGQHJZKH.js +272 -0
- package/dist/grin2-OUZN5LOU.js +66 -0
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- package/dist/hierCluster-3ERW47JJ.js +51 -0
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- package/dist/isoformExpression-K5BCDJLL.js +31 -0
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- package/dist/matrix.groups-3UH2KOIY.js +25 -0
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- /package/dist/{samplelst-RIC5E2W4.js.map → samplelst-7XXJTJ4J.js.map} +0 -0
- /package/dist/{samplematrix-WLCFCPBR.js.map → samplematrix-JN35HJBG.js.map} +0 -0
- /package/dist/{sc-TXRF7D6F.js.map → sc-6ZHDNPYP.js.map} +0 -0
- /package/dist/{scatter-YQ47446T.js.map → scatter-4MP6TG67.js.map} +0 -0
- /package/dist/{scatter-JUGGPR4B.js.map → scatter-TRMY47CC.js.map} +0 -0
- /package/dist/{selectGenomeWithTklst-2ELB6HQK.js.map → selectGenomeWithTklst-UDNTL544.js.map} +0 -0
- /package/dist/{singleCellCellType-DUTH4SZF.js.map → singleCellCellType-UXABRPQQ.js.map} +0 -0
- /package/dist/{singleCellCellType.unit.spec-PWP6I5PZ.js.map → singleCellCellType.unit.spec-N22EQMZW.js.map} +0 -0
- /package/dist/{singleCellGeneExpression-3563T7GE.js.map → singleCellGeneExpression-OBPVP6IU.js.map} +0 -0
- /package/dist/{singleCellGeneExpression.unit.spec-66IDCFJC.js.map → singleCellGeneExpression.unit.spec-NVCFU5B4.js.map} +0 -0
- /package/dist/{singleCellNumericValue-XVQTKLTS.js.map → singleCellNumericValue-Z2X3LLRB.js.map} +0 -0
- /package/dist/{singleCellNumericValue.unit.spec-LJSTGKNS.js.map → singleCellNumericValue.unit.spec-Q7DCQHEE.js.map} +0 -0
- /package/dist/{singleCellPlot-MKYJJXSG.js.map → singleCellPlot-S5N6ZEEA.js.map} +0 -0
- /package/dist/{singlecell-ANCWPAAO.js.map → singlecell-OK2P4AS2.js.map} +0 -0
- /package/dist/{singlecell-KMRVFOC5.js.map → singlecell-RI6HA3NI.js.map} +0 -0
- /package/dist/{snp-B5UHGWVD.js.map → snp-XRM2UAEJ.js.map} +0 -0
- /package/dist/{snp.unit.spec-YAHITASM.js.map → snp.unit.spec-CDTYGH4K.js.map} +0 -0
- /package/dist/{snplocus-MLGICRGT.js.map → snplocus-CAUGDRZE.js.map} +0 -0
- /package/dist/{snplst-DZPIQEKI.js.map → snplst-DP533FL2.js.map} +0 -0
- /package/dist/{spliceevent.a53ss.diagram-4NYPSFC2.js.map → spliceevent.a53ss.diagram-XWEN4UMO.js.map} +0 -0
- /package/dist/{spliceevent.exonskip.diagram-WLLTP7NP.js.map → spliceevent.exonskip.diagram-HBXQOUT4.js.map} +0 -0
- /package/dist/{spliceevent.noeventdiagram-NOSO752Y.js.map → spliceevent.noeventdiagram-ORQJ62ON.js.map} +0 -0
- /package/dist/{ssGSEA-4DVY6Z5U.js.map → ssGSEA-PLDZ2556.js.map} +0 -0
- /package/dist/{ssGSEA.unit.spec-UDXV4Q7S.js.map → ssGSEA.unit.spec-ORFJFZJY.js.map} +0 -0
- /package/dist/{stattable-T5X76Q32.js.map → stattable-GVRVRO2Y.js.map} +0 -0
- /package/dist/{studyCatalog-O3EPBJPW.js.map → studyCatalog-K46WJHC6.js.map} +0 -0
- /package/dist/{summarizeCnvGeneexp-ST36TPEJ.js.map → summarizeCnvGeneexp-7WSJTWKH.js.map} +0 -0
- /package/dist/{summarizeGeneexpSurvival-AZOFCBMT.js.map → summarizeGeneexpSurvival-H3TW7I4I.js.map} +0 -0
- /package/dist/{summarizeMutationCnv-HRCW6BYV.js.map → summarizeMutationCnv-JOYXEMFP.js.map} +0 -0
- /package/dist/{summarizeMutationDiagnosis-RQQO2MOR.js.map → summarizeMutationDiagnosis-GBIGXFY5.js.map} +0 -0
- /package/dist/{summarizeMutationSurvival-UHSUJ7FU.js.map → summarizeMutationSurvival-3RULG3KW.js.map} +0 -0
- /package/dist/{summary-ZMM5ET67.js.map → summary-VKLFTPC2.js.map} +0 -0
- /package/dist/{summary.integration.spec-GW5UGDDU.js.map → summary.integration.spec-EK3MPFVD.js.map} +0 -0
- /package/dist/{summaryInput-ZO5TPARQ.js.map → summaryInput-POI5KQSP.js.map} +0 -0
- /package/dist/{sunburst-LXRG2SFE.js.map → sunburst-BIVYHF5R.js.map} +0 -0
- /package/dist/{sunburst-6VJS2SUY.js.map → sunburst-SYHQOCGQ.js.map} +0 -0
