@sjcrh/proteinpaint-client 2.208.0 → 2.209.0
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-VTMPVZGT.js +1367 -0
- package/dist/AggMatrixInput-CH3RQ2QC.js +406 -0
- package/dist/AggregateMatrix-DPCHUOMF.js +41 -0
- package/dist/AppHeader-RA7T467G.js +830 -0
- package/dist/BoxPlot-7Q7SMT26.js +1211 -0
- package/dist/CorrelationVolcano-YV4UHOAX.js +617 -0
- package/dist/Cuminc-ZN53C3MD.js +1219 -0
- package/dist/DE-BEWW5AIG.js +89 -0
- package/dist/DEinput-SJITUJF2.js +499 -0
- package/dist/DM-2LBNE4WE.js +90 -0
- package/dist/DifferentialAnalysis-WE4LBHEF.js +239 -0
- package/dist/DifferentialAnalysis-WE4LBHEF.js.map +7 -0
- package/dist/Disco-PTZQF7IM.js +3389 -0
- package/dist/Disco.UI-NBR67N5M.js +243 -0
- package/dist/DmrPlot-QROLI66S.js +362 -0
- package/dist/DmrPlot-QROLI66S.js.map +7 -0
- package/dist/GB-FEBSFX5U.js +1428 -0
- package/dist/GB-FEBSFX5U.js.map +7 -0
- package/dist/GSEA-KOXOVC5V.js +875 -0
- package/dist/GSEA-KOXOVC5V.js.map +7 -0
- package/dist/GeneExpInput-DYBK54HC.js +42 -0
- package/dist/Geomap-QRD2WZVL.js +84 -0
- package/dist/HicApp-VKET4QHD.js +2245 -0
- package/dist/IDCViewer-RLLTXGD7.js +10812 -0
- package/dist/NumBinaryEditor-GYHOYPQL.js +279 -0
- package/dist/NumBinaryEditor.unit.spec-E2HKBWOO.js +312 -0
- package/dist/NumContEditor-3V76ZSEY.js +105 -0
- package/dist/NumContEditor.unit.spec-RTT5Q5E5.js +164 -0
- package/dist/NumCustomBinEditor-O5DMPY7H.js +33 -0
- package/dist/NumCustomBinEditor.unit.spec-5LZBP2JL.js +397 -0
- package/dist/NumDiscreteEditor-DFOJ7AIH.js +170 -0
- package/dist/NumDiscreteEditor.unit.spec-PPJGEBFX.js +233 -0
- package/dist/NumRegularBinEditor-O6RDO32C.js +33 -0
- package/dist/NumRegularBinEditor.unit.spec-GOB3BF25.js +278 -0
- package/dist/NumSplineEditor-PUXJF2RW.js +210 -0
- package/dist/NumSplineEditor.unit.spec-4VOAAMOU.js +224 -0
- package/dist/NumericDensity-E6MH2THZ.js +33 -0
- package/dist/NumericDensity.unit.spec-IRPFBQUS.js +418 -0
- package/dist/NumericHandler-42RR54X3.js +34 -0
- package/dist/NumericHandler.unit.spec-YYOO7XVT.js +214 -0
- package/dist/ProteomeInput-4N2G6IFX.js +388 -0
- package/dist/Regression-LIWUWAGQ.js +1416 -0
- package/dist/Regression-LIWUWAGQ.js.map +7 -0
- package/dist/RunChart2-VAX5JGZY.js +749 -0
- package/dist/SC-UHBZ3HRO.js +1183 -0
- package/dist/SC-UHBZ3HRO.js.map +7 -0
- package/dist/Violin-V23VZR6B.js +1081 -0
- package/dist/Violin-V23VZR6B.js.map +7 -0
- package/dist/Volcano-64S4AW66.js +2443 -0
- package/dist/Volcano-64S4AW66.js.map +7 -0
- package/dist/Wsi-FOJCKDCP.js +629 -0
- package/dist/adSandbox-CLMUYNC3.js +33 -0
- package/dist/animatedBubbleChart-GMLNYTQC.js +547 -0
- package/dist/app-2SFDRDN2.js +32 -0
- package/dist/app-QOZ36UR4.js +42 -0
- package/dist/app.js +14 -14
- package/dist/bam-LLAK7FVG.js +876 -0
- package/dist/barchart-SEC6VKQ2.js +42 -0
- package/dist/barchart2-D4FXZCTU.js +309 -0
- package/dist/block-XGK6TEGH.js +6250 -0
- package/dist/block-XGK6TEGH.js.map +7 -0
- package/dist/block.init-UMRCAKCF.js +33 -0
- package/dist/block.mds.expressionrank-LFPJ52SX.js +354 -0
- package/dist/block.mds.geneboxplot-2QIEN6AH.js +823 -0
- package/dist/block.mds.junction-Z4HUFSG2.js +1539 -0
- package/dist/block.mds.svcnv-3GXGY6ET.js +6796 -0
- package/dist/block.svg-7RCJLMAP.js +159 -0
- package/dist/block.tk.aicheck-5N6EGZ6F.js +278 -0
- package/dist/block.tk.ase-V3AJRYT6.js +360 -0
- package/dist/block.tk.bam-W6QOVVEU.js +1901 -0
- package/dist/block.tk.bedgraphdot-FKTPJZTH.js +379 -0
- package/dist/block.tk.bigwig.ui-Y3M2TDM2.js +206 -0
- package/dist/block.tk.hicstraw-3SWYTMFQ.js +818 -0
- package/dist/block.tk.junction-OXB22PDS.js +2358 -0
- package/dist/block.tk.junction.textmatrixui-PWBLRGCO.js +194 -0
- package/dist/block.tk.ld-NTRJL5GA.js +94 -0
- package/dist/block.tk.menu-JIHSGGIO.js +1024 -0
- package/dist/block.tk.pgv-4Q6CY6QN.js +938 -0
- package/dist/brainImaging-MBI4XTTU.js +555 -0
- package/dist/brainRegions-YVTAESRP.js +217 -0
- package/dist/bubbleHeatmap-ZKTA3AIG.js +378 -0
- package/dist/cellTypeBubbleHeatmap-GJZNXDG4.js +278 -0
- package/dist/chunk-2PDBU42F.js +4375 -0
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- package/dist/chunk-33BE7AYS.js +299 -0
- package/dist/chunk-3FEP6B5T.js +119 -0
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- package/dist/chunk-BCCFJYPE.js +54 -0
- package/dist/chunk-BG3SGGVB.js +134 -0
- package/dist/chunk-C3HEDQPT.js +24921 -0
- package/dist/chunk-C3HEDQPT.js.map +7 -0
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- package/dist/chunk-CKOU3P27.js +26 -0
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- package/dist/chunk-FSLOUTTK.js.map +7 -0
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- package/dist/chunk-JMDUO47F.js +5071 -0
- package/dist/chunk-JTANDSTD.js +54 -0
