@sjcrh/proteinpaint-client 2.196.0 → 2.197.0
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-HV22W5N3.js +1373 -0
- package/dist/AIProjectAdmin-7QGTPN3B.js +958 -0
- package/dist/AppHeader-NOKET4YE.js +835 -0
- package/dist/BoxPlot-SPG66F4C.js +1217 -0
- package/dist/CorrelationVolcano-3LEMTFXP.js +619 -0
- package/dist/DE-WCCADMXA.js +95 -0
- package/dist/DEinput-IZNPYPKH.js +301 -0
- package/dist/DifferentialAnalysis-SDZXIUXP.js +242 -0
- package/dist/DifferentialAnalysis-SDZXIUXP.js.map +7 -0
- package/dist/Disco-M5RNUOWG.js +3297 -0
- package/dist/Disco.UI-RVUOPT6Y.js +249 -0
- package/dist/DmrPlot-R2N534FS.js +642 -0
- package/dist/GB-DY6XWOJE.js +1356 -0
- package/dist/GB-DY6XWOJE.js.map +7 -0
- package/dist/GSEA-3TB3PYEV.js +846 -0
- package/dist/GSEA-3TB3PYEV.js.map +7 -0
- package/dist/GeneExpInput-VWCPHOVO.js +367 -0
- package/dist/HicApp-F2MY3NXP.js +2250 -0
- package/dist/IDCViewer-PT7IV6T2.js +10799 -0
- package/dist/IDCViewer-PT7IV6T2.js.map +7 -0
- package/dist/NumBinaryEditor-AL2NWII2.js +271 -0
- package/dist/NumBinaryEditor.unit.spec-NFRJHFNX.js +286 -0
- package/dist/NumContEditor-CTFJVIHU.js +109 -0
- package/dist/NumContEditor.unit.spec-FXGGCMTD.js +169 -0
- package/dist/NumCustomBinEditor-JFIJ2X6E.js +38 -0
- package/dist/NumCustomBinEditor.unit.spec-ZKIZXS53.js +284 -0
- package/dist/NumDiscreteEditor-E7SPHF55.js +179 -0
- package/dist/NumDiscreteEditor.unit.spec-QKKRZJMU.js +202 -0
- package/dist/NumRegularBinEditor-JSLTZIAQ.js +38 -0
- package/dist/NumRegularBinEditor.unit.spec-W73BA6L4.js +227 -0
- package/dist/NumSplineEditor-ZEXYGKKF.js +198 -0
- package/dist/NumSplineEditor.unit.spec-EHKI4CY7.js +199 -0
- package/dist/NumericDensity-ZXM6TB33.js +38 -0
- package/dist/NumericDensity.unit.spec-PUFRE5XA.js +221 -0
- package/dist/NumericHandler-73TUDM3R.js +39 -0
- package/dist/NumericHandler.unit.spec-EITBD47U.js +219 -0
- package/dist/ProteomeInput-QICOUSRW.js +395 -0
- package/dist/ProteomeInput-QICOUSRW.js.map +7 -0
- package/dist/RunChart2-4JYV2Z7B.js +758 -0
- package/dist/SC-77HA6SBW.js +1120 -0
- package/dist/SC-77HA6SBW.js.map +7 -0
- package/dist/Volcano-3546I4MG.js +1385 -0
- package/dist/Volcano-3546I4MG.js.map +7 -0
- package/dist/WSIViewer-DQAXX7QJ.js +48562 -0
- package/dist/WsiSamplesPlot-AGOLPLK3.js +165 -0
- package/dist/adSandbox-ZE5QOTN5.js +38 -0
- package/dist/animatedBubbleChart-ILMDNAVK.js +555 -0
- package/dist/app-JBFRJ5OO.js +49 -0
- package/dist/app-YVNRAZWU.js +37 -0
- package/dist/app.js +16 -16
- package/dist/bam-A2PVAF3J.js +860 -0
- package/dist/barchart-2XQ7F6LT.js +47 -0
- package/dist/barchart.data-6XLK7D63.js +22 -0
- package/dist/barchart.events-DKJDKSPN.js +47 -0
- package/dist/barchart.integration.spec-UTTCQJRL.js +2196 -0
- package/dist/barchart2-2FRVUVJG.js +314 -0
- package/dist/block-3KOPYQ25.js +6255 -0
- package/dist/block-3KOPYQ25.js.map +7 -0
- package/dist/block.init-3KLLFGGV.js +38 -0
- package/dist/block.mds.expressionrank-XU3MBIOX.js +359 -0
- package/dist/block.mds.geneboxplot-VQTBL7T4.js +828 -0
- package/dist/block.mds.junction-IYWWRIJD.js +1545 -0
- package/dist/block.mds.svcnv-BMY5DCAM.js +6801 -0
- package/dist/block.svg-AT4GYQHX.js +164 -0
- package/dist/block.tk.aicheck-RANOFGDZ.js +283 -0
- package/dist/block.tk.ase-CBWJA3RN.js +365 -0
- package/dist/block.tk.bam-D7JBRNFQ.js +1906 -0
- package/dist/block.tk.bedgraphdot-IEHNIGVI.js +384 -0
- package/dist/block.tk.bigwig.ui-3SAXUJU4.js +212 -0
- package/dist/block.tk.hicstraw-R5EHQFGM.js +823 -0
- package/dist/block.tk.junction-JFCEXZZC.js +2364 -0
- package/dist/block.tk.junction.textmatrixui-4V7MV6TD.js +199 -0
- package/dist/block.tk.ld-LP4DIHAJ.js +99 -0
- package/dist/block.tk.menu-FTVZU2HA.js +1029 -0
- package/dist/block.tk.pgv-CRAMVKU4.js +944 -0
- package/dist/brainImaging-DXLK5XZ6.js +423 -0
- package/dist/brainRegions-AMSXQT3T.js +221 -0
- package/dist/bubbleHeatmap-SXBARILL.js +383 -0
