@sjcrh/proteinpaint-client 2.203.0 → 2.203.1
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-6CEBP4SA.js +1366 -0
- package/dist/AIProjectAdmin-2CKKFC3A.js +951 -0
- package/dist/AggregateMatrix-5TBUMFE5.js +665 -0
- package/dist/AppHeader-5YBPWF44.js +829 -0
- package/dist/BoxPlot-UOJS5SJV.js +1210 -0
- package/dist/CorrelationVolcano-KX6JPZMT.js +613 -0
- package/dist/Cuminc-TLOOLZWR.js +1208 -0
- package/dist/DE-HUQLQ2Z3.js +87 -0
- package/dist/DEinput-WWUISAF2.js +404 -0
- package/dist/DifferentialAnalysis-6DTAGCEY.js +237 -0
- package/dist/Disco-P6ZLPYLF.js +3388 -0
- package/dist/Disco.UI-WGTMAFK2.js +242 -0
- package/dist/DmrPlot-3FRU5KUK.js +636 -0
- package/dist/GB-NWOBARL3.js +1390 -0
- package/dist/GSEA-DEEUAAMI.js +850 -0
- package/dist/GeneExpInput-6QWGEAFV.js +361 -0
- package/dist/Geomap-6HT2B7RH.js +83 -0
- package/dist/HicApp-PCNOUULF.js +2244 -0
- package/dist/IDCViewer-H3QPXVM3.js +10811 -0
- package/dist/NumBinaryEditor-IU6OLMKN.js +278 -0
- package/dist/NumBinaryEditor.unit.spec-YUPUILIV.js +311 -0
- package/dist/NumContEditor-KFDA76QN.js +104 -0
- package/dist/NumContEditor.unit.spec-QBOT5QHU.js +163 -0
- package/dist/NumCustomBinEditor-EOSTEXLB.js +32 -0
- package/dist/NumCustomBinEditor.unit.spec-B46XWFYH.js +396 -0
- package/dist/NumDiscreteEditor-Y4EAADXC.js +169 -0
- package/dist/NumDiscreteEditor.unit.spec-SJGHLWSM.js +232 -0
- package/dist/NumRegularBinEditor-3BNG7DIN.js +32 -0
- package/dist/NumRegularBinEditor.unit.spec-KM45QXXG.js +277 -0
- package/dist/NumSplineEditor-K4KPDC4S.js +209 -0
- package/dist/NumSplineEditor.unit.spec-TKQP5XTS.js +223 -0
- package/dist/NumericDensity-Z6JFVN3D.js +32 -0
- package/dist/NumericDensity.unit.spec-YEYBVLEP.js +417 -0
- package/dist/NumericHandler-ITT6HMPN.js +33 -0
- package/dist/NumericHandler.unit.spec-QVONMXY4.js +213 -0
- package/dist/ProteomeInput-PRS3DEMZ.js +387 -0
- package/dist/Regression-LJJJBBT6.js +1413 -0
- package/dist/Regression-LJJJBBT6.js.map +7 -0
- package/dist/RunChart2-AMM2JFF5.js +749 -0
- package/dist/SC-F7IE66VZ.js +1106 -0
- package/dist/Violin-RJ6OJZ4F.js +1073 -0
- package/dist/Volcano-BJA5HN5Y.js +1414 -0
- package/dist/WSIViewer-RJZGRUIR.js +26194 -0
- package/dist/Wsi-DXP6KOQA.js +232 -0
- package/dist/WsiSamplesPlot-2IAWV2B6.js +159 -0
- package/dist/adSandbox-RGWOIV3W.js +32 -0
- package/dist/animatedBubbleChart-J4Q2NAEW.js +546 -0
- package/dist/app-3QXNR4VG.js +31 -0
- package/dist/app-B4B7YNP3.js +41 -0
- package/dist/app.js +12 -12
- package/dist/bam-LRUMN45P.js +875 -0
- package/dist/barchart-L2G6GEHK.js +41 -0
- package/dist/barchart2-DWNVAZAJ.js +308 -0
- package/dist/block-TVEVAXNP.js +6248 -0
- package/dist/block.init-YOHAKPRI.js +32 -0
- package/dist/block.mds.expressionrank-PU6JH4W5.js +353 -0
- package/dist/block.mds.geneboxplot-WYYFDNE3.js +822 -0
- package/dist/block.mds.junction-4WCTL7Y4.js +1538 -0
- package/dist/block.mds.svcnv-MR3VCYUW.js +6795 -0
- package/dist/block.svg-LR3Y4ZO7.js +158 -0
- package/dist/block.tk.aicheck-A5AWKJZI.js +277 -0
- package/dist/block.tk.ase-AQBBAQEH.js +359 -0
- package/dist/block.tk.bam-QBTA2O3V.js +1900 -0
- package/dist/block.tk.bedgraphdot-4ALZG2MY.js +378 -0
- package/dist/block.tk.bigwig.ui-32W6XW37.js +205 -0
- package/dist/block.tk.hicstraw-PKBHBAG2.js +817 -0
- package/dist/block.tk.junction-AO5CXUCU.js +2357 -0
- package/dist/block.tk.junction.textmatrixui-RORVUIPI.js +193 -0
- package/dist/block.tk.ld-TNBSR4FT.js +93 -0
- package/dist/block.tk.menu-QDJO54J5.js +1023 -0
- package/dist/block.tk.pgv-6222WWYR.js +937 -0
- package/dist/brainImaging-2TPE7MXB.js +426 -0
- package/dist/brainImaging-2TPE7MXB.js.map +7 -0
- package/dist/brainRegions-KTFH6DE2.js +215 -0
- package/dist/bubbleHeatmap-LNXZLFY6.js +377 -0
- package/dist/cellTypeBubbleHeatmap-SRHUNX3S.js +277 -0
- package/dist/chunk-3TXVDBGN.js +626 -0
- package/dist/chunk-4HLHKBHP.js +274 -0
- package/dist/chunk-5GG7Q2ZG.js +397 -0
- package/dist/chunk-5HVAVJKW.js +518 -0
- package/dist/chunk-5HVAVJKW.js.map +7 -0
- package/dist/chunk-5PMFCQKC.js +98 -0
- package/dist/chunk-67URJYN7.js +84 -0
- package/dist/chunk-67URJYN7.js.map +7 -0
- package/dist/chunk-6AKSOLBX.js +5071 -0
- package/dist/chunk-6AKSOLBX.js.map +7 -0
- package/dist/chunk-6X7PP7A4.js +2126 -0
- package/dist/chunk-A3EDLRUN.js +54 -0
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- package/dist/chunk-EO6M3LY3.js +339 -0
- package/dist/chunk-EO6M3LY3.js.map +7 -0
- package/dist/chunk-F4PMOAQK.js +494 -0
- package/dist/chunk-FISQTHD4.js +2327 -0
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- package/dist/chunk-FXT2XM4E.js.map +7 -0