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- package/dist/chunk-NDOKW2HJ.js +31 -0
- package/dist/chunk-NGMM2MNC.js +518 -0
- package/dist/chunk-OASGOTRM.js +80 -0
- package/dist/chunk-OASGOTRM.js.map +7 -0
- package/dist/chunk-OBDIJ4QS.js +2146 -0
- package/dist/chunk-OBDIJ4QS.js.map +7 -0
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- package/dist/chunk-WGDJX7WZ.js +2327 -0
- package/dist/chunk-WIQVSCD5.js +294 -0
- package/dist/chunk-WXXRVJSP.js +56 -0
- package/dist/chunk-X4MV2M5F.js +129 -0
- package/dist/chunk-XVVVNCXS.js +217 -0
- package/dist/chunk-XVVVNCXS.js.map +7 -0
- package/dist/chunk-YHP7MYB7.js +49 -0
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- package/dist/chunk-YKZOQTT4.js +1233 -0
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- package/dist/cohort-GVAJTICQ.js +70 -0
- package/dist/condition-EGPNMM47.js +327 -0
- package/dist/controls-HBROSXHF.js +34 -0
- package/dist/controls.config-FWKV66TU.js +34 -0
- package/dist/correlation-CEHE66EC.js +95 -0
- package/dist/customdata.inputui-LFT3N5FD.js +284 -0
- package/dist/dataDownload-ZPAIAAE4.js +329 -0
- package/dist/databrowser.ui-W5JGFBE6.js +425 -0
- package/dist/dictionary-RBE2CIZI.js +113 -0
- package/dist/dnaMethylation-CX22TSRO.js +33 -0
- package/dist/dnaMethylation.integration.spec-KEE6ZZRT.js +198 -0
- package/dist/dofetch-6NAGX5EG.js +48 -0
- package/dist/e2pca-XDGPTEXL.js +344 -0
- package/dist/ep-IUIDMIGW.js +1249 -0
- package/dist/expclust.gdc.spec-BMN2PTJX.js +302 -0
- package/dist/facet-DTJKZOBA.js +519 -0
- package/dist/gb-MV7MUJWO.js +81 -0
- package/dist/geneExpClustering-NFH5FS3S.js +244 -0
- package/dist/geneExpression-XVOLNYVN.js +310 -0
- package/dist/geneExpression-ZP2VWHED.js +33 -0
- package/dist/geneExpression.unit.spec-2NSK4ARK.js +128 -0
- package/dist/geneExpression.unit.spec-2NSK4ARK.js.map +7 -0
- package/dist/geneORA-HQ7FLMEJ.js +273 -0
- package/dist/geneRanking-MIABUKTN.js +548 -0
- package/dist/geneVariant-H52UUK6Z.js +289 -0
- package/dist/geneVariant-H52UUK6Z.js.map +7 -0
- package/dist/geneVariant-HDFWLALZ.js +36 -0
- package/dist/geneVariant.integration.spec-O36JK4B7.js +503 -0
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- package/dist/genefusion.ui-HSDZQHJA.js +303 -0
- package/dist/geneset-WKV3X2EJ.js +203 -0
- package/dist/genomeBrowser.spec-UTAHAU76.js +276 -0
- package/dist/grin2-M2JDZVYU.js +70 -0
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- package/dist/hierCluster.interactivity-4HP3JCON.js +49 -0
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- package/dist/imagePlot-OA4WTMLU.js +156 -0
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- package/dist/isoformExpression-LZ5RTUS5.js +35 -0
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- /package/dist/{scatter-ZOWFPGIS.js.map → scatter-IGFBIZ3B.js.map} +0 -0
- /package/dist/{selectGenomeWithTklst-EF7WYEAJ.js.map → selectGenomeWithTklst-HBHRXEDY.js.map} +0 -0
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- /package/dist/{singleCellCellType.unit.spec-JZ6UHC5F.js.map → singleCellCellType.unit.spec-ZLYDUDIY.js.map} +0 -0
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- /package/dist/{snp-2WPJYPDE.js.map → snp-BHG4NVK4.js.map} +0 -0
- /package/dist/{snp.unit.spec-PPWIIOX6.js.map → snp.unit.spec-Q3AZHQRC.js.map} +0 -0
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- /package/dist/{spliceevent.noeventdiagram-CPXQSX3Z.js.map → spliceevent.noeventdiagram-LGLXCF25.js.map} +0 -0
- /package/dist/{ssGSEA-FSX6P7HA.js.map → ssGSEA-BIEEKAKX.js.map} +0 -0
- /package/dist/{ssGSEA.unit.spec-TXYT665R.js.map → ssGSEA.unit.spec-YD4UDIRH.js.map} +0 -0
- /package/dist/{stattable-BD64SFYV.js.map → stattable-LFR3RSD6.js.map} +0 -0
- /package/dist/{studyCatalog-6BOWO4PO.js.map → studyCatalog-RINIZ277.js.map} +0 -0
- /package/dist/{summarizeCnvGeneexp-AMLYJIPU.js.map → summarizeCnvGeneexp-ZQFNPR65.js.map} +0 -0
- /package/dist/{summarizeGeneexpSurvival-IDM7T333.js.map → summarizeGeneexpSurvival-GIS7XMMH.js.map} +0 -0
- /package/dist/{summarizeMutationCnv-R6SYSJQC.js.map → summarizeMutationCnv-FWF7YIGR.js.map} +0 -0
- /package/dist/{summarizeMutationDiagnosis-XZJ4JLW2.js.map → summarizeMutationDiagnosis-V5L2OKTK.js.map} +0 -0
- /package/dist/{summarizeMutationSurvival-ABJ5RL4L.js.map → summarizeMutationSurvival-LAUUF6XN.js.map} +0 -0
- /package/dist/{summary-NVYCTE6P.js.map → summary-OMU3ACNE.js.map} +0 -0
- /package/dist/{summary.integration.spec-SSLTLVNW.js.map → summary.integration.spec-6JZAT73L.js.map} +0 -0
- /package/dist/{summaryInput-SJOZETRP.js.map → summaryInput-QIKL3HDD.js.map} +0 -0
- /package/dist/{sunburst-RU5ZPJKW.js.map → sunburst-32IW2R57.js.map} +0 -0
- /package/dist/{survival-BHJQMXKI.js.map → survival-BMOPVAN2.js.map} +0 -0
- /package/dist/{survival-DVG6Y2FV.js.map → survival-H5AWMQ36.js.map} +0 -0