- /package/dist/{survival-U6J6KFN2.js.map → survival-CG2GQ4YY.js.map} +0 -0
- /package/dist/{survival-QXHY7JRR.js.map → survival-NEO3E2HS.js.map} +0 -0
- /package/dist/{survival.integration.spec-HN3LL6IY.js.map → survival.integration.spec-PPK5KO4V.js.map} +0 -0
- /package/dist/{svgraph-CVI27CTM.js.map → svgraph-Q2U2HEMF.js.map} +0 -0
- /package/dist/{swimmer-M4JGBO72.js.map → swimmer-GA4C6YH7.js.map} +0 -0
- /package/dist/{table-QO22C2ER.js.map → table-DJJIES6L.js.map} +0 -0
- /package/dist/{termCollection-EN73BZV5.js.map → termCollection-CHVUM5C6.js.map} +0 -0
- /package/dist/{termCollection-KWNFLRWJ.js.map → termCollection-R3LTBPJ4.js.map} +0 -0
- /package/dist/{termCollection.unit.spec-Z27AZUE6.js.map → termCollection.unit.spec-B7KAAOFT.js.map} +0 -0
- /package/dist/{termCollectionFractionSelection-Q7QFEPKA.js.map → termCollectionFractionSelection-A72QM36J.js.map} +0 -0
- /package/dist/{termCollectionFractionSelection.unit.spec-PYLIFZN5.js.map → termCollectionFractionSelection.unit.spec-JR77QEIG.js.map} +0 -0
- /package/dist/{tk-WVEDS5OU.js.map → tk-GRGKFATN.js.map} +0 -0
- /package/dist/{tp.ui-CG36YXBY.js.map → tp.ui-NATRJ5EN.js.map} +0 -0
- /package/dist/{tvs.categorical-GCJISWBS.js.map → tvs.categorical-U2ZYLPSW.js.map} +0 -0
- /package/dist/{tvs.condition-YTCVMB3I.js.map → tvs.condition-6EBZALR4.js.map} +0 -0
- /package/dist/{tvs.dt-UCSZ5S44.js.map → tvs.dt-H626ESMQ.js.map} +0 -0
- /package/dist/{tvs.dtcnv.categorical-KYB6XPL3.js.map → tvs.dtcnv.categorical-6S7INDYC.js.map} +0 -0
- /package/dist/{tvs.dtcnv.continuous-MJWJNMKJ.js.map → tvs.dtcnv.continuous-MLYNEMHI.js.map} +0 -0
- /package/dist/{tvs.dtfusion-IZCEMTH5.js.map → tvs.dtfusion-2OLY6X7G.js.map} +0 -0
- /package/dist/{tvs.dtitd-DZ4WWGNO.js.map → tvs.dtitd-Z6MEL5SH.js.map} +0 -0
- /package/dist/{tvs.dtsnvindel-PMJCV4E7.js.map → tvs.dtsnvindel-HPBQSCYV.js.map} +0 -0
- /package/dist/{tvs.dtsv-5K2RNWDH.js.map → tvs.dtsv-BRRNX64J.js.map} +0 -0
- /package/dist/{tvs.multivalue-6NSC6JPR.js.map → tvs.multivalue-H2G7WKAL.js.map} +0 -0
- /package/dist/{tvs.numeric-7U2NDY4A.js.map → tvs.numeric-OKYGMQSK.js.map} +0 -0
- /package/dist/{tvs.samplelst-3SIYTFWZ.js.map → tvs.samplelst-46FGACU7.js.map} +0 -0
- /package/dist/{tvs.survival-Q3F5SLBW.js.map → tvs.survival-QL4KC3SQ.js.map} +0 -0
- /package/dist/{tvs.termCollection-OR73LBNX.js.map → tvs.termCollection-22DFW3PF.js.map} +0 -0
- /package/dist/{vocabulary-RWRAQ4VJ.js.map → vocabulary-LJEERZJ6.js.map} +0 -0
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i = htry("sample", "sampleid");
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i = htry("snv4");
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header[i] = "coverage";
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header[i] = "maf";
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}
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function parseline(i, line, header, badlines, data) {
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const lst = line.split(" ");
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m[header[j]] = lst[j];
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}
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if (!m.patient) {
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badlines.push([i, "missing patient", lst]);
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return;
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}
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if (!data[m.patient]) {
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data[m.patient] = {
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snv4: {},
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show: false