- package/dist/chunk-HIWTGMTE.js +1721 -0
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- package/dist/chunk-KLWSW6CC.js +203 -0
- package/dist/chunk-KNNSOOTG.js +194 -0
- package/dist/chunk-KTPXQH2N.js +170 -0
- package/dist/chunk-LGKXSWY4.js +276 -0
- package/dist/chunk-LP2GIXVK.js +4274 -0
- package/dist/chunk-M2ZZL5EV.js +2669 -0
- package/dist/chunk-M2ZZL5EV.js.map +7 -0
- package/dist/chunk-MBHERRJR.js +302 -0
- package/dist/chunk-MLYQDJUQ.js +480 -0
- package/dist/chunk-NBGDLLMX.js +446 -0
- package/dist/chunk-OPMMU6DQ.js +183 -0
- package/dist/chunk-OPMMU6DQ.js.map +7 -0
- package/dist/chunk-P3JEXVBT.js +50 -0
- package/dist/chunk-PZPPJY4K.js +34 -0
- package/dist/chunk-Q6JF4ZLT.js +141 -0
- package/dist/chunk-QF5IH7PC.js +263 -0
- package/dist/chunk-QJ6SO7CF.js +465 -0
- package/dist/chunk-QQUOVIOM.js +2899 -0
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- package/dist/chunk-SNCZRDS5.js +557 -0
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- package/dist/chunk-SPDNUC76.js +70 -0
- package/dist/chunk-T3663ZQL.js +37 -0
- package/dist/chunk-TSK4ZTFK.js +340 -0
- package/dist/chunk-USW6WRDZ.js +217 -0
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- package/dist/chunk-XE6E526E.js +129 -0
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- package/dist/chunk-YCECQV3T.js +160 -0
- package/dist/chunk-YROOKO3Q.js +1954 -0
- package/dist/chunk-YROOKO3Q.js.map +7 -0
- package/dist/chunk-Z4NADGZX.js +243 -0
- package/dist/chunk-Z53KOPRJ.js +102 -0
- package/dist/cohort-U7M6Q2UX.js +69 -0
- package/dist/condition-EGAV2PMJ.js +326 -0
- package/dist/controls-PTMYWUZV.js +33 -0
- package/dist/controls.config-DOA6PTP2.js +33 -0
- package/dist/correlation-Y3EL6GB7.js +94 -0
- package/dist/customdata.inputui-4NDDG6FL.js +283 -0
- package/dist/dataDownload-EQGUAOK2.js +328 -0
- package/dist/databrowser.ui-ABGOJUWQ.js +424 -0
- package/dist/dictionary-YOLLEDE5.js +112 -0
- package/dist/dnaMethylation-JZT63UHO.js +32 -0
- package/dist/dnaMethylation.integration.spec-EATCABJW.js +197 -0
- package/dist/dofetch-YNBIUFV5.js +48 -0
- package/dist/e2pca-RD6COCRL.js +343 -0
- package/dist/ep-BAI7WUET.js +1248 -0
- package/dist/expclust.gdc.spec-LKV2CQA5.js +301 -0
- package/dist/facet-X3SXQIAC.js +518 -0
- package/dist/gb-K324K7XB.js +80 -0
- package/dist/geneExpClustering-BJD5U3KG.js +243 -0
- package/dist/geneExpression-2TK3XLZ5.js +310 -0
- package/dist/geneExpression-F6NRTHZ4.js +32 -0
- package/dist/geneExpression.unit.spec-IFZN3J6A.js +96 -0
- package/dist/geneORA-DUEP735U.js +272 -0
- package/dist/geneRanking-LURDNT7L.js +547 -0
- package/dist/geneVariant-EAVCWQAZ.js +35 -0
- package/dist/geneVariant-IZTFYAG6.js +284 -0
- package/dist/geneVariant-IZTFYAG6.js.map +7 -0
- package/dist/geneVariant.integration.spec-LHL4ERFO.js +192 -0
- package/dist/genefusion.ui-4T5R7DT7.js +302 -0
- package/dist/geneset-3PWXPBG2.js +202 -0
- package/dist/genomeBrowser.spec-5SEN7R2P.js +275 -0
- package/dist/grin2-EXBG7TMS.js +1136 -0
- package/dist/grin2-XIXVFVWO.js +69 -0
- package/dist/hierCluster-5XQIWXAY.js +57 -0
- package/dist/hierCluster-I4TAQWPF.js +53 -0
- package/dist/hierCluster.config-T7HVAWES.js +34 -0
- package/dist/hierCluster.integration.spec-XWX43K4D.js +482 -0
- package/dist/hierCluster.interactivity-MYIDHFSL.js +48 -0
- package/dist/hierCluster.renderers-YRXA5ZUK.js +19 -0
- package/dist/imagePlot-4JQB6JUG.js +155 -0
- package/dist/importPlot-D3MXCCLN.js +8 -0
- package/dist/isoformExpression-WNGGUVIZ.js +34 -0
- package/dist/isoformExpression.unit.spec-NVJ5TIKM.js +236 -0
- package/dist/junction-O7N57JE3.js +35 -0
- package/dist/junction.unit.spec-Z63DRTRR.js +181 -0
- package/dist/launch.adhoc-MBDRXD3B.js +36 -0
- package/dist/leftlabel.sample-IG6FOQ26.js +257 -0
- package/dist/lollipop-ZUYBLPGN.js +165 -0
- package/dist/maf-QOS5LURG.js +454 -0
- package/dist/maftimeline-FEHP2J55.js +586 -0
- package/dist/matrix-BG4J4RXA.js +57 -0
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- package/dist/matrix.cells-PTIDQVCI.js +26 -0
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- package/dist/matrix.data-FMIQRXOA.js +23 -0
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- package/dist/multivalue-OZALSBFW.js +82 -0
- package/dist/numericDictTermCluster-7PGJ7KV4.js +63 -0
- package/dist/oncomatrix-Q2EQZPLS.js +289 -0
- package/dist/oncomatrix.spec-YEQOQRPW.js +442 -0
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- package/dist/plot.app-AEUR6XGI.js +35 -0
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- package/dist/plot.disco-LUFC5GGC.js +99 -0