- /package/dist/{survival.integration.spec-OJUPTY5N.js.map → survival.integration.spec-66UOWSZG.js.map} +0 -0
- /package/dist/{svgraph-ETFA4GRX.js.map → svgraph-B75FS3BB.js.map} +0 -0
- /package/dist/{svmr-AI3RU4JK.js.map → svmr-IUEUOHVO.js.map} +0 -0
- /package/dist/{table-YCTSMLQL.js.map → table-YAAH7WR6.js.map} +0 -0
- /package/dist/{termCollection-GMKEZR6D.js.map → termCollection-7F5ZG2DB.js.map} +0 -0
- /package/dist/{termCollection-VEVKKJZD.js.map → termCollection-KNFUELYY.js.map} +0 -0
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- /package/dist/{termCollectionFractionSelection-UBS74X36.js.map → termCollectionFractionSelection-X22VMJWY.js.map} +0 -0
- /package/dist/{termCollectionFractionSelection.unit.spec-Y5OJFGDD.js.map → termCollectionFractionSelection.unit.spec-ELU6SD7P.js.map} +0 -0
- /package/dist/{tk-W6Z4FJMW.js.map → tk-TT666UVE.js.map} +0 -0
- /package/dist/{tk-HMF4HCNV.js.map → tk-UOPNJ323.js.map} +0 -0
- /package/dist/{tp.ui-NECRDJCS.js.map → tp.ui-HGAHRKO5.js.map} +0 -0
- /package/dist/{tvs.dt-2JEH3F35.js.map → tvs.dt-H7YYR4EB.js.map} +0 -0
- /package/dist/{tvs.dtcnv.categorical-YBXKEBR2.js.map → tvs.dtcnv.categorical-IPJTKGMF.js.map} +0 -0
- /package/dist/{tvs.dtcnv.continuous-AD3SJ6BY.js.map → tvs.dtcnv.continuous-XY5XZ4GH.js.map} +0 -0
- /package/dist/{tvs.dtfusion-ODI3CLQS.js.map → tvs.dtfusion-VFCBMXRM.js.map} +0 -0
- /package/dist/{tvs.dtitd-V3LYLPJY.js.map → tvs.dtitd-RZVW6FTR.js.map} +0 -0
- /package/dist/{tvs.dtsnvindel-R3V5LTNL.js.map → tvs.dtsnvindel-IDPJWSGC.js.map} +0 -0
- /package/dist/{tvs.dtsv-ZQLKEDLJ.js.map → tvs.dtsv-QERP756F.js.map} +0 -0
- /package/dist/{tvs.samplelst-G25A7HM6.js.map → tvs.samplelst-6KNDHBIU.js.map} +0 -0
- /package/dist/{tvs.termCollection-WLVCWDEJ.js.map → tvs.termCollection-GWPJK3NE.js.map} +0 -0
- /package/dist/{vocabulary-6K537FJM.js.map → vocabulary-C5FIZMPQ.js.map} +0 -0
- /package/dist/{wsi.direct-SNPPQPVO.js.map → wsi.direct-2RBCBXDA.js.map} +0 -0
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select_default
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// src/maftimeline.js
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var zerovalue = 1e-5;
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function maftimelineui(genomes, holder, sandbox_header) {
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;
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"<a href=https://docs.google.com/document/d/1WXlCVHLq_P2jGiRGJ55uzXCC6p-6Jqn7h406RUID_xo/edit?usp=sharing target=_blank>File format</a>"
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inputdiv.append("p").html("<a href=https://www.dropbox.com/s/940wfo6rd1ttlim/example.maftimeline?dl=0 target=_blank>Example file</a>");
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{
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const id = Math.random().toString();
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const pane2 = newpane({ x: 100, y: 100, toshrink: true });
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pane2.header.html('<span style="opacity:.5;font-size:.7em">MAF TIMELINE</span> ' + file.name);
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visual_holder = visualdiv.html('<span style="opacity:.5;font-size:.7em">MAF TIMELINE</span> ' + file.name);
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render(data, header, visual_holder);
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};
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setTimeout(() => butt.node().focus(), 1100);
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};
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}
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function parseheader(line) {
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const header = line.toLowerCase().split(" ");
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if (header.length <= 1) return ["columns must be separated by tab"];
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const htry = (...lst) => {
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}
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return -1;
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};
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let i = htry("person", "patient", "caseid");
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if (i == -1) return ["person missing"];
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header[i] = "patient";
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i = htry("sample", "sampleid");
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if (i == -1) return ["sample missing"];
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header[i] = "sample";
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i = htry("snv4");