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};
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}
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if (!m.snv4) {
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badlines.push([i, "missing snv4", lst]);
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return;
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}
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if (!data[m.patient].snv4[m.snv4]) {
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data[m.patient].snv4[m.snv4] = {
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mutationname: m.snv4,
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samples: [],
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subidx: void 0
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};
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|
202
|
+
}
|
|
203
|
+
if (m.gene) {
|
|
204
|
+
data[m.patient].snv4[m.snv4].gene = m.gene;
|
|
205
|
+
}
|
|
206
|
+
if (!m.maf) {
|
|
207
|
+
badlines.push([i, "missing maf", lst]);
|
|
208
|
+
return;
|
|
209
|
+
}
|
|
210
|
+
let v = Number.parseFloat(m.maf);
|
|
211
|
+
if (Number.isNaN(v)) {
|
|
212
|
+
badlines.push([i, "invalid maf", lst]);
|
|
213
|
+
return;
|
|
214
|
+
}
|
|
215
|
+
if (v < zerovalue) {
|
|
216
|
+
v = zerovalue;
|
|
217
|
+
}
|
|
218
|
+
m.maf = v;
|
|
219
|
+
if (!m.coverage) {
|
|
220
|
+
badlines.push([i, "missing total_readcount", lst]);
|
|
221
|
+
return;
|
|
222
|
+
}
|
|
223
|
+
if (m.call_manual && m.call_manual == "wildtype") {
|
|
224
|
+
m.maf = zerovalue;
|
|
225
|
+
}
|
|
226
|
+
v = Number.parseInt(m.coverage);
|
|
227
|
+
if (Number.isNaN(v)) {
|
|
228
|
+
badlines.push([i, "invalid total_readcount", lst]);
|
|
229
|
+
return;
|
|
230
|
+
}
|
|
231
|
+
m.coverage = v;
|
|
232
|
+
let date;
|
|
233
|
+
if (m.date) {
|
|
234
|
+
const f = timeParse("%m/%d/%Y");
|
|
235
|
+
date = f(m.date);
|
|
236
|
+
m.Date = m.date;
|
|
237
|
+
} else {
|
|
238
|
+
badlines.push([i, "missing date", lst]);
|
|
239
|
+
return;
|
|
240
|
+
}
|
|
241
|
+
if (date == null) {
|
|
242
|
+
badlines.push([i, "cannot parse date", lst]);
|
|
243
|
+
return;
|
|
244
|
+
}
|
|
245
|
+
m.date = date;
|
|
246
|
+
if (!m.sample) {
|
|
247
|
+
badlines.push([i, "missing sample", lst]);
|
|
248
|
+
return;
|
|
249
|
+
}
|
|
250
|
+
data[m.patient].snv4[m.snv4].samples.push(m);
|
|
251
|
+
return true;
|
|
252
|
+
}
|
|
253
|
+
function render(data, header, holder) {
|
|
254
|
+
const table = holder.append("table").style("margin", "20px");
|
|
255
|
+
const tr1 = table.append("tr");
|
|
256
|
+
let td = tr1.append("td").style("vertical-align", "top").attr("rowspan", 2);
|
|
257
|
+
td.append("button").text("Toggle circle visibility").on("click", () => {
|
|
258
|
+
showcircle = !showcircle;
|
|
259
|
+
for (const n in data) {
|
|
260
|
+
if (data[n].show) {
|
|
261
|
+
data[n].handle.node().click();
|
|
262
|
+
break;
|
|
263
|
+
}
|
|
264
|
+
}
|
|
265
|
+
});
|
|
266
|
+
const patientholder = td.append("div").style("margin-top", "10px");
|
|
267
|
+
const td1 = tr1.append("td").style("vertical-align", "top");
|
|
268
|
+
const graphholder = td1.append("div").style("display", "inline-block");
|
|
269
|
+
const controlholder = td1.append("div").style("display", "inline-block").style("vertical-align", "top");
|
|
270
|
+
const tr2 = table.append("tr");
|
|
271
|
+
const tiantable = tr2.append("td").append("table").style("border-spacing", "20px").style("border-collapse", "separate");
|
|
272
|
+
const gtr1 = tiantable.append("tr");
|
|
273
|
+
td = gtr1.append("td").style("vertical-align", "top");
|
|
274
|
+
td.append("div").text("Shared").style("font-size", "2em");