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- package/dist/polar2-AB6SVYRS.js +231 -0
- package/dist/profileForms-AIEHZ4GC.js +933 -0
- package/dist/profilePlot-PZDFGXKZ.js +48 -0
- package/dist/proteinView-7GWHQYXC.js +1561 -0
- package/dist/proteomeCohortCompare-BTN4HHFL.js +779 -0
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- package/dist/singleCellCellType-EZYESBVZ.js +32 -0
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- /package/dist/{summary.integration.spec-52WP6SNY.js.map → summary.integration.spec-JJDE6SRV.js.map} +0 -0
- /package/dist/{summaryInput-WUJNHCGH.js.map → summaryInput-JG4AW6FW.js.map} +0 -0
- /package/dist/{sunburst-IJ3ZG2BC.js.map → sunburst-YKB42RZX.js.map} +0 -0
- /package/dist/{survival-SQRYWGWZ.js.map → survival-3IFFTDQA.js.map} +0 -0
- /package/dist/{survival-F2B5JKOO.js.map → survival-HOFNJENX.js.map} +0 -0
- /package/dist/{svgraph-HVCMF6KI.js.map → svgraph-WFEY4ZIZ.js.map} +0 -0
- /package/dist/{svmr-PROHTMTP.js.map → svmr-44EIX7YD.js.map} +0 -0
- /package/dist/{table-3E64OJNV.js.map → table-6MKVJUNC.js.map} +0 -0
- /package/dist/{termCollection-WKT6ESMI.js.map → termCollection-6JBVQL6Y.js.map} +0 -0
- /package/dist/{summary-U3YKEMZC.js.map → termCollection-TTELZVC5.js.map} +0 -0
- /package/dist/{termCollection.unit.spec-XMOCMVER.js.map → termCollection.unit.spec-6Z7X646L.js.map} +0 -0
- /package/dist/{termCollection-MUH7P6B5.js.map → termCollectionFractionSelection-5DVIJBM5.js.map} +0 -0
- /package/dist/{termCollectionFractionSelection.unit.spec-MG7E3EIZ.js.map → termCollectionFractionSelection.unit.spec-3HIM5BIF.js.map} +0 -0
- /package/dist/{termCollectionFractionSelection-P5G6WIJJ.js.map → tk-HSYWJCGQ.js.map} +0 -0
- /package/dist/{tk-HWUPUGOS.js.map → tk-PNOVG2XS.js.map} +0 -0
- /package/dist/{tp.ui-RRB5MJRD.js.map → tp.ui-COBBSUPB.js.map} +0 -0
- /package/dist/{tk-SBM2GN3S.js.map → tvs.dt-35AKURFI.js.map} +0 -0
- /package/dist/{tvs.dtcnv.categorical-7RJPQKMX.js.map → tvs.dtcnv.categorical-3EHXYROL.js.map} +0 -0
- /package/dist/{tvs.dtcnv.continuous-FW4ZXIYY.js.map → tvs.dtcnv.continuous-AXQ2GU6S.js.map} +0 -0
- /package/dist/{tvs.dtfusion-3GDWW3ML.js.map → tvs.dtfusion-PLJIMPNX.js.map} +0 -0
- /package/dist/{tvs.dtitd-FER4H4UO.js.map → tvs.dtitd-JS6RFBV5.js.map} +0 -0
- /package/dist/{tvs.dtsnvindel-ISEOJ5UA.js.map → tvs.dtsnvindel-MDEM5MPT.js.map} +0 -0
- /package/dist/{tvs.dtsv-JDML7EWE.js.map → tvs.dtsv-OU756YLO.js.map} +0 -0
- /package/dist/{tvs.samplelst-MJTM6GSV.js.map → tvs.samplelst-5NDICES4.js.map} +0 -0
- /package/dist/{tvs.termCollection-GMOXBJWF.js.map → tvs.termCollection-5URPDPH6.js.map} +0 -0
- /package/dist/{tvs.dt-I2ECKHQ2.js.map → vocabulary-CHCVMPK5.js.map} +0 -0
- /package/dist/{wsi.direct-IVPACPNT.js.map → wsi.direct-JSKV4H4X.js.map} +0 -0
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to_svg
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// src/mds.survivalplot.js
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async function init(obj, holder, debugmode) {
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if (debugmode) {
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window.obj = obj;
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obj.plots = [];
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obj.menu = new Menu({ padding: "5px" });
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obj.tip = new Menu({ padding: "5px" });
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sayerror(obj.errordiv, typeof e == "string" ? e : e.message);
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obj.plotdiv = holder.append("div").style("margin", "20px");
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obj.legendtable = holder.append("table").style("border-spacing", "5px");
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holder.append("button").text("SVG").on("click", () => {
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to_svg(obj.plotlist[0].svg.node(), "Survival");
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});
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try {
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await init_dataset_config(obj);
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if (!obj.plotlist) {
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obj.plotlist = [];
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if (!Array.isArray(obj.plotlist)) throw ".plotlist should be array";
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const p = {
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obj.plotlist.push(p);