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if (i == -1) return ["snv4 missing"];
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header[i] = "snv4";
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i = htry("date", "dateofsample");
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if (i == -1) return ["date missing"];
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header[i] = "date";
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i = htry("mutant_readcount", "mutantcount");
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if (i != -1) header[i] = "mutant_readcount";
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i = htry("ref_readcount", "refcount");
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if (i != -1) header[i] = "ref_readcount";
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i = htry("total_readcount", "coveragecount");
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if (i == -1) return ["total_readcount missing"];
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header[i] = "coverage";
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i = htry("maf");
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if (i == -1) return ["maf missing"];
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header[i] = "maf";
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i = htry("call_manual");
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if (i != -1) header[i] = "call_manual";
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return [null, header];
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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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const m = {};
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for (let j = 0; j < header.length; j++) {
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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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}
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if (m.gene) {
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data[m.patient].snv4[m.snv4].gene = m.gene;
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}
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if (!m.maf) {
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badlines.push([i, "missing maf", lst]);
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return;
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}
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let v = Number.parseFloat(m.maf);
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if (Number.isNaN(v)) {
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|
+
badlines.push([i, "invalid maf", lst]);
|
|
217
|
+
return;
|
|
218
|
+
}
|
|
219
|
+
if (v < zerovalue) {
|
|
220
|
+
v = zerovalue;
|
|
221
|
+
}
|
|
222
|
+
m.maf = v;
|
|
223
|
+
if (!m.coverage) {
|
|
224
|
+
badlines.push([i, "missing total_readcount", lst]);
|
|
225
|
+
return;
|
|
226
|
+
}
|
|
227
|
+
if (m.call_manual && m.call_manual == "wildtype") {
|
|
228
|
+
m.maf = zerovalue;
|
|
229
|
+
}
|
|
230
|
+
v = Number.parseInt(m.coverage);
|
|
231
|
+
if (Number.isNaN(v)) {
|
|
232
|
+
badlines.push([i, "invalid total_readcount", lst]);
|
|
233
|
+
return;
|
|
234
|
+
}
|
|
235
|
+
m.coverage = v;
|
|
236
|
+
let date;
|
|
237
|
+
if (m.date) {
|
|
238
|
+
const f = timeParse("%m/%d/%Y");
|
|
239
|
+
date = f(m.date);
|
|
240
|
+
m.Date = m.date;
|
|
241
|
+
} else {
|
|
242
|
+
badlines.push([i, "missing date", lst]);
|
|
243
|
+
return;
|
|
244
|
+
}
|
|
245
|
+
if (date == null) {
|
|
246
|
+
badlines.push([i, "cannot parse date", lst]);
|
|
247
|
+
return;
|
|
248
|
+
}
|
|
249
|
+
m.date = date;
|
|
250
|
+
if (!m.sample) {
|
|
251
|
+
badlines.push([i, "missing sample", lst]);
|
|
252
|
+
return;
|
|
253
|
+
}
|
|
254
|
+
data[m.patient].snv4[m.snv4].samples.push(m);
|
|
255
|
+
return true;
|
|
256
|
+
}
|
|
257
|
+
function render(data, header, holder) {
|
|
258
|
+
const table = holder.append("table").style("margin", "20px");
|
|
259
|
+
const tr1 = table.append("tr");
|
|
260
|
+
let td = tr1.append("td").style("vertical-align", "top").attr("rowspan", 2);
|
|
261
|
+
td.append("button").text("Toggle circle visibility").on("click", () => {
|
|
262
|
+
showcircle = !showcircle;
|
|
263
|
+
for (const n in data) {
|
|
264
|
+
if (data[n].show) {
|
|
265
|
+
data[n].handle.node().click();
|
|
266
|
+
break;
|
|
267
|
+
}
|
|
268
|
+
}
|
|
269
|
+
});
|
|
270
|
+
const patientholder = td.append("div").style("margin-top", "10px");
|
|
271
|
+
const td1 = tr1.append("td").style("vertical-align", "top");
|
|
272
|
+
const graphholder = td1.append("div").style("display", "inline-block");
|
|
273
|
+