|
|
275
|
+
const graph1holder = td.append("div").style("border", "solid 1px black");
|
|
276
|
+
td = gtr1.append("td").style("vertical-align", "top");
|
|
277
|
+
td.append("div").text("Rising").style("font-size", "2em");
|
|
278
|
+
const graph2holder = td.append("div").style("border", "solid 1px black");
|
|
279
|
+
const gtr2 = tiantable.append("tr");
|
|
280
|
+
td = gtr2.append("td").style("vertical-align", "top");
|
|
281
|
+
td.append("div").text("Falling").style("font-size", "2em");
|
|
282
|
+
const graph3holder = td.append("div").style("border", "solid 1px black");
|
|
283
|
+
td = gtr2.append("td").style("vertical-align", "top");
|
|
284
|
+
td.append("div").text("R-only").style("font-size", "2em");
|
|
285
|
+
const graph4holder = td.append("div").style("border", "solid 1px black");
|
|
286
|
+
for (const patient in data) {
|
|
287
|
+
const snvlst = [];
|
|
288
|
+
const colors = ordinal(category10_default);
|
|
289
|
+
for (const x in data[patient].snv4) {
|
|
290
|
+
const snv = data[patient].snv4[x];
|
|
291
|
+
snv.show = true;
|
|
292
|
+
snv.color = colors(snv.mutationname);
|
|
293
|
+
snv.samples.sort((a, b) => a.date - b.date);
|
|
294
|
+
for (const s of snv.samples) {
|
|
295
|
+
s.color = snv.color;
|
|
296
|
+
}
|
|
297
|
+
snvlst.push(snv);
|
|
298
|
+
}
|
|
299
|
+
const div = patientholder.append("div").classed("sja_menuoption", true).style("color", "black").text(patient).on("click", () => {
|
|
300
|
+
for (const pn in data) {
|
|
301
|
+
data[pn].handle.style("color", "black");
|
|
302
|
+
data[pn].show = false;
|
|
303
|
+
}
|
|
304
|
+
data[patient].handle.style("color", "red");
|
|
305
|
+
data[patient].show = true;
|
|
306
|
+
makegraph(snvlst, header, graphholder);
|
|
307
|
+
makesubgraph(snvlst, graph1holder, graph2holder, graph3holder, graph4holder);
|
|
308
|
+
makecontrol(snvlst, header, controlholder, graphholder, graph1holder, graph2holder, graph3holder, graph4holder);
|
|
309
|
+
});
|
|
310
|
+
data[patient].handle = div;
|
|
311
|
+
}
|
|
312
|
+
for (const n in data) {
|
|
313
|
+
data[n].handle.node().click();
|
|
314
|
+
break;
|
|
315
|
+
}
|
|
316
|
+
}
|
|
317
|
+
function makesubgraph(snvlst, g1, g2, g3, g4) {
|
|
318
|
+
g1.selectAll("*").remove();
|
|
319
|
+
g2.selectAll("*").remove();
|
|
320
|
+
g3.selectAll("*").remove();
|
|
321
|
+
g4.selectAll("*").remove();
|
|
322
|
+
const l1 = [];
|
|
323
|
+
const l2 = [];
|
|
324
|
+
const l3 = [];
|
|
325
|
+
const l4 = [];
|
|
326
|
+
for (const snv of snvlst) {
|
|
327
|
+
switch (snv.subidx) {
|
|
328
|
+
case 1:
|
|
329
|
+
l1.push(snv);
|
|
330
|
+
break;
|
|
331
|
+
case 2:
|
|
332
|
+
l2.push(snv);
|
|
333
|
+
break;
|
|
334
|
+
case 3:
|
|
335
|
+
l3.push(snv);
|
|
336
|
+
break;
|
|
337
|
+
case 4:
|
|
338
|
+
l4.push(snv);
|
|
339
|
+
break;
|
|
340
|
+
}
|
|
341
|
+
}
|
|
342
|
+
if (l1.length) {
|
|
343
|
+
makegraph(l1, null, g1, true);
|
|
344
|
+
} else {
|
|
345
|
+
g1.append("div").style("padding", "60px").style("background-color", "#ededed").text("no data");
|
|
346
|
+
}
|
|
347
|
+
if (l2.length) {
|
|
348
|
+
makegraph(l2, null, g2, true);
|
|
349
|
+
} else {
|
|
350
|
+
g2.append("div").style("padding", "60px").style("background-color", "#ededed").text("no data");
|
|
351
|
+
}
|
|
352
|
+
if (l3.length) {
|
|
353
|
+
makegraph(l3, null, g3, true);
|
|
354
|
+
} else {
|
|
355
|
+
g3.append("div").style("padding", "60px").style("background-color", "#ededed").text("no data");
|
|
356
|
+
}
|
|
357
|
+
if (l4.length) {
|
|
358
|
+
makegraph(l4, null, g4, true);
|
|
359
|
+
} else {
|
|
360
|
+
g4.append("div").style("padding", "60px").style("background-color", "#ededed").text("no data");