- package/dist/chunk-23AEAG37.js +314 -0
- package/dist/chunk-23AEAG37.js.map +7 -0
- package/dist/chunk-2AHDWWQO.js +276 -0
- package/dist/chunk-2OJ577BB.js +299 -0
- package/dist/chunk-433DTQ6C.js +26 -0
- package/dist/chunk-46CPDZSW.js +617 -0
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- package/dist/chunk-H42SJNXA.js +1535 -0
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- package/dist/chunk-JT7HC65V.js.map +7 -0
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- package/dist/chunk-K7QY24X2.js +1223 -0
- package/dist/chunk-K7QY24X2.js.map +7 -0
- package/dist/chunk-KOLVLBMI.js +100 -0
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- package/dist/chunk-KTKZSYIH.js.map +7 -0
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- package/dist/chunk-M2PPUO4E.js +315 -0
- package/dist/chunk-M2PPUO4E.js.map +7 -0
- package/dist/chunk-MCXQL4W2.js +226 -0
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- package/dist/chunk-ZPXSPJV2.js +263 -0
- package/dist/chunk-ZRSJVACE.js +1500 -0
- package/dist/chunk-ZRSJVACE.js.map +7 -0
- package/dist/condition-YCPNILTV.js +332 -0
- package/dist/controls-RW5MWSLN.js +41 -0
- package/dist/controls.config-MP3CSYR4.js +39 -0
- package/dist/correlation-7AQRU4YR.js +102 -0
- package/dist/cuminc-WYLKIOXR.js +1149 -0
- package/dist/cuminc.integration.spec-MSAWDLD7.js +678 -0
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- package/dist/customdata.inputui-YU4IQJOV.js +289 -0
- package/dist/dataDownload-72DIPZ45.js +330 -0
- package/dist/dataDownload.integration.spec-HRLMWQN7.js +193 -0
- package/dist/databrowser.ui-3PE25HK4.js +433 -0
- package/dist/dictionary-Y3ICL4AE.js +118 -0
- package/dist/dnaMethylation-SVGDW64U.js +38 -0
- package/dist/dnaMethylation.integration.spec-B7GLAFZI.js +203 -0
- package/dist/dofetch-42KOXNPF.js +51 -0
- package/dist/e2pca-CLFGEFJH.js +350 -0
- package/dist/ep-PUHV2DMO.js +1256 -0
- package/dist/expclust.gdc.spec-N7YDJAOZ.js +307 -0
- package/dist/facet-JFFJJCNT.js +521 -0
- package/dist/forms2-XZAWW3RN.js +539 -0
- package/dist/gb-SQJ5PWOH.js +88 -0
- package/dist/geneExpClustering-EG2BLMQX.js +249 -0
- package/dist/geneExpression-J42BGP3B.js +38 -0
- package/dist/geneExpression-QRK3LNMV.js +313 -0
- package/dist/geneExpression.unit.spec-X7HVIFZA.js +102 -0
- package/dist/geneORA-SVBPO66K.js +278 -0
- package/dist/geneRanking-HNMMLZIX.js +553 -0
- package/dist/geneVariant-RVQKNVQO.js +39 -0
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- package/dist/geneVariant.integration.spec-DOMX4GMP.js +198 -0
- package/dist/genefusion.ui-QS7AG46F.js +309 -0
- package/dist/geneset-JKOX3VIW.js +208 -0
- package/dist/genomeBrowser.spec-IRSTT2OX.js +281 -0
- package/dist/grin2-G6DA4M7Q.js +1095 -0
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- /package/dist/{selectGenomeWithTklst-WF2XZ6GH.js.map → selectGenomeWithTklst-IJTCLRIN.js.map} +0 -0
- /package/dist/{sampleView-WKZT5ZFE.js.map → singleCellCellType-FJ53DRXD.js.map} +0 -0
- /package/dist/{singleCellCellType.unit.spec-DCGHNRJI.js.map → singleCellCellType.unit.spec-VOE4KY6L.js.map} +0 -0
- /package/dist/{singleCellCellType-2SRGROMS.js.map → singleCellGeneExpression-RZE5UVL4.js.map} +0 -0
- /package/dist/{singleCellGeneExpression.unit.spec-5MRGH2OO.js.map → singleCellGeneExpression.unit.spec-2DASF7PD.js.map} +0 -0
- /package/dist/{singleCellGeneExpression-RASZA4NO.js.map → singleCellPlot-Q5UNIW3M.js.map} +0 -0
- /package/dist/{singlecell-CFA43TTU.js.map → singlecell-N7F5KVIB.js.map} +0 -0
- /package/dist/{singlecell-JS5SIZHY.js.map → singlecell-TX5AQ4WM.js.map} +0 -0
- /package/dist/{singleCellPlot-TIYA3GNM.js.map → snp-S4O7SVDD.js.map} +0 -0
- /package/dist/{snp.unit.spec-TR5TCO7X.js.map → snp.unit.spec-WSQMZSTE.js.map} +0 -0
- /package/dist/{snplocus-VLPH5Y65.js.map → snplocus-Y2R5C4ZP.js.map} +0 -0
- /package/dist/{spliceevent.a53ss.diagram-PATK67SH.js.map → spliceevent.a53ss.diagram-FGRQR73W.js.map} +0 -0