const controlholder = td1.append("div").style("display", "inline-block").style("vertical-align", "top");
|
|
274
|
+
const tr2 = table.append("tr");
|
|
275
|
+
const tiantable = tr2.append("td").append("table").style("border-spacing", "20px").style("border-collapse", "separate");
|
|
276
|
+
const gtr1 = tiantable.append("tr");
|
|
277
|
+
td = gtr1.append("td").style("vertical-align", "top");
|
|
278
|
+
td.append("div").text("Shared").style("font-size", "2em");
|
|
279
|
+
const graph1holder = td.append("div").style("border", "solid 1px black");
|
|
280
|
+
td = gtr1.append("td").style("vertical-align", "top");
|
|
281
|
+
td.append("div").text("Rising").style("font-size", "2em");
|
|
282
|
+
const graph2holder = td.append("div").style("border", "solid 1px black");
|
|
283
|
+
const gtr2 = tiantable.append("tr");
|
|
284
|
+
td = gtr2.append("td").style("vertical-align", "top");
|
|
285
|
+
td.append("div").text("Falling").style("font-size", "2em");
|
|
286
|
+
const graph3holder = td.append("div").style("border", "solid 1px black");
|
|
287
|
+
td = gtr2.append("td").style("vertical-align", "top");
|
|
288
|
+
td.append("div").text("R-only").style("font-size", "2em");
|
|
289
|
+
const graph4holder = td.append("div").style("border", "solid 1px black");
|
|
290
|
+
for (const patient in data) {
|
|
291
|
+
const snvlst = [];
|
|
292
|
+
const colors = ordinal(category10_default);
|
|
293
|
+
for (const x in data[patient].snv4) {
|
|
294
|
+
const snv = data[patient].snv4[x];
|
|
295
|
+
snv.show = true;
|
|
296
|
+
snv.color = colors(snv.mutationname);
|
|
297
|
+
snv.samples.sort((a, b) => a.date - b.date);
|
|
298
|
+
for (const s of snv.samples) {
|
|
299
|
+
s.color = snv.color;
|
|
300
|
+
}
|
|
301
|
+
snvlst.push(snv);
|
|
302
|
+
}
|
|
303
|
+
const div = patientholder.append("div").classed("sja_menuoption", true).style("color", "black").text(patient).on("click", () => {
|
|
304
|
+
for (const pn in data) {
|
|
305
|
+
data[pn].handle.style("color", "black");
|
|
306
|
+
data[pn].show = false;
|
|
307
|
+
}
|
|
308
|
+
data[patient].handle.style("color", "red");
|
|
309
|
+
data[patient].show = true;
|
|
310
|
+
makegraph(snvlst, header, graphholder);
|
|
311
|
+
makesubgraph(snvlst, graph1holder, graph2holder, graph3holder, graph4holder);
|
|
312
|
+
makecontrol(snvlst, header, controlholder, graphholder, graph1holder, graph2holder, graph3holder, graph4holder);
|
|
313
|
+
});
|
|
314
|
+
data[patient].handle = div;
|
|
315
|
+
}
|
|
316
|
+
for (const n in data) {
|
|
317
|
+
data[n].handle.node().click();
|
|
318
|
+
break;
|
|
319
|
+
}
|
|
320
|
+
}
|
|
321
|
+
function makesubgraph(snvlst, g1, g2, g3, g4) {
|
|
322
|
+
g1.selectAll("*").remove();
|
|
323
|
+
g2.selectAll("*").remove();
|
|
324
|
+
g3.selectAll("*").remove();
|
|
325
|
+
g4.selectAll("*").remove();
|
|
326
|
+
const l1 = [];
|
|
327
|
+
const l2 = [];
|
|
328
|
+
const l3 = [];
|
|
329
|
+
const l4 = [];
|
|
330
|
+
for (const snv of snvlst) {
|
|
331
|
+
switch (snv.subidx) {
|
|
332
|
+
case 1:
|
|
333
|
+
l1.push(snv);
|
|
334
|
+
break;
|
|
335
|
+
case 2:
|
|
336
|
+
l2.push(snv);
|
|
337
|
+
break;
|
|
338
|
+
case 3:
|
|
339
|
+
l3.push(snv);
|
|
340
|
+
break;
|
|
341
|
+
case 4:
|
|
342
|
+
l4.push(snv);
|
|
343
|
+
break;
|
|
344
|
+
}
|
|
345
|
+
}
|
|
346
|
+
if (l1.length) {
|
|
347
|
+
makegraph(l1, null, g1, true);
|
|
348
|
+
} else {
|
|
349
|
+
g1.append("div").style("padding", "60px").style("background-color", "#ededed").text("no data");
|
|
350
|
+
}
|
|
351
|
+
if (l2.length) {
|
|
352
|
+
makegraph(l2, null, g2, true);
|
|
353
|
+
} else {
|
|
354
|
+
g2.append("div").style("padding", "60px").style("background-color", "#ededed").text("no data");
|
|
355
|
+
}
|
|
356
|
+
if (l3.length) {
|
|
357
|
+
makegraph(l3, null, g3, true);
|
|
358
|
+
} else {
|
|
359
|
+
g3.append("div").style("padding", "60px").style("background-color", "#ededed").text("no data");
|
|
360
|
+
}
|
|
361
|
+
if (l4.length) {
|
|
362
|
+
makegraph(l4, null, g4, true);
|
|
363
|
+
} else {
|
|
364
|
+
g4.append("div").style("padding", "60px").style("background-color", "#ededed").text("no data");
|
|
365
|
+
}
|
|
366
|
+
}
|
|
367
|
+
function makegraph(snvlst0, header, holder, issub) {
|
|
368
|
+
holder.selectAll("*").remove();
|
|
369
|
+
const samples = [];
|
|
370
|
+
const snvlst = [];
|
|
371
|
+
for (const snv of snvlst0) {
|
|
372
|
+
if (!issub && !snv.show) continue;
|
|
373
|
+
snvlst.push(snv);
|
|
374
|
+
for (const s of snv.samples) {
|
|
375
|
+
samples.push(s);
|
|
376
|
+
}
|
|
377
|
+
}
|
|
378
|
+
if (snvlst.length == 0) return;
|
|
379
|
+
let mindate = snvlst[0].samples[0].date;
|
|
380
|
+
let maxdate = snvlst[0].samples[0].date;
|
|
381
|
+
let maxmaf = snvlst[0].samples[0].maf;
|
|
382
|
+