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obj.sayerror("Cannot make plot: " + (e.message || e));
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function init_dataset_config(obj) {
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const par = {
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genome: obj.genome.name,
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init: 1
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};
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return dofetch("mdssurvivalplot", par).then((data) => {
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obj.plottypes = data.plottypes;
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obj.samplegroupings = data.samplegroupings;
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}
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function init_a_plot(p, obj) {
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const div = obj.uidiv.append("div").style("margin", "20px");
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const s = div.append("div").style("margin-bottom", "10px").append("select").on("change", (event) => {
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p.type = event.target.options[event.target.selectedIndex].value;
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const custom_input_row = div.append("div").style("display", "none");
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row.append("span").html("Choose samples from ").style("opacity", 0.5);
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const s = row.append("select").style("margin-right", "5px").on("change", (event) => {
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}
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const o = event.target.options[event.target.selectedIndex];
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}
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p.samplerule.full.usesampleset = 1;
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show_sampleinput(p, custom_input_row);
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}
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delete p.samplerule.full.useall;
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p.samplerule.full.byattr = 1;
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p.samplerule.key = o.key;
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s3.style("display", "inline");
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p.samplerule.full.value = s3.node().options[s3.node().selectedIndex].value;
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});
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for (const [i, attr] of obj.samplegroupings.entries()) {
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s.append("option").text(attr.label).property("key", attr.key);
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const usingthisattr = p.samplerule.full.byattr && p.samplerule.full.key == attr.key;
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if (usingthisattr) {
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s.node().selectedIndex = i;
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}
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const s2 = row.append("select").on("change", (event) => {
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p.samplerule.full.value = event.target.options[event.target.selectedIndex].value;
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});
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attr2select[attr.key] = s2;
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s2.style("display", usingthisattr ? "inline" : "none");
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for (const [j, v] of attr.values.entries()) {
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s2.append("option").text(v.value + " (n=" + v.count + ")").property("value", v.value);
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if (usingthisattr && v.value == p.samplerule.full.value) {
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s2.node().selectedIndex = j;
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}
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}
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}
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s.append("option").text("all samples").property("useall", 1);
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if (p.samplerule.full.useall) {
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s.node().selectedIndex = obj.samplegroupings.length;