- /package/dist/{spliceevent.exonskip.diagram-7B3SEOAJ.js.map → spliceevent.exonskip.diagram-TVH44RNL.js.map} +0 -0
- /package/dist/{spliceevent.noeventdiagram-4NPNZUEN.js.map → spliceevent.noeventdiagram-G2CMYYE7.js.map} +0 -0
- /package/dist/{snp-VXZXPMKS.js.map → ssGSEA-BH53XGEZ.js.map} +0 -0
- /package/dist/{ssGSEA.unit.spec-ASUWKVUT.js.map → ssGSEA.unit.spec-BYIVB7FZ.js.map} +0 -0
- /package/dist/{summarizeCnvGeneexp-KWRFGX32.js.map → summarizeCnvGeneexp-IZNOX4E7.js.map} +0 -0
- /package/dist/{summarizeGeneexpSurvival-FIPIMEJR.js.map → summarizeGeneexpSurvival-DJZ2R24E.js.map} +0 -0
- /package/dist/{summarizeMutationCnv-IUYRVLZG.js.map → summarizeMutationCnv-CO2TVWOI.js.map} +0 -0
- /package/dist/{ssGSEA-XMW5BLAU.js.map → summarizeMutationDiagnosis-EUZXCSZP.js.map} +0 -0
- /package/dist/{summarizeMutationSurvival-HFHYB7DT.js.map → summarizeMutationSurvival-CXFT3HWL.js.map} +0 -0
- /package/dist/{summarizeMutationDiagnosis-ZFJPCABL.js.map → summary-JHZCDE35.js.map} +0 -0
- /package/dist/{summary.integration.spec-WLBAJL44.js.map → summary.integration.spec-WBEYSDCA.js.map} +0 -0
- /package/dist/{summaryInput-NJWVXDXW.js.map → summaryInput-JVH3R54R.js.map} +0 -0
- /package/dist/{sunburst-PXGF4WM6.js.map → sunburst-CTJTXHSA.js.map} +0 -0
- /package/dist/{summary-AZUNEZ5I.js.map → survival-DLLVUG2P.js.map} +0 -0
- /package/dist/{survival-RAU4XCKG.js.map → survival-XFVYNI6S.js.map} +0 -0
- /package/dist/{svgraph-7UCFRL6A.js.map → svgraph-ACEBMDIX.js.map} +0 -0
- /package/dist/{svmr-DB3RY2ID.js.map → svmr-IQEDSZ2C.js.map} +0 -0
- /package/dist/{table-HJRWWXGM.js.map → table-2IF6UGHR.js.map} +0 -0
- /package/dist/{survival-ZZ4QLZHK.js.map → termCollection-JOLQJYJ3.js.map} +0 -0
- /package/dist/{termCollection-WPON7RG3.js.map → termCollection-PSXFFR32.js.map} +0 -0
- /package/dist/{termCollection.unit.spec-254ESHOE.js.map → termCollection.unit.spec-4SOZP4FY.js.map} +0 -0
- /package/dist/{termCollection-AW7M6DTP.js.map → tk-AAIHEQO6.js.map} +0 -0
- /package/dist/{tp.ui-ELEQGSK2.js.map → tp.ui-6STLQEXX.js.map} +0 -0
- /package/dist/{tk-SUAFM5YA.js.map → tvs.dt-FSA7KPSQ.js.map} +0 -0
- /package/dist/{tvs.dtcnv.categorical-SFQZMYX7.js.map → tvs.dtcnv.categorical-FSPGH7DP.js.map} +0 -0
- /package/dist/{tvs.dtcnv.continuous-AUZNJMC3.js.map → tvs.dtcnv.continuous-T4ZMSDB4.js.map} +0 -0
- /package/dist/{tvs.dtfusion-5F7MYFHZ.js.map → tvs.dtfusion-UL3YENUM.js.map} +0 -0
- /package/dist/{tvs.dtsnvindel-JJSPL4PH.js.map → tvs.dtsnvindel-5TPUT5RJ.js.map} +0 -0
- /package/dist/{tvs.dtsv-DARTSV5H.js.map → tvs.dtsv-OTNHXYOJ.js.map} +0 -0
- /package/dist/{tvs.samplelst-HHBIO26C.js.map → tvs.samplelst-FQKTAQZF.js.map} +0 -0
- /package/dist/{tvs.termCollection-KCMALH6B.js.map → tvs.termCollection-ZAPCUMUW.js.map} +0 -0
- /package/dist/{tvs.dt-DCXY66YY.js.map → violin-HEFFKPL5.js.map} +0 -0
- /package/dist/{violin.integration.spec-QQ43XWHQ.js.map → violin.integration.spec-774N4G5A.js.map} +0 -0
- /package/dist/{violin-C26FW5WK.js.map → violin.interactivity-XNYJSK53.js.map} +0 -0
- /package/dist/{violin.interactivity-H2BHC6M4.js.map → violin.renderer-R74VSGRC.js.map} +0 -0
- /package/dist/{violin.renderer-GSG2I7AV.js.map → vocabulary-OHMC6NWL.js.map} +0 -0
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// src/maftimeline.js
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function maftimelineui(genomes, holder, sandbox_header) {
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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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{
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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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render(data, header, visual_holder);
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};
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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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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]);