let maxcoverage = snvlst[0].samples[0].coverage;
|
|
383
|
+
for (const snv of snvlst) {
|
|
384
|
+
for (const s of snv.samples) {
|
|
385
|
+
mindate = Math.min(mindate, s.date);
|
|
386
|
+
maxdate = Math.max(maxdate, s.date);
|
|
387
|
+
maxmaf = Math.max(maxmaf, s.maf);
|
|
388
|
+
maxcoverage = Math.max(maxcoverage, s.coverage);
|
|
389
|
+
}
|
|
390
|
+
}
|
|
391
|
+
const svg = holder.append("svg");
|
|
392
|
+
const toppad = 30, rightpad = 200, yaxisw = 100, xaxish = 50;
|
|
393
|
+
let width = 600;
|
|
394
|
+
let height = 400;
|
|
395
|
+
let xpad, ypad, minradius;
|
|
396
|
+
const xaxisg = svg.append("g");
|
|
397
|
+
const yaxisg = svg.append("g");
|
|
398
|
+
const drag = svg.append("text").text("drag to resize").attr("class", "sja_clb").attr("text-anchor", "end").on("mousedown", (event) => {
|
|
399
|
+
event.preventDefault();
|
|
400
|
+
const x = event.clientX;
|
|
401
|
+
const y = event.clientY;
|
|
402
|
+
const w0 = width;
|
|
403
|
+
const h0 = height;
|
|
404
|
+
const body = select_default(document.body);
|
|
405
|
+
body.on("mousemove", (event2) => {
|
|
406
|
+
setsize(w0 + event2.clientX - x, h0 + event2.clientY - y);
|
|
407
|
+
}).on("mouseup", () => {
|
|
408
|
+
body.on("mousemove", null).on("mouseup", null);
|
|
409
|
+
});
|
|
410
|
+
});
|
|
411
|
+
const xscale = time().domain([mindate, maxdate]);
|
|
412
|
+
const yscale = (maflogscale ? log() : linear()).domain([zerovalue, 1]);
|
|
413
|
+
const rscale = linear().domain([1, maxcoverage]);
|
|
414
|
+
const g = svg.append("g");
|
|
415
|
+
const lines = g.selectAll().data(snvlst).enter().append("path").attr("stroke", (d) => d.color).attr("fill", "none");
|
|
416
|
+
let circles;
|
|
417
|
+
if (showcircle) {
|
|
418
|
+
circles = g.selectAll().data(samples).enter().append("circle").attr("fill", (d) => d.color).attr("fill-opacity", 0.1).on("mouseover", (event, d) => {
|
|
419
|
+
event.target.setAttribute("fill-opacity", 0.4);
|
|
420
|
+
tip.clear();
|
|
421
|
+
tip.show(event.clientX, event.clientY);
|
|
422
|
+
const lst = [];
|
|
423
|
+
for (const k in d) {
|
|
424
|
+
if (k == "color") continue;
|
|
425
|
+
if (k == "gene") {
|
|
426
|
+
lst.push({ k: "gene", v: '<span style="color:' + d.color + '">' + d.gene + "</span>" });
|
|
427
|
+
continue;
|
|
428
|
+
}
|
|
429
|
+
if (k == "date") continue;
|
|
430
|
+
if (k == "url") {
|
|
431
|
+
lst.push({ k: "URL", v: "<a href=" + d.url + " target=_blank>LINK</a>" });
|
|
432
|
+
continue;
|
|
433
|
+
}
|
|
434
|
+
lst.push({ k, v: d[k] });
|
|
435
|
+
}
|
|
436
|
+
make_table_2col(tip.d, lst);
|
|
437
|
+
}).on("mouseout", (event) => {
|
|
438
|
+
event.target.setAttribute("fill-opacity", 0.1);
|
|
439
|
+
});
|
|
440
|
+
}
|
|
441
|
+
const legend = svg.append("g");
|
|
442
|
+
const setsize = (w, h) => {
|
|
443
|
+
width = w;
|
|
444
|
+
height = h;
|
|
445
|
+
minradius = 2;
|
|
446
|
+
const maxradius = Math.max(width, height) / 30;
|
|
447
|
+
xpad = maxradius;
|
|
448
|
+
ypad = maxradius;
|
|
449
|
+
rscale.range([Math.pow(minradius, 2), Math.pow(maxradius, 2)]);
|
|
450
|
+
xscale.range([0, width]);
|
|
451
|
+
yscale.range([height, 0]);
|
|
452
|
+
svg.attr("width", yaxisw + xpad + width + rightpad).attr("height", toppad + height + ypad + xaxish);
|
|
453
|
+
xaxisg.attr("transform", "translate(" + (yaxisw + xpad) + "," + (toppad + height + ypad) + ")");
|
|
454
|
+
yaxisg.attr("transform", "translate(" + yaxisw + "," + toppad + ")");
|
|
455
|
+
drag.attr("x", yaxisw + xpad + width).attr("y", toppad + height + ypad + xaxish - 4);
|
|
456
|
+
axisstyle({
|
|
457
|
+
axis: xaxisg.call(axisBottom().scale(xscale)),
|
|
458
|
+
showline: true,
|
|
459
|
+
color: "black",
|
|
460
|
+
fontsize: Math.max(12, Math.min(20, width / 100))
|
|
461
|
+
});
|
|
462
|
+
axisstyle({
|
|
463
|
+
axis: yaxisg.call(
|
|
464
|
+
axisLeft().scale(yscale).tickValues([1, 0.1, 0.01, 1e-3, 1e-4, zerovalue]).tickFormat(format(" "))
|
|
465
|
+
),
|
|
466
|
+
showline: true,
|
|
467
|
+
color: "black",
|
|
468
|
+
fontsize: Math.max(12, Math.min(20, height / 100))
|
|
469
|
+
});
|
|
470
|
+
g.attr("transform", "translate(" + (yaxisw + xpad) + "," + toppad + ")");
|
|
471
|
+
lines.attr("d", (d) => {
|
|
472
|
+
const lst = [];
|
|
473
|
+
for (let i = 0; i < d.samples.length; i++) {
|
|
474
|
+
const s = d.samples[i];
|
|
475
|
+
lst.push((i == 0 ? "M" : "L") + " " + xscale(s.date) + " " + yscale(s.maf));
|
|
476
|
+
}
|
|
477
|
+
return lst.join(" ");
|
|
478
|
+
});
|
|
479
|
+
if (showcircle) {
|
|
480
|
+
circles.attr("cx", (d) => xscale(d.date)).attr("cy", (d) => yscale(d.maf)).attr("r", (d) => Math.sqrt(rscale(d.coverage)));
|
|
481
|
+
}
|
|
482
|
+
legend.attr("transform", "translate(" + (yaxisw + xpad + width + maxradius + 5) + "," + toppad + ")");
|
|
483
|
+