|
|
361
|
+
}
|
|
362
|
+
}
|
|
363
|
+
function makegraph(snvlst0, header, holder, issub) {
|
|
364
|
+
holder.selectAll("*").remove();
|
|
365
|
+
const samples = [];
|
|
366
|
+
const snvlst = [];
|
|
367
|
+
for (const snv of snvlst0) {
|
|
368
|
+
if (!issub && !snv.show) continue;
|
|
369
|
+
snvlst.push(snv);
|
|
370
|
+
for (const s of snv.samples) {
|
|
371
|
+
samples.push(s);
|
|
372
|
+
}
|
|
373
|
+
}
|
|
374
|
+
if (snvlst.length == 0) return;
|
|
375
|
+
let mindate = snvlst[0].samples[0].date;
|
|
376
|
+
let maxdate = snvlst[0].samples[0].date;
|
|
377
|
+
let maxmaf = snvlst[0].samples[0].maf;
|
|
378
|
+
let maxcoverage = snvlst[0].samples[0].coverage;
|
|
379
|
+
for (const snv of snvlst) {
|
|
380
|
+
for (const s of snv.samples) {
|
|
381
|
+
mindate = Math.min(mindate, s.date);
|
|
382
|
+
maxdate = Math.max(maxdate, s.date);
|
|
383
|
+
maxmaf = Math.max(maxmaf, s.maf);
|
|
384
|
+
maxcoverage = Math.max(maxcoverage, s.coverage);
|
|
385
|
+
}
|
|
386
|
+
}
|
|
387
|
+
const svg = holder.append("svg");
|
|
388
|
+
const toppad = 30, rightpad = 200, yaxisw = 100, xaxish = 50;
|
|
389
|
+
let width = 600;
|
|
390
|
+
let height = 400;
|
|
391
|
+
let xpad, ypad, minradius;
|
|
392
|
+
const xaxisg = svg.append("g");
|
|
393
|
+
const yaxisg = svg.append("g");
|
|
394
|
+
const drag = svg.append("text").text("drag to resize").attr("class", "sja_clb").attr("text-anchor", "end").on("mousedown", (event) => {
|
|
395
|
+
event.preventDefault();
|
|
396
|
+
const x = event.clientX;
|
|
397
|
+
const y = event.clientY;
|
|
398
|
+
const w0 = width;
|
|
399
|
+
const h0 = height;
|
|
400
|
+
const body = select_default(document.body);
|
|
401
|
+
body.on("mousemove", (event2) => {
|
|
402
|
+
setsize(w0 + event2.clientX - x, h0 + event2.clientY - y);
|
|
403
|
+
}).on("mouseup", () => {
|
|
404
|
+
body.on("mousemove", null).on("mouseup", null);
|
|
405
|
+
});
|
|
406
|
+
});
|
|
407
|
+
const xscale = time().domain([mindate, maxdate]);
|
|
408
|
+
const yscale = (maflogscale ? log() : linear()).domain([zerovalue, 1]);
|
|
409
|
+
const rscale = linear().domain([1, maxcoverage]);
|
|
410
|
+
const g = svg.append("g");
|
|
411
|
+
const lines = g.selectAll().data(snvlst).enter().append("path").attr("stroke", (d) => d.color).attr("fill", "none");
|
|
412
|
+
let circles;
|
|
413
|
+
if (showcircle) {
|
|
414
|
+
circles = g.selectAll().data(samples).enter().append("circle").attr("fill", (d) => d.color).attr("fill-opacity", 0.1).on("mouseover", (event, d) => {
|
|
415
|
+
event.target.setAttribute("fill-opacity", 0.4);
|
|
416
|
+
tip.clear();
|
|
417
|
+
tip.show(event.clientX, event.clientY);
|
|
418
|
+
const lst = [];
|
|
419
|
+
for (const k in d) {
|
|
420
|
+
if (k == "color") continue;
|
|
421
|
+
if (k == "gene") {
|
|
422
|
+
lst.push({ k: "gene", v: '<span style="color:' + d.color + '">' + d.gene + "</span>" });
|
|
423
|
+
continue;
|
|
424
|
+
}
|
|
425
|
+
if (k == "date") continue;
|
|
426
|
+
if (k == "url") {
|
|
427
|
+
lst.push({ k: "URL", v: "<a href=" + d.url + " target=_blank>LINK</a>" });
|
|
428
|
+
continue;
|
|
429
|
+
}
|
|
430
|
+
lst.push({ k, v: d[k] });
|
|
431
|
+
}
|
|
432
|
+
make_table_2col(tip.d, lst);
|
|
433
|
+
}).on("mouseout", (event) => {
|
|
434
|
+
event.target.setAttribute("fill-opacity", 0.1);
|
|
435
|
+
});
|
|
436
|
+
}
|
|
437
|
+
const legend = svg.append("g");
|
|
438
|
+
const setsize = (w, h) => {
|
|
439
|
+
width = w;
|
|
440
|
+
height = h;
|
|
441
|
+
minradius = 2;
|
|
442
|
+
const maxradius = Math.max(width, height) / 30;
|
|
443
|
+
xpad = maxradius;
|
|
444
|
+
ypad = maxradius;
|
|
445
|
+
rscale.range([Math.pow(minradius, 2), Math.pow(maxradius, 2)]);
|
|