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return;
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}
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if (v < zerovalue) {
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v = zerovalue;
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}
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m.maf = v;
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+
if (!m.coverage) {
|
|
230
|
+
badlines.push([i, "missing total_readcount", lst]);
|
|
231
|
+
return;
|
|
232
|
+
}
|
|
233
|
+
if (m.call_manual && m.call_manual == "wildtype") {
|
|
234
|
+
m.maf = zerovalue;
|
|
235
|
+
}
|
|
236
|
+
v = Number.parseInt(m.coverage);
|
|
237
|
+
if (Number.isNaN(v)) {
|
|
238
|
+
badlines.push([i, "invalid total_readcount", lst]);
|
|
239
|
+
return;
|
|
240
|
+
}
|
|
241
|
+
m.coverage = v;
|
|
242
|
+
let date;
|
|
243
|
+
if (m.date) {
|
|
244
|
+
const f = timeParse("%m/%d/%Y");
|
|
245
|
+
date = f(m.date);
|
|
246
|
+
m.Date = m.date;
|
|
247
|
+
} else {
|
|
248
|
+
badlines.push([i, "missing date", lst]);
|
|
249
|
+
return;
|
|
250
|
+
}
|
|
251
|
+
if (date == null) {
|
|
252
|
+
badlines.push([i, "cannot parse date", lst]);
|
|
253
|
+
return;
|
|
254
|
+
}
|
|
255
|
+
m.date = date;
|
|
256
|
+
if (!m.sample) {
|
|
257
|
+
badlines.push([i, "missing sample", lst]);
|
|
258
|
+
return;
|
|
259
|
+
}
|
|
260
|
+
data[m.patient].snv4[m.snv4].samples.push(m);
|
|
261
|
+
return true;
|
|
262
|
+
}
|
|
263
|
+
function render(data, header, holder) {
|
|
264
|
+
const table = holder.append("table").style("margin", "20px");
|
|
265
|
+
const tr1 = table.append("tr");
|
|
266
|
+
let td = tr1.append("td").style("vertical-align", "top").attr("rowspan", 2);
|
|
267
|
+
td.append("button").text("Toggle circle visibility").on("click", () => {
|
|
268
|
+
showcircle = !showcircle;
|
|
269
|
+
for (const n in data) {
|
|
270
|
+
if (data[n].show) {
|
|
271
|
+
data[n].handle.node().click();
|
|
272
|
+
break;
|
|
273
|
+
}
|
|
274
|
+
}
|
|
275
|
+
});
|
|
276
|
+
const patientholder = td.append("div").style("margin-top", "10px");
|
|
277
|
+
const td1 = tr1.append("td").style("vertical-align", "top");
|
|
278
|
+
const graphholder = td1.append("div").style("display", "inline-block");
|
|
279
|
+
const controlholder = td1.append("div").style("display", "inline-block").style("vertical-align", "top");
|
|
280
|
+
const tr2 = table.append("tr");
|
|
281
|
+
const tiantable = tr2.append("td").append("table").style("border-spacing", "20px").style("border-collapse", "separate");
|
|
282
|
+
const gtr1 = tiantable.append("tr");
|
|
283
|
+
td = gtr1.append("td").style("vertical-align", "top");
|
|
284
|
+
td.append("div").text("Shared").style("font-size", "2em");
|
|
285
|
+
const graph1holder = td.append("div").style("border", "solid 1px black");
|
|
286
|
+
td = gtr1.append("td").style("vertical-align", "top");
|
|
287
|
+
td.append("div").text("Rising").style("font-size", "2em");
|
|
288
|
+
const graph2holder = td.append("div").style("border", "solid 1px black");
|
|
289
|
+
const gtr2 = tiantable.append("tr");
|
|
290
|
+
td = gtr2.append("td").style("vertical-align", "top");
|
|
291
|
+
td.append("div").text("Falling").style("font-size", "2em");
|
|
292
|
+
const graph3holder = td.append("div").style("border", "solid 1px black");
|
|
293
|
+
td = gtr2.append("td").style("vertical-align", "top");
|
|
294
|
+
td.append("div").text("R-only").style("font-size", "2em");
|
|
295
|
+
const graph4holder = td.append("div").style("border", "solid 1px black");
|
|
296
|
+
for (const patient in data) {
|
|
297
|
+
const snvlst = [];
|
|
298
|
+
const colors = ordinal(category10_default);
|
|
299
|
+
for (const x in data[patient].snv4) {
|
|
300
|
+
const snv = data[patient].snv4[x];
|
|
301
|
+
snv.show = true;
|
|
302
|
+