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}
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s.append("option").text("custom sampleset").property("usesampleset", 1);
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}
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show_dividerules(p, div);
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p.button = div.append("button").text("Make plot").on("click", () => {
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loadPlot(p, obj);
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});
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p.d = obj.plotdiv.append("div").style("margin", "20px"), p.legend = {
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d_pvalue: p.d.append("div").style("margin", "10px"),
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d_samplefull: p.d.append("div").style("margin", "10px"),
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d_curves: p.d.append("div").style("margin", "10px")
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};
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p.svg = p.d.append("svg");
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p.resize_handle = p.d.append("div").append("div").attr("class", "sja_clbtext").text("drag to resize").style("float", "right");
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if (p.renderplot) {
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loadPlot(p, obj);
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}
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}
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function init_a_plot_filldefault(p, obj) {
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if (!p.type) {
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p.type = obj.plottypes[0].key;
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}
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if (!p.samplerule) {
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p.samplerule = {};
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}
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if (!p.samplerule.full) {
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p.samplerule.full = {};
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}
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if (obj.samplegroupings) {
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if (!p.samplerule.full.useall) {
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p.samplerule.full.byattr = 1;
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if (!p.samplerule.full.key) {
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p.samplerule.full.key = obj.samplegroupings[0].key;
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p.samplerule.full.value = obj.samplegroupings[0].values[0].value;
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}
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}
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} else {
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p.samplerule.full.useall = 1;
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}
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if (p.samplerule.set) {
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const st = p.samplerule.set;
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if (st.geneexpression) {
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if (!st.bymedian && !st.byquartile) {
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st.bymedian = 1;
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}
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}
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}
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if (!p.width) p.width = 500;
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if (!p.height) p.height = 500;
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if (!p.toppad) p.toppad = 10;
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if (!p.rightpad) p.rightpad = 10;
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if (!p.xaxispad) p.xaxispad = 10;
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if (!p.yaxispad) p.yaxispad = 10;
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if (!p.xaxish) p.xaxish = 40;
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if (!p.yaxisw) p.yaxisw = 65;
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if (!p.censorticksize) p.censorticksize = 6;
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if (!p.tickfontsize) p.tickfontsize = 14;