446
|
+
xscale.range([0, width]);
|
|
447
|
+
yscale.range([height, 0]);
|
|
448
|
+
svg.attr("width", yaxisw + xpad + width + rightpad).attr("height", toppad + height + ypad + xaxish);
|
|
449
|
+
xaxisg.attr("transform", "translate(" + (yaxisw + xpad) + "," + (toppad + height + ypad) + ")");
|
|
450
|
+
yaxisg.attr("transform", "translate(" + yaxisw + "," + toppad + ")");
|
|
451
|
+
drag.attr("x", yaxisw + xpad + width).attr("y", toppad + height + ypad + xaxish - 4);
|
|
452
|
+
axisstyle({
|
|
453
|
+
axis: xaxisg.call(axisBottom().scale(xscale)),
|
|
454
|
+
showline: true,
|
|
455
|
+
color: "black",
|
|
456
|
+
fontsize: Math.max(12, Math.min(20, width / 100))
|
|
457
|
+
});
|
|
458
|
+
axisstyle({
|
|
459
|
+
axis: yaxisg.call(
|
|
460
|
+
axisLeft().scale(yscale).tickValues([1, 0.1, 0.01, 1e-3, 1e-4, zerovalue]).tickFormat(format(" "))
|
|
461
|
+
),
|
|
462
|
+
showline: true,
|
|
463
|
+
color: "black",
|
|
464
|
+
fontsize: Math.max(12, Math.min(20, height / 100))
|
|
465
|
+
});
|
|
466
|
+
g.attr("transform", "translate(" + (yaxisw + xpad) + "," + toppad + ")");
|
|
467
|
+
lines.attr("d", (d) => {
|
|
468
|
+
const lst = [];
|
|
469
|
+
for (let i = 0; i < d.samples.length; i++) {
|
|
470
|
+
const s = d.samples[i];
|
|
471
|
+
lst.push((i == 0 ? "M" : "L") + " " + xscale(s.date) + " " + yscale(s.maf));
|
|
472
|
+
}
|
|
473
|
+
return lst.join(" ");
|
|
474
|
+
});
|
|
475
|
+
if (showcircle) {
|
|
476
|
+
circles.attr("cx", (d) => xscale(d.date)).attr("cy", (d) => yscale(d.maf)).attr("r", (d) => Math.sqrt(rscale(d.coverage)));
|
|
477
|
+
}
|
|
478
|
+
legend.attr("transform", "translate(" + (yaxisw + xpad + width + maxradius + 5) + "," + toppad + ")");
|
|
479
|
+
legend.selectAll("*").remove();
|
|
480
|
+
let y = minradius;
|
|
481
|
+
if (showcircle) {
|
|
482
|
+
legend.append("circle").attr("r", minradius).attr("cx", minradius).attr("cy", y).attr("fill", "#ccc");
|
|
483
|
+
legend.append("text").text(1).attr("x", minradius * 2 + 10).attr("y", y).attr("font-size", 10).attr("dominant-baseline", "central");
|
|
484
|
+
y += 5 + minradius + maxradius;
|
|
485
|
+
legend.append("circle").attr("r", maxradius).attr("cx", maxradius).attr("cy", y).attr("fill", "#ccc");
|
|
486
|
+
legend.append("text").text(maxcoverage).attr("x", maxradius * 2 + 10).attr("y", y).attr("font-size", 15).attr("dominant-baseline", "central");
|
|
487
|
+
y += 15 + maxradius;
|
|
488
|
+
}
|
|
489
|
+
const fontsize = 12;
|
|
490
|
+
for (const snv of snvlst) {
|
|
491
|
+
legend.append("line").attr("x2", 30).attr("y1", y).attr("y2", y).attr("stroke", snv.color);
|
|
492
|
+
if (showcircle) {
|
|
493
|
+
legend.append("circle").attr("cx", 15).attr("cy", y).attr("r", 8).attr("fill", snv.color).attr("fill-opacity", 0.1);
|
|
494
|
+
}
|
|
495
|
+
legend.append("text").text(snv.gene).attr("dominant-baseline", "central").attr("font-size", fontsize).attr("x", 30 + 10).attr("y", y).attr("fill", snv.color).style("cursor", "default").on("mouseover", (event) => {
|
|
496
|
+
event.target.setAttribute("font-weight", "bold");
|
|
497
|
+
lines.filter((d) => d.mutationname == snv.mutationname).attr("stroke-width", 3);
|
|
498
|
+
}).on("mouseout", (event) => {
|
|
499
|
+
event.target.setAttribute("font-weight", "normal");
|
|
500
|
+
lines.filter((d) => d.mutationname == snv.mutationname).attr("stroke-width", 1);
|
|
501
|
+
});
|
|
502
|
+
y += fontsize + 10;
|
|
503
|
+
}
|
|
504
|
+
};
|
|
505
|
+
setsize(width, height);
|
|
506
|
+
holder.append("div").style("text-align", "right").append("button").text("SVG").on("click", () => {
|
|
507
|
+
to_svg(svg.node(), "maf-timeline");
|
|
508
|
+
});
|
|
509
|
+
}
|
|
510
|
+