snv.color = colors(snv.mutationname);
|
|
303
|
+
snv.samples.sort((a, b) => a.date - b.date);
|
|
304
|
+
for (const s of snv.samples) {
|
|
305
|
+
s.color = snv.color;
|
|
306
|
+
}
|
|
307
|
+
snvlst.push(snv);
|
|
308
|
+
}
|
|
309
|
+
const div = patientholder.append("div").classed("sja_menuoption", true).style("color", "black").text(patient).on("click", () => {
|
|
310
|
+
for (const pn in data) {
|
|
311
|
+
data[pn].handle.style("color", "black");
|
|
312
|
+
data[pn].show = false;
|
|
313
|
+
}
|
|
314
|
+
data[patient].handle.style("color", "red");
|
|
315
|
+
data[patient].show = true;
|
|
316
|
+
makegraph(snvlst, header, graphholder);
|
|
317
|
+
makesubgraph(snvlst, graph1holder, graph2holder, graph3holder, graph4holder);
|
|
318
|
+
makecontrol(snvlst, header, controlholder, graphholder, graph1holder, graph2holder, graph3holder, graph4holder);
|
|
319
|
+
});
|
|
320
|
+
data[patient].handle = div;
|
|
321
|
+
}
|
|
322
|
+
for (const n in data) {
|
|
323
|
+
data[n].handle.node().click();
|
|
324
|
+
break;
|
|
325
|
+
}
|
|
326
|
+
}
|
|
327
|
+
function makesubgraph(snvlst, g1, g2, g3, g4) {
|
|
328
|
+
g1.selectAll("*").remove();
|
|
329
|
+
g2.selectAll("*").remove();
|
|
330
|
+
g3.selectAll("*").remove();
|
|
331
|
+
g4.selectAll("*").remove();
|
|
332
|
+
const l1 = [];
|
|
333
|
+
const l2 = [];
|
|
334
|
+
const l3 = [];
|
|
335
|
+
const l4 = [];
|
|
336
|
+
for (const snv of snvlst) {
|
|
337
|
+
switch (snv.subidx) {
|
|
338
|
+
case 1:
|
|
339
|
+
l1.push(snv);
|
|
340
|
+
break;
|
|
341
|
+
case 2:
|
|
342
|
+
l2.push(snv);
|
|
343
|
+
break;
|
|
344
|
+
case 3:
|
|
345
|
+
l3.push(snv);
|
|
346
|
+
break;
|
|
347
|
+
case 4:
|
|
348
|
+
l4.push(snv);
|
|
349
|
+
break;
|
|
350
|
+
}
|
|
351
|
+
}
|
|
352
|
+
if (l1.length) {
|
|
353
|
+
makegraph(l1, null, g1, true);
|
|
354
|
+
} else {
|
|
355
|
+
g1.append("div").style("padding", "60px").style("background-color", "#ededed").text("no data");
|
|
356
|
+
}
|
|
357
|
+
if (l2.length) {
|
|
358
|
+
makegraph(l2, null, g2, true);
|
|
359
|
+
} else {
|
|
360
|
+
g2.append("div").style("padding", "60px").style("background-color", "#ededed").text("no data");
|
|
361
|
+
}
|
|
362
|
+
if (l3.length) {
|
|
363
|
+
makegraph(l3, null, g3, true);
|
|
364
|
+
} else {
|
|
365
|
+
g3.append("div").style("padding", "60px").style("background-color", "#ededed").text("no data");
|
|
366
|
+
}
|
|
367
|
+
if (l4.length) {
|
|
368
|
+
makegraph(l4, null, g4, true);
|
|
369
|
+
} else {
|
|
370
|
+
g4.append("div").style("padding", "60px").style("background-color", "#ededed").text("no data");
|
|
371
|
+
}
|
|
372
|
+
}
|
|
373
|
+
function makegraph(snvlst0, header, holder, issub) {
|
|
374
|
+
holder.selectAll("*").remove();
|
|
375
|
+
const samples = [];
|
|
376
|
+
const snvlst = [];
|
|
377
|
+
for (const snv of snvlst0) {
|
|
378
|
+
if (!issub && !snv.show) continue;
|
|
379
|
+
snvlst.push(snv);
|
|
380
|
+
for (const s of snv.samples) {
|
|
381
|
+
samples.push(s);
|
|
382
|
+
}
|
|
383
|
+
}
|
|
384
|
+
if (snvlst.length == 0) return;
|
|
385
|
+
let mindate = snvlst[0].samples[0].date;
|
|
386
|
+
let maxdate = snvlst[0].samples[0].date;
|
|
387
|
+
let maxmaf = snvlst[0].samples[0].maf;
|
|
388
|
+
let maxcoverage = snvlst[0].samples[0].coverage;
|
|
389
|
+
for (const snv of snvlst) {
|
|
390
|
+
for (const s of snv.samples) {
|
|
391
|
+
mindate = Math.min(mindate, s.date);
|
|
392
|
+
maxdate = Math.max(maxdate, s.date);
|
|
393
|
+
maxmaf = Math.max(maxmaf, s.maf);
|
|
394
|
+
maxcoverage = Math.max(maxcoverage, s.coverage);
|
|
395
|
+
}
|
|
396
|
+
}
|
|
397
|
+
const svg = holder.append("svg");
|
|
398
|
+
const toppad = 30, rightpad = 200, yaxisw = 100, xaxish = 50;
|
|
399
|
+
let width = 600;
|
|
400
|
+
let height = 400;
|
|
401
|
+
let xpad, ypad, minradius;
|
|
402
|
+
const xaxisg = svg.append("g");
|
|
403
|
+
const yaxisg = svg.append("g");
|
|
404
|
+