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if (!p.labfontsize) p.labfontsize = 15;
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}
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function doPlot(plot, obj) {
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const colorfunc = ordinal(category10_default);
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const minx = 0;
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let maxx = 0;
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for (const curve of plot.samplesets) {
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curve.color = colorfunc(curve.name);
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for (const s of curve.steps) {
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maxx = Math.max(maxx, s.x);
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}
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}
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plot.svg.selectAll("*").remove();
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const curves_g = plot.svg.append("g");
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for (const curve of plot.samplesets) {
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curve.path = curves_g.append("path").attr("stroke", curve.color).attr("fill", "none");
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curve.ticks = curves_g.append("path").attr("stroke", curve.color).attr("fill", "none");
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}
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const yaxis_g = plot.svg.append("g");
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const yaxis_scale = linear().domain([0, 1]);
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const yaxis_lab_g = plot.svg.append("g");
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const yaxis_lab = yaxis_lab_g.append("text").text("Survival").attr("transform", "rotate(-90)");
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const xaxis_g = plot.svg.append("g");
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const xaxis_scale = linear().domain([minx, maxx]);
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const xaxis_lab = plot.svg.append("text").attr("font-size", plot.labfontsize).text(obj.plottypes.find((i) => i.key == plot.type).timelabel).attr("x", plot.yaxisw + plot.yaxispad + plot.width / 2).attr("y", plot.toppad + plot.height + plot.xaxispad + plot.xaxish - 3);
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function resize() {
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curves_g.attr("transform", "translate(" + (plot.yaxisw + plot.yaxispad) + "," + plot.toppad + ")");
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247
|
-
for (const curve of plot.samplesets) {
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248
|
-
const ticks = [];
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249
|
-
const pathd = ["M 0 0"];
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|
250
|
-
for (const s of curve.steps) {
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251
|
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pathd.push("H " + plot.width * s.x / maxx);
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252
|
-
const y = plot.height * (s.y + s.drop);
|
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253
|
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pathd.push("V " + y);
|
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254
|
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if (s.censored) {
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255
|
-
const y2 = plot.height * s.y;
|
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256
|
-
for (const c of s.censored) {
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257
|
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const x = plot.width * c / maxx;
|
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258
|
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ticks.push(
|
|
259
|
-
"M " + (x - plot.censorticksize / 2) + " " + (y2 - plot.censorticksize / 2) + " l " + plot.censorticksize + " " + plot.censorticksize + " M " + (x + plot.censorticksize / 2) + " " + (y2 - plot.censorticksize / 2) + " l -" + plot.censorticksize + " " + plot.censorticksize
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260
|
-
);
|
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261
|
-
}
|
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262
|
-
}
|
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263
|
-
}
|