legend.selectAll("*").remove();
|
|
484
|
+
let y = minradius;
|
|
485
|
+
if (showcircle) {
|
|
486
|
+
legend.append("circle").attr("r", minradius).attr("cx", minradius).attr("cy", y).attr("fill", "#ccc");
|
|
487
|
+
legend.append("text").text(1).attr("x", minradius * 2 + 10).attr("y", y).attr("font-size", 10).attr("dominant-baseline", "central");
|
|
488
|
+
y += 5 + minradius + maxradius;
|
|
489
|
+
legend.append("circle").attr("r", maxradius).attr("cx", maxradius).attr("cy", y).attr("fill", "#ccc");
|
|
490
|
+
legend.append("text").text(maxcoverage).attr("x", maxradius * 2 + 10).attr("y", y).attr("font-size", 15).attr("dominant-baseline", "central");
|
|
491
|
+
y += 15 + maxradius;
|
|
492
|
+
}
|
|
493
|
+
const fontsize = 12;
|
|
494
|
+
for (const snv of snvlst) {
|
|
495
|
+
legend.append("line").attr("x2", 30).attr("y1", y).attr("y2", y).attr("stroke", snv.color);
|
|
496
|
+
if (showcircle) {
|
|
497
|
+
legend.append("circle").attr("cx", 15).attr("cy", y).attr("r", 8).attr("fill", snv.color).attr("fill-opacity", 0.1);
|
|
498
|
+
}
|
|
499
|
+
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) => {
|
|
500
|
+
event.target.setAttribute("font-weight", "bold");
|
|
501
|
+
lines.filter((d) => d.mutationname == snv.mutationname).attr("stroke-width", 3);
|
|
502
|
+
}).on("mouseout", (event) => {
|
|
503
|
+
event.target.setAttribute("font-weight", "normal");
|
|
504
|
+
lines.filter((d) => d.mutationname == snv.mutationname).attr("stroke-width", 1);
|
|
505
|
+
});
|
|
506
|
+
y += fontsize + 10;
|
|
507
|
+
}
|
|
508
|
+
};
|
|
509
|
+
setsize(width, height);
|
|
510
|
+
holder.append("div").style("text-align", "right").append("button").text("SVG").on("click", () => {
|
|
511
|
+
to_svg(svg.node(), "maf-timeline");
|
|
512
|
+
});
|
|
513
|
+
}
|
|
514
|
+
function makecontrol(snvlst, header, holder, graphholder, g1, g2, g3, g4) {
|
|
515
|
+
holder.selectAll("*").remove();
|
|
516
|
+
const table = holder.append("table");
|
|
517
|
+
for (const snv of snvlst) {
|
|
518
|
+
const tr = table.append("tr");
|
|
519
|
+
const td1 = tr.append("td");
|
|
520
|
+
td1.text(snv.gene).style("color", snv.color);
|
|
521
|
+
const td2 = tr.append("td");
|
|
522
|
+
const checkbox = td2.append("input").attr("type", "checkbox").style("zoom", "150%").property("checked", snv.show);
|
|
523
|
+
snv.checkbox = checkbox;
|
|
524
|
+
checkbox.on("change", (event) => {
|
|
525
|
+
snv.show = event.target.checked;
|
|
526
|
+
makegraph(snvlst, header, graphholder);
|
|
527
|
+
});
|
|
528
|
+
const butt = td2.append("button").style("margin-left", "5px").text("Only").on("click", () => {
|
|
529
|
+
for (const s2 of snvlst) {
|
|
530
|
+
s2.show = false;
|
|
531
|
+
s2.checkbox.property("checked", false);
|
|
532
|
+
}
|
|
533
|
+
snv.show = true;
|
|
534
|
+
snv.checkbox.property("checked", true);
|
|
535
|
+
makegraph(snvlst, header, graphholder);
|
|
536
|
+
});
|
|
537
|
+
let cname = Math.random();
|
|
538
|
+
const td11 = tr.append("td");
|
|
539
|
+
const c1 = td11.append("input").attr("type", "checkbox").attr("id", cname).on("change", (event) => cchange(1, event.target));
|
|
540
|
+
td11.append("label").html(" shared").attr("for", cname);
|
|
541
|
+
cname = Math.random();
|
|
542
|
+
const td22 = tr.append("td");
|
|
543
|
+
const c2 = td22.append("input").attr("type", "checkbox").attr("id", cname).on("change", (event) => cchange(2, event.target));
|
|
544
|
+
td22.append("label").html(" rising").attr("for", cname);
|
|
545
|
+
cname = Math.random();
|
|
546
|
+
const td33 = tr.append("td");
|
|
547
|
+
const c3 = td33.append("input").attr("type", "checkbox").attr("id", cname).on("change", (event) => cchange(3, event.target));
|
|
548
|
+
td33.append("label").html(" falling").attr("for", cname);
|
|
549
|
+
cname = Math.random();
|
|
550
|
+
const td44 = tr.append("td");
|
|
551
|
+
const c4 = td44.append("input").attr("type", "checkbox").attr("id", cname).on("change", (event) => cchange(4, event.target));
|
|
552
|
+
td44.append("label").html(" R-only").attr("for", cname);
|
|
553
|
+
if (snv.subidx == 1) c1.property("checked", true);
|
|
554
|
+
if (snv.subidx == 2) c2.property("checked", true);
|
|
555
|
+
if (snv.subidx == 3) c3.property("checked", true);
|
|
556
|
+
if (snv.subidx == 4) c4.property("checked", true);
|
|
557
|
+
const cchange = (which, check) => {
|
|
558
|
+
if (!check.checked) {
|
|
559
|
+
snv.subidx = -1;
|
|
560
|
+
} else {
|
|
561
|
+
snv.subidx = which;
|
|
562
|
+
if (which == 1) {
|
|
563
|
+
c2.property("checked", false);
|
|
564
|
+
c3.property("checked", false);
|
|
565
|
+
c4.property("checked", false);
|
|
566
|
+
} else if (which == 2) {
|
|
567
|
+
c1.property("checked", false);
|
|
568
|
+
c3.property("checked", false);
|
|
569
|
+
c4.property("checked", false);