const drag = svg.append("text").text("drag to resize").attr("class", "sja_clb").attr("text-anchor", "end").on("mousedown", (event) => {
|
|
405
|
+
event.preventDefault();
|
|
406
|
+
const x = event.clientX;
|
|
407
|
+
const y = event.clientY;
|
|
408
|
+
const w0 = width;
|
|
409
|
+
const h0 = height;
|
|
410
|
+
const body = select_default(document.body);
|
|
411
|
+
body.on("mousemove", (event2) => {
|
|
412
|
+
setsize(w0 + event2.clientX - x, h0 + event2.clientY - y);
|
|
413
|
+
}).on("mouseup", () => {
|
|
414
|
+
body.on("mousemove", null).on("mouseup", null);
|
|
415
|
+
});
|
|
416
|
+
});
|
|
417
|
+
const xscale = time().domain([mindate, maxdate]);
|
|
418
|
+
const yscale = (maflogscale ? log() : linear()).domain([zerovalue, 1]);
|
|
419
|
+
const rscale = linear().domain([1, maxcoverage]);
|
|
420
|
+
const g = svg.append("g");
|
|
421
|
+
const lines = g.selectAll().data(snvlst).enter().append("path").attr("stroke", (d) => d.color).attr("fill", "none");
|
|
422
|
+
let circles;
|
|
423
|
+
if (showcircle) {
|
|
424
|
+
circles = g.selectAll().data(samples).enter().append("circle").attr("fill", (d) => d.color).attr("fill-opacity", 0.1).on("mouseover", (event, d) => {
|
|
425
|
+
event.target.setAttribute("fill-opacity", 0.4);
|
|
426
|
+
tip.clear();
|
|
427
|
+
tip.show(event.clientX, event.clientY);
|
|
428
|
+
const lst = [];
|
|
429
|
+
for (const k in d) {
|
|
430
|
+
if (k == "color") continue;
|
|
431
|
+
if (k == "gene") {
|
|
432
|
+
lst.push({ k: "gene", v: '<span style="color:' + d.color + '">' + d.gene + "</span>" });
|
|
433
|
+
continue;
|
|
434
|
+
}
|
|
435
|
+
if (k == "date") continue;
|
|
436
|
+
if (k == "url") {
|
|
437
|
+
lst.push({ k: "URL", v: "<a href=" + d.url + " target=_blank>LINK</a>" });
|
|
438
|
+
continue;
|
|
439
|
+
}
|
|
440
|
+
lst.push({ k, v: d[k] });
|
|
441
|
+
}
|
|
442
|
+
make_table_2col(tip.d, lst);
|
|
443
|
+
}).on("mouseout", (event) => {
|
|
444
|
+
event.target.setAttribute("fill-opacity", 0.1);
|
|
445
|
+
});
|
|
446
|
+
}
|
|
447
|
+
const legend = svg.append("g");
|
|
448
|
+
const setsize = (w, h) => {
|
|
449
|
+
width = w;
|
|
450
|
+
height = h;
|
|
451
|
+
minradius = 2;
|
|
452
|
+
const maxradius = Math.max(width, height) / 30;
|
|
453
|
+
xpad = maxradius;
|
|
454
|
+
ypad = maxradius;
|
|
455
|
+
rscale.range([Math.pow(minradius, 2), Math.pow(maxradius, 2)]);
|
|
456
|
+
xscale.range([0, width]);
|
|
457
|
+
yscale.range([height, 0]);
|
|
458
|
+
svg.attr("width", yaxisw + xpad + width + rightpad).attr("height", toppad + height + ypad + xaxish);
|
|
459
|
+
xaxisg.attr("transform", "translate(" + (yaxisw + xpad) + "," + (toppad + height + ypad) + ")");
|
|
460
|
+
yaxisg.attr("transform", "translate(" + yaxisw + "," + toppad + ")");
|
|
461
|
+
drag.attr("x", yaxisw + xpad + width).attr("y", toppad + height + ypad + xaxish - 4);
|
|
462
|
+
axisstyle({
|
|
463
|
+
axis: xaxisg.call(axisBottom().scale(xscale)),
|
|
464
|
+
showline: true,
|
|
465
|
+
color: "black",
|
|
466
|
+
fontsize: Math.max(12, Math.min(20, width / 100))
|
|
467
|
+
});
|
|
468
|
+
axisstyle({
|
|
469
|
+
axis: yaxisg.call(
|
|
470
|
+
axisLeft().scale(yscale).tickValues([1, 0.1, 0.01, 1e-3, 1e-4, zerovalue]).tickFormat(format(" "))
|
|
471
|
+
),
|
|
472
|
+
showline: true,
|
|
473
|
+
color: "black",
|
|
474
|
+
fontsize: Math.max(12, Math.min(20, height / 100))
|
|
475
|
+
});
|
|
476
|
+
g.attr("transform", "translate(" + (yaxisw + xpad) + "," + toppad + ")");
|
|
477
|
+
lines.attr("d", (d) => {
|
|
478
|
+
const lst = [];
|
|
479
|
+
for (let i = 0; i < d.samples.length; i++) {
|
|
480
|
+
const s = d.samples[i];
|
|
481
|
+
lst.push((i == 0 ? "M" : "L") + " " + xscale(s.date) + " " + yscale(s.maf));
|
|
482
|
+
}
|
|
483
|
+
return lst.join(" ");
|
|
484
|
+
});
|
|
485
|
+
if (showcircle) {
|
|
486
|
+
circles.attr("cx", (d) => xscale(d.date)).attr("cy", (d) => yscale(d.maf)).attr("r", (d) => Math.sqrt(rscale(d.coverage)));