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264
|
-
curve.path.attr("d", pathd.join(" "));
|
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265
|
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if (ticks.length) {
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266
|
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curve.ticks.attr("d", ticks.join(" "));
|
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267
|
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}
|
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268
|
-
}
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269
|
-
yaxis_g.attr("transform", "translate(" + plot.yaxisw + "," + plot.toppad + ")");
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270
|
-
axisstyle({
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271
|
-
axis: yaxis_g.call(
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272
|
-
axisLeft().scale(yaxis_scale.range([plot.height, 0])).ticks(Math.floor(plot.height / (plot.tickfontsize + 20)))
|
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273
|
-
),
|
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274
|
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showline: 1,
|
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275
|
-
fontsize: plot.tickfontsize
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276
|
-
});
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277
|
-
yaxis_lab_g.attr("transform", "translate(" + plot.labfontsize + "," + (plot.toppad + plot.height / 2) + ")");
|
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278
|
-
yaxis_lab.attr("font-size", plot.labfontsize);
|
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279
|
-
xaxis_g.attr(
|
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280
|
-
"transform",
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281
|
-
"translate(" + (plot.yaxisw + plot.yaxispad) + "," + (plot.toppad + plot.height + plot.xaxispad) + ")"
|
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282
|
-
);
|
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283
|
-
let xticknumber;
|
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284
|
-
xaxis_g.append("text").text(maxx).attr("font-size", plot.tickfontsize).each(function() {
|
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285
|
-
xticknumber = Math.floor(plot.width / (this.getBBox().width + 30));
|
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286
|
-
}).remove();
|
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287
|
-
axisstyle({
|
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288
|
-
axis: xaxis_g.call(
|
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289
|
-
axisBottom().scale(xaxis_scale.range([0, plot.width])).ticks(xticknumber)
|
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290
|
-
),
|
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291
|
-
showline: 1,
|
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292
|
-
fontsize: plot.tickfontsize
|
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293
|
-
});
|
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294
|
-
xaxis_lab.attr("font-size", plot.labfontsize).attr("x", plot.yaxisw + plot.yaxispad + plot.width / 2).attr("y", plot.toppad + plot.height + plot.xaxispad + plot.xaxish - 3);
|
|
295
|
-
plot.svg.attr("width", plot.yaxisw + plot.yaxispad + plot.width + plot.rightpad).attr("height", plot.toppad + plot.height + plot.xaxispad + plot.xaxish);
|
|
296
|
-
}
|
|
297
|
-
resize();
|
|
298
|
-
plot.resize_handle.on("mousedown", (event) => {
|
|
299
|
-
event.preventDefault();
|
|
300
|
-
const b = select_default(document.body);
|
|
301
|
-
const x = event.clientX;
|
|
302
|
-
const y = event.clientY;
|
|
303
|
-
const w0 = plot.width;
|
|
304
|
-
const h0 = plot.height;
|
|
305
|
-
b.on("mousemove", () => {
|
|
306
|
-
plot.width = w0 + event.clientX - x;
|
|
307
|
-
plot.height = h0 + event.clientY - y;
|
|
308
|
-
resize();
|
|
309
|
-
});
|
|
310
|
-
b.on("mouseup", () => {
|
|
311
|
-
b.on("mousemove", null).on("mouseup", null);
|
|
312
|
-
});
|
|
313
|
-
});
|
|
314
|
-
if (Number.isFinite(plot.pvalue)) {
|
|
315
|
-
plot.legend.d_pvalue.style("display", "block").text("P-value: " + plot.pvalue);
|
|
316
|
-
} else {
|
|
317
|
-
plot.legend.d_pvalue.style("display", "none");
|
|
318
|
-
}
|
|
319
|
-
plot.legend.d_curves.selectAll("*").remove();
|
|
320
|
-
for (const c of plot.samplesets) {
|
|
321
|
-
plot.legend.d_curves.append("div").style("margin", "3px").html(
|
|
322
|
-
'<span style="background:' + c.color + '"> </span> ' + c.name