function makecontrol(snvlst, header, holder, graphholder, g1, g2, g3, g4) {
|
|
511
|
+
holder.selectAll("*").remove();
|
|
512
|
+
const table = holder.append("table");
|
|
513
|
+
for (const snv of snvlst) {
|
|
514
|
+
const tr = table.append("tr");
|
|
515
|
+
const td1 = tr.append("td");
|
|
516
|
+
td1.text(snv.gene).style("color", snv.color);
|
|
517
|
+
const td2 = tr.append("td");
|
|
518
|
+
const checkbox = td2.append("input").attr("type", "checkbox").style("zoom", "150%").property("checked", snv.show);
|
|
519
|
+
snv.checkbox = checkbox;
|
|
520
|
+
checkbox.on("change", (event) => {
|
|
521
|
+
snv.show = event.target.checked;
|
|
522
|
+
makegraph(snvlst, header, graphholder);
|
|
523
|
+
});
|
|
524
|
+
const butt = td2.append("button").style("margin-left", "5px").text("Only").on("click", () => {
|
|
525
|
+
for (const s2 of snvlst) {
|
|
526
|
+
s2.show = false;
|
|
527
|
+
s2.checkbox.property("checked", false);
|
|
528
|
+
}
|
|
529
|
+
snv.show = true;
|
|
530
|
+
snv.checkbox.property("checked", true);
|
|
531
|
+
makegraph(snvlst, header, graphholder);
|
|
532
|
+
});
|
|
533
|
+
let cname = Math.random();
|
|
534
|
+
const td11 = tr.append("td");
|
|
535
|
+
const c1 = td11.append("input").attr("type", "checkbox").attr("id", cname).on("change", (event) => cchange(1, event.target));
|
|
536
|
+
td11.append("label").html(" shared").attr("for", cname);
|
|
537
|
+
cname = Math.random();
|
|
538
|
+
const td22 = tr.append("td");
|
|
539
|
+
const c2 = td22.append("input").attr("type", "checkbox").attr("id", cname).on("change", (event) => cchange(2, event.target));
|
|
540
|
+
td22.append("label").html(" rising").attr("for", cname);
|
|
541
|
+
cname = Math.random();
|
|
542
|
+
const td33 = tr.append("td");
|
|
543
|
+
const c3 = td33.append("input").attr("type", "checkbox").attr("id", cname).on("change", (event) => cchange(3, event.target));
|
|
544
|
+
td33.append("label").html(" falling").attr("for", cname);
|
|
545
|
+
cname = Math.random();
|
|
546
|
+
const td44 = tr.append("td");
|
|
547
|
+
const c4 = td44.append("input").attr("type", "checkbox").attr("id", cname).on("change", (event) => cchange(4, event.target));
|
|
548
|
+
td44.append("label").html(" R-only").attr("for", cname);
|
|
549
|
+
if (snv.subidx == 1) c1.property("checked", true);
|
|
550
|
+
if (snv.subidx == 2) c2.property("checked", true);
|
|
551
|
+
if (snv.subidx == 3) c3.property("checked", true);
|
|
552
|
+
if (snv.subidx == 4) c4.property("checked", true);
|
|
553
|
+
const cchange = (which, check) => {
|
|
554
|
+
if (!check.checked) {
|
|
555
|
+
snv.subidx = -1;
|
|
556
|
+
} else {
|
|
557
|
+
snv.subidx = which;
|
|
558
|
+
if (which == 1) {
|
|
559
|
+
c2.property("checked", false);
|
|
560
|
+
c3.property("checked", false);
|
|
561
|
+
c4.property("checked", false);
|
|
562
|
+
} else if (which == 2) {
|
|
563
|
+
c1.property("checked", false);
|
|
564
|
+
c3.property("checked", false);
|
|
565
|
+
c4.property("checked", false);
|
|
566
|
+
} else if (which == 3) {
|
|
567
|
+
c1.property("checked", false);
|
|
568
|
+
c2.property("checked", false);
|
|
569
|
+
c4.property("checked", false);
|
|
570
|
+
} else {
|
|
571
|
+
c1.property("checked", false);
|
|
572
|
+
c2.property("checked", false);
|
|
573
|
+
c3.property("checked", false);
|
|
574
|
+
}
|
|
575
|
+
}
|
|
576
|
+
makesubgraph(snvlst, g1, g2, g3, g4);
|
|
577
|
+
};
|
|
578
|
+
}
|
|
579
|
+
}
|
|
580
|
+
export {
|
|
581
|
+
maftimelineui as default
|
|
582
|
+
};
|
|
583
|
+
//# sourceMappingURL=maftimeline-HE7XLJWG.js.map
|
|
@@ -0,0 +1,50 @@
|
|
|
1
|
+
import {
|
|
2
|
+
Matrix,
|
|
3
|
+
componentInit,
|
|
4
|
+
makeChartBtnMenu,
|
|
5
|
+
matrixInit
|
|
6
|
+
} from "./chunk-BKJLRLQQ.js";
|