|
|
487
|
+
}
|
|
488
|
+
legend.attr("transform", "translate(" + (yaxisw + xpad + width + maxradius + 5) + "," + toppad + ")");
|
|
489
|
+
legend.selectAll("*").remove();
|
|
490
|
+
let y = minradius;
|
|
491
|
+
if (showcircle) {
|
|
492
|
+
legend.append("circle").attr("r", minradius).attr("cx", minradius).attr("cy", y).attr("fill", "#ccc");
|
|
493
|
+
legend.append("text").text(1).attr("x", minradius * 2 + 10).attr("y", y).attr("font-size", 10).attr("dominant-baseline", "central");
|
|
494
|
+
y += 5 + minradius + maxradius;
|
|
495
|
+
legend.append("circle").attr("r", maxradius).attr("cx", maxradius).attr("cy", y).attr("fill", "#ccc");
|
|
496
|
+
legend.append("text").text(maxcoverage).attr("x", maxradius * 2 + 10).attr("y", y).attr("font-size", 15).attr("dominant-baseline", "central");
|
|
497
|
+
y += 15 + maxradius;
|
|
498
|
+
}
|
|
499
|
+
const fontsize = 12;
|
|
500
|
+
for (const snv of snvlst) {
|
|
501
|
+
legend.append("line").attr("x2", 30).attr("y1", y).attr("y2", y).attr("stroke", snv.color);
|
|
502
|
+
if (showcircle) {
|
|
503
|
+
legend.append("circle").attr("cx", 15).attr("cy", y).attr("r", 8).attr("fill", snv.color).attr("fill-opacity", 0.1);
|
|
504
|
+
}
|
|
505
|
+
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) => {
|
|
506
|
+
event.target.setAttribute("font-weight", "bold");
|
|
507
|
+
lines.filter((d) => d.mutationname == snv.mutationname).attr("stroke-width", 3);
|
|
508
|
+
}).on("mouseout", (event) => {
|
|
509
|
+
event.target.setAttribute("font-weight", "normal");
|
|
510
|
+
lines.filter((d) => d.mutationname == snv.mutationname).attr("stroke-width", 1);
|
|
511
|
+
});
|
|
512
|
+
y += fontsize + 10;
|
|
513
|
+
}
|
|
514
|
+
};
|
|
515
|
+
setsize(width, height);
|
|
516
|
+
holder.append("div").style("text-align", "right").append("button").text("SVG").on("click", () => {
|
|
517
|
+
to_svg(svg.node(), "maf-timeline");
|
|
518
|
+
});
|
|
519
|
+
}
|
|
520
|
+
function makecontrol(snvlst, header, holder, graphholder, g1, g2, g3, g4) {
|
|
521
|
+
holder.selectAll("*").remove();
|
|
522
|
+
const table = holder.append("table");
|
|
523
|
+
for (const snv of snvlst) {
|
|
524
|
+
const tr = table.append("tr");
|
|
525
|
+
const td1 = tr.append("td");
|
|
526
|
+
td1.text(snv.gene).style("color", snv.color);
|
|
527
|
+
const td2 = tr.append("td");
|
|
528
|
+
const checkbox = td2.append("input").attr("type", "checkbox").style("zoom", "150%").property("checked", snv.show);
|
|
529
|
+
snv.checkbox = checkbox;
|
|
530
|
+
checkbox.on("change", (event) => {
|
|
531
|
+
snv.show = event.target.checked;
|
|
532
|
+
makegraph(snvlst, header, graphholder);
|
|
533
|
+
});
|
|
534
|
+
const butt = td2.append("button").style("margin-left", "5px").text("Only").on("click", () => {
|
|
535
|
+
for (const s2 of snvlst) {
|
|
536
|
+
s2.show = false;
|
|
537
|
+
s2.checkbox.property("checked", false);
|
|
538
|
+
}
|
|
539
|
+
snv.show = true;
|
|
540
|
+
snv.checkbox.property("checked", true);
|
|
541
|
+
makegraph(snvlst, header, graphholder);
|
|
542
|
+
});
|
|
543
|
+
let cname = Math.random();
|
|
544
|
+
const td11 = tr.append("td");
|
|
545
|
+
const c1 = td11.append("input").attr("type", "checkbox").attr("id", cname).on("change", (event) => cchange(1, event.target));
|
|
546
|
+
td11.append("label").html(" shared").attr("for", cname);
|
|
547
|
+
cname = Math.random();
|
|
548
|
+
const td22 = tr.append("td");
|
|
549
|
+
const c2 = td22.append("input").attr("type", "checkbox").attr("id", cname).on("change", (event) => cchange(2, event.target));
|
|
550
|
+
td22.append("label").html(" rising").attr("for", cname);
|
|
551
|
+
cname = Math.random();
|
|
552
|
+
const td33 = tr.append("td");
|
|
553
|
+
const c3 = td33.append("input").attr("type", "checkbox").attr("id", cname).on("change", (event) => cchange(3, event.target));
|
|
554
|
+
td33.append("label").html(" falling").attr("for", cname);
|
|