|
|
570
|
+
} else if (which == 3) {
|
|
571
|
+
c1.property("checked", false);
|
|
572
|
+
c2.property("checked", false);
|
|
573
|
+
c4.property("checked", false);
|
|
574
|
+
} else {
|
|
575
|
+
c1.property("checked", false);
|
|
576
|
+
c2.property("checked", false);
|
|
577
|
+
c3.property("checked", false);
|
|
578
|
+
}
|
|
579
|
+
}
|
|
580
|
+
makesubgraph(snvlst, g1, g2, g3, g4);
|
|
581
|
+
};
|
|
582
|
+
}
|
|
583
|
+
}
|
|
584
|
+
export {
|
|
585
|
+
maftimelineui as default
|
|
586
|
+
};
|
|
587
|
+
//# sourceMappingURL=maftimeline-75N6ZXEM.js.map
|
|
@@ -0,0 +1,54 @@
|
|
|
1
|
+
import {
|
|
2
|
+
Matrix,
|
|
3
|
+
componentInit,
|
|
4
|
+
makeChartBtnMenu,
|
|
5
|
+
matrixInit
|
|
6
|
+
} from "./chunk-A2UUXYH6.js";
|
|
7
|
+
import "./chunk-5LYVIIYR.js";
|
|
8
|
+
import "./chunk-CN6KJORZ.js";
|
|
9
|
+
import "./chunk-5FRETII3.js";
|
|
10
|
+
import "./chunk-WIQVSCD5.js";
|
|
11
|
+
import "./chunk-AR3HXZIW.js";
|
|
12
|
+
import "./chunk-67URJYN7.js";
|
|
13
|
+
import "./chunk-OEBGQKQR.js";
|
|
14
|
+
import "./chunk-JTQPPUDG.js";
|
|
15
|
+
import "./chunk-C2MCQZWH.js";
|
|
16
|
+
import "./chunk-DDKS3MV3.js";
|
|
17
|
+
import "./chunk-CFZ2ZW3E.js";
|
|
18
|
+
import "./chunk-Z6MCBFDM.js";
|
|
19
|
+
import "./chunk-NGMM2MNC.js";
|
|
20
|
+
import "./chunk-AVCEHJG7.js";
|
|
21
|
+
import "./chunk-V2OJLJSK.js";
|
|
22
|
+
import "./chunk-C3HEDQPT.js";
|
|
23
|
+
import "./chunk-HJ6L54YS.js";
|
|
24
|
+
import "./chunk-KV4W2ACA.js";
|
|
25
|
+
import "./chunk-B6UXFX73.js";
|
|
26
|
+
import "./chunk-ELJX3QIQ.js";
|
|
27
|
+
import "./chunk-3FEP6B5T.js";
|
|
28
|
+
import "./chunk-EEB5VE2A.js";
|
|
29
|
+
import "./chunk-6RRZRISL.js";
|
|
30
|
+
import "./chunk-2KM4PRQM.js";
|
|
31
|
+
import "./chunk-OBDIJ4QS.js";
|
|
32
|
+
import "./chunk-6FG6JFZP.js";
|
|
33
|
+
import "./chunk-3XBG5HIV.js";
|
|
34
|
+
import "./chunk-SB36AUG7.js";
|
|
35
|
+
import "./chunk-WINIL2KN.js";
|
|
36
|
+
import "./chunk-PF4DSFDR.js";
|
|
37
|
+
import "./chunk-7X6NF7NI.js";
|
|
38
|
+
import "./chunk-W5J3LTYS.js";
|
|
39
|
+
import "./chunk-Z2ZITHT4.js";
|
|
40
|
+
import "./chunk-4OLM3KSB.js";
|
|
41
|
+
import "./chunk-FXQXCOII.js";
|
|
42
|
+
import "./chunk-TLT4YIG3.js";
|
|
43
|
+
import "./chunk-5R63Q5KH.js";
|
|
44
|
+
import "./chunk-I6Y4O3RR.js";
|
|
45
|
+
import "./chunk-Q5RDQNIT.js";
|
|
46
|
+
import "./chunk-DQC5FFGV.js";
|
|
47
|
+
import "./chunk-HS5PO5ZQ.js";
|
|
48
|
+
export {
|
|
49
|
+
Matrix,
|
|
50
|
+
componentInit,
|
|
51
|
+
makeChartBtnMenu,
|
|
52
|
+
matrixInit
|
|
53
|
+
};
|
|
54
|
+
//# sourceMappingURL=matrix-QFKGEW5A.js.map
|
|
@@ -0,0 +1,59 @@
|
|
|
1
|
+
import {
|
|
2
|
+
Matrix,
|
|
3
|
+
componentInit,
|
|
4
|
+
makeChartBtnMenu,
|
|
5
|
+
matrixInit
|
|
6
|
+
} from "./chunk-A2UUXYH6.js";
|
|
7
|
+
import "./chunk-5LYVIIYR.js";
|
|
8
|
+
import "./chunk-CN6KJORZ.js";
|
|
9
|
+
import "./chunk-5FRETII3.js";
|
|
10
|
+
import {
|
|
11
|
+
getPlotConfig,
|
|
12
|
+
setComputedConfig
|
|
13
|
+
} from "./chunk-WIQVSCD5.js";
|
|
14
|
+
import "./chunk-AR3HXZIW.js";
|
|
15
|
+
import "./chunk-67URJYN7.js";
|
|
16
|
+
import "./chunk-OEBGQKQR.js";
|
|
17
|
+
import "./chunk-JTQPPUDG.js";
|
|
18
|
+
import "./chunk-C2MCQZWH.js";
|
|
19
|
+
import "./chunk-DDKS3MV3.js";
|
|
20
|
+
import "./chunk-CFZ2ZW3E.js";
|
|
21
|
+
import "./chunk-Z6MCBFDM.js";
|
|
22
|
+
import "./chunk-NGMM2MNC.js";
|
|
23
|
+
import "./chunk-AVCEHJG7.js";
|
|
24
|
+
import "./chunk-V2OJLJSK.js";
|
|
25
|
+
import "./chunk-C3HEDQPT.js";
|
|
26
|
+
import "./chunk-HJ6L54YS.js";
|
|
27
|
+
import "./chunk-KV4W2ACA.js";
|
|
28
|
+
import "./chunk-B6UXFX73.js";
|
|
29
|
+
import "./chunk-ELJX3QIQ.js";
|
|
30
|
+
import "./chunk-3FEP6B5T.js";
|
|
31
|
+
import "./chunk-EEB5VE2A.js";
|
|
32
|
+
import "./chunk-6RRZRISL.js";
|
|
33
|
+
import "./chunk-2KM4PRQM.js";
|
|
34
|
+
import "./chunk-OBDIJ4QS.js";
|
|
35
|
+
import "./chunk-6FG6JFZP.js";
|
|
36
|
+
import "./chunk-3XBG5HIV.js";
|
|
37
|
+
import "./chunk-SB36AUG7.js";
|
|
38
|
+
import "./chunk-WINIL2KN.js";
|
|
39
|
+
import "./chunk-PF4DSFDR.js";
|
|
40
|
+
import "./chunk-7X6NF7NI.js";
|
|
41
|
+
import "./chunk-W5J3LTYS.js";
|
|
42
|
+
import "./chunk-Z2ZITHT4.js";
|
|
43
|
+
import "./chunk-4OLM3KSB.js";
|
|
44
|
+
import "./chunk-FXQXCOII.js";
|
|
45
|
+
import "./chunk-TLT4YIG3.js";
|
|
46
|
+
import "./chunk-5R63Q5KH.js";
|
|
47
|
+
import "./chunk-I6Y4O3RR.js";
|
|
48
|
+
import "./chunk-Q5RDQNIT.js";
|
|
49
|
+
import "./chunk-DQC5FFGV.js";
|
|
50
|
+
import "./chunk-HS5PO5ZQ.js";
|
|
51
|
+
export {
|
|
52
|
+
Matrix,
|
|
53
|
+
componentInit,
|
|
54
|
+
getPlotConfig,
|
|
55
|
+
makeChartBtnMenu,
|
|
56
|
+
matrixInit,
|
|
57
|
+
setComputedConfig
|
|
58
|
+
};
|
|
59
|
+
//# sourceMappingURL=matrix-XT7LUV5K.js.map
|