|
7
|
+
import "./chunk-WENNRY5E.js";
|
|
8
|
+
import "./chunk-JG5CF5Q3.js";
|
|
9
|
+
import "./chunk-UHZDDPUU.js";
|
|
10
|
+
import "./chunk-UYA5LCAR.js";
|
|
11
|
+
import "./chunk-JWWLSDVM.js";
|
|
12
|
+
import "./chunk-SB5DR4NL.js";
|
|
13
|
+
import "./chunk-W5SPLFIG.js";
|
|
14
|
+
import "./chunk-CW3IVTRX.js";
|
|
15
|
+
import "./chunk-VHEXNBCO.js";
|
|
16
|
+
import "./chunk-C2MCQZWH.js";
|
|
17
|
+
import "./chunk-DDKS3MV3.js";
|
|
18
|
+
import "./chunk-WUCIHN7D.js";
|
|
19
|
+
import "./chunk-2W6U53AG.js";
|
|
20
|
+
import "./chunk-D7KZWYP5.js";
|
|
21
|
+
import "./chunk-V2OJLJSK.js";
|
|
22
|
+
import "./chunk-YBXQBSFY.js";
|
|
23
|
+
import "./chunk-HJ6L54YS.js";
|
|
24
|
+
import "./chunk-QKVKQD6S.js";
|
|
25
|
+
import "./chunk-CNFTQSNE.js";
|
|
26
|
+
import "./chunk-DOC3HBOV.js";
|
|
27
|
+
import "./chunk-TVJOSRCH.js";
|
|
28
|
+
import "./chunk-3CIL7KH7.js";
|
|
29
|
+
import "./chunk-T4XPCSLP.js";
|
|
30
|
+
import "./chunk-VVWZ4BOI.js";
|
|
31
|
+
import "./chunk-W5J3LTYS.js";
|
|
32
|
+
import "./chunk-2IAELUCN.js";
|
|
33
|
+
import "./chunk-CFYWQJ7F.js";
|
|
34
|
+
import "./chunk-2N345NXD.js";
|
|
35
|
+
import "./chunk-HBNB5TRH.js";
|
|
36
|
+
import "./chunk-PF4DSFDR.js";
|
|
37
|
+
import "./chunk-4OLM3KSB.js";
|
|
38
|
+
import "./chunk-PWYMHUXY.js";
|
|
39
|
+
import "./chunk-TLT4YIG3.js";
|
|
40
|
+
import "./chunk-5R63Q5KH.js";
|
|
41
|
+
import "./chunk-I6Y4O3RR.js";
|
|
42
|
+
import "./chunk-Q5RDQNIT.js";
|
|
43
|
+
import "./chunk-HS5PO5ZQ.js";
|
|
44
|
+
export {
|
|
45
|
+
Matrix,
|
|
46
|
+
componentInit,
|
|
47
|
+
makeChartBtnMenu,
|
|
48
|
+
matrixInit
|
|
49
|
+
};
|
|
50
|
+
//# sourceMappingURL=matrix-IAM6SA7K.js.map
|
|
@@ -0,0 +1,55 @@
|
|
|
1
|
+
import {
|
|
2
|
+
Matrix,
|
|
3
|
+
componentInit,
|
|
4
|
+
makeChartBtnMenu,
|
|
5
|
+
matrixInit
|
|
6
|
+
} from "./chunk-BKJLRLQQ.js";
|
|
7
|
+
import "./chunk-WENNRY5E.js";
|
|
8
|
+
import "./chunk-JG5CF5Q3.js";
|
|
9
|
+
import "./chunk-UHZDDPUU.js";
|
|
10
|
+
import "./chunk-UYA5LCAR.js";
|
|
11
|
+
import {
|
|
12
|
+
getPlotConfig,
|
|
13
|
+
setComputedConfig
|
|
14
|
+
} from "./chunk-JWWLSDVM.js";
|
|
15
|
+
import "./chunk-SB5DR4NL.js";
|
|
16
|
+
import "./chunk-W5SPLFIG.js";
|
|
17
|
+
import "./chunk-CW3IVTRX.js";
|
|
18
|
+
import "./chunk-VHEXNBCO.js";
|
|
19
|
+
import "./chunk-C2MCQZWH.js";
|
|
20
|
+
import "./chunk-DDKS3MV3.js";
|
|
21
|
+
import "./chunk-WUCIHN7D.js";
|
|
22
|
+
import "./chunk-2W6U53AG.js";
|
|
23
|
+
import "./chunk-D7KZWYP5.js";
|
|
24
|
+
import "./chunk-V2OJLJSK.js";
|
|
25
|
+
import "./chunk-YBXQBSFY.js";
|
|
26
|
+
import "./chunk-HJ6L54YS.js";
|
|
27
|
+
import "./chunk-QKVKQD6S.js";
|
|
28
|
+
import "./chunk-CNFTQSNE.js";
|
|
29
|
+
import "./chunk-DOC3HBOV.js";
|
|
30
|
+
import "./chunk-TVJOSRCH.js";
|
|
31
|
+
import "./chunk-3CIL7KH7.js";
|
|
32
|
+
import "./chunk-T4XPCSLP.js";
|
|
33
|
+
import "./chunk-VVWZ4BOI.js";
|
|
34
|
+
import "./chunk-W5J3LTYS.js";
|
|
35
|
+
import "./chunk-2IAELUCN.js";
|
|
36
|
+
import "./chunk-CFYWQJ7F.js";
|
|
37
|
+
import "./chunk-2N345NXD.js";
|
|
38
|
+
import "./chunk-HBNB5TRH.js";
|
|
39
|
+
import "./chunk-PF4DSFDR.js";
|
|
40
|
+
import "./chunk-4OLM3KSB.js";
|
|
41
|
+
import "./chunk-PWYMHUXY.js";
|
|
42
|
+
import "./chunk-TLT4YIG3.js";
|
|
43
|
+
import "./chunk-5R63Q5KH.js";
|
|
44
|
+
import "./chunk-I6Y4O3RR.js";
|
|
45
|
+
import "./chunk-Q5RDQNIT.js";
|
|
46
|
+
import "./chunk-HS5PO5ZQ.js";
|
|
47
|
+
export {
|
|
48
|
+
Matrix,
|
|
49
|
+
componentInit,
|
|
50
|
+
getPlotConfig,
|
|
51
|
+
makeChartBtnMenu,
|
|
52
|
+
matrixInit,
|
|
53
|
+
setComputedConfig
|
|
54
|
+
};
|
|
55
|
+
//# sourceMappingURL=matrix-QF5MBV5Y.js.map
|