555
|
+
cname = Math.random();
|
|
556
|
+
const td44 = tr.append("td");
|
|
557
|
+
const c4 = td44.append("input").attr("type", "checkbox").attr("id", cname).on("change", (event) => cchange(4, event.target));
|
|
558
|
+
td44.append("label").html(" R-only").attr("for", cname);
|
|
559
|
+
if (snv.subidx == 1) c1.property("checked", true);
|
|
560
|
+
if (snv.subidx == 2) c2.property("checked", true);
|
|
561
|
+
if (snv.subidx == 3) c3.property("checked", true);
|
|
562
|
+
if (snv.subidx == 4) c4.property("checked", true);
|
|
563
|
+
const cchange = (which, check) => {
|
|
564
|
+
if (!check.checked) {
|
|
565
|
+
snv.subidx = -1;
|
|
566
|
+
} else {
|
|
567
|
+
snv.subidx = which;
|
|
568
|
+
if (which == 1) {
|
|
569
|
+
c2.property("checked", false);
|
|
570
|
+
c3.property("checked", false);
|
|
571
|
+
c4.property("checked", false);
|
|
572
|
+
} else if (which == 2) {
|
|
573
|
+
c1.property("checked", false);
|
|
574
|
+
c3.property("checked", false);
|
|
575
|
+
c4.property("checked", false);
|
|
576
|
+
} else if (which == 3) {
|
|
577
|
+
c1.property("checked", false);
|
|
578
|
+
c2.property("checked", false);
|
|
579
|
+
c4.property("checked", false);
|
|
580
|
+
} else {
|
|
581
|
+
c1.property("checked", false);
|
|
582
|
+
c2.property("checked", false);
|
|
583
|
+
c3.property("checked", false);
|
|
584
|
+
}
|
|
585
|
+
}
|
|
586
|
+
makesubgraph(snvlst, g1, g2, g3, g4);
|
|
587
|
+
};
|
|
588
|
+
}
|
|
589
|
+
}
|
|
590
|
+
export {
|
|
591
|
+
maftimelineui as default
|
|
592
|
+
};
|
|
593
|
+
//# sourceMappingURL=maftimeline-D7UENAP5.js.map
|
|
@@ -0,0 +1,63 @@
|
|
|
1
|
+
import {
|
|
2
|
+
Matrix,
|
|
3
|
+
componentInit,
|
|
4
|
+
makeChartBtnMenu,
|
|
5
|
+
matrixInit
|
|
6
|
+
} from "./chunk-Q555GFBW.js";
|
|
7
|
+
import "./chunk-CJJA6RVM.js";
|
|
8
|
+
import {
|
|
9
|
+
getPlotConfig,
|
|
10
|
+
setComputedConfig
|
|
11
|
+
} from "./chunk-HCNF7EFT.js";
|
|
12
|
+
import "./chunk-JT7HC65V.js";
|
|
13
|
+
import "./chunk-XVYSEXFV.js";
|
|
14
|
+
import "./chunk-DDKS3MV3.js";
|
|
15
|
+
import "./chunk-UF6ZP6UR.js";
|
|
16
|
+
import "./chunk-4YDERN37.js";
|
|
17
|
+
import "./chunk-SFIX7XVT.js";
|
|
18
|
+
import "./chunk-DA6RR5IR.js";
|
|
19
|
+
import "./chunk-XB6F5OUB.js";
|
|
20
|
+
import "./chunk-DXM5IMGV.js";
|
|
21
|
+
import "./chunk-HUBO743S.js";
|
|
22
|
+
import "./chunk-JD2ECQ3Z.js";
|
|
23
|
+
import "./chunk-V2OJLJSK.js";
|
|
24
|
+
import "./chunk-JHZK6IDA.js";
|
|
25
|
+
import "./chunk-HJ6L54YS.js";
|
|
26
|
+
import "./chunk-LSEFWW72.js";
|
|
27
|
+
import "./chunk-FYY3T565.js";
|
|
28
|
+
import "./chunk-HYOEWQ5P.js";
|
|
29
|
+
import "./chunk-HBW42TDT.js";
|
|
30
|
+
import "./chunk-FN5XPUPH.js";
|
|
31
|
+
import "./chunk-LQJMCE7G.js";
|
|
32
|
+
import "./chunk-IIT367QZ.js";
|
|
33
|
+
import "./chunk-RZGEKL77.js";
|
|
34
|
+
import "./chunk-7Z6E3NA5.js";
|
|
35
|
+
import "./chunk-V2ET64EJ.js";
|
|
36
|
+
import "./chunk-5ERYRSVV.js";
|
|
37
|
+
import "./chunk-7IYJZZQI.js";
|
|
38
|
+
import "./chunk-M3J4MINX.js";
|
|
39
|
+
import "./chunk-PF4DSFDR.js";
|
|
40
|
+
import "./chunk-23AEAG37.js";
|
|
41
|
+
import "./chunk-M2PPUO4E.js";
|
|
42
|
+
import "./chunk-ZRSJVACE.js";
|
|
43
|
+
import "./chunk-BKPDYW5T.js";
|
|
44
|
+
import "./chunk-JNITUVXP.js";
|
|
45
|
+
import "./chunk-TJYRBEBK.js";
|
|
46
|
+
import "./chunk-LOZEKOES.js";
|
|
47
|
+
import "./chunk-VQZ2Z5YU.js";
|
|
48
|
+
import "./chunk-SOTB4FRE.js";
|
|
49
|
+
import "./chunk-TLT4YIG3.js";
|
|
50
|
+
import "./chunk-KYBIQBXE.js";
|
|
51
|
+
import "./chunk-I6Y4O3RR.js";
|
|
52
|
+
import "./chunk-OMR2DT66.js";
|
|
53
|
+
import "./chunk-DQC5FFGV.js";
|
|
54
|
+
import "./chunk-HFNDKYVF.js";
|
|
55
|
+
export {
|
|
56
|
+
Matrix,
|
|
57
|
+
componentInit,
|
|
58
|
+
getPlotConfig,
|
|
59
|
+
makeChartBtnMenu,
|
|
60
|
+
matrixInit,
|
|
61
|
+
setComputedConfig
|
|
62
|
+
};
|
|
63
|
+
//# sourceMappingURL=matrix-77LNADX2.js.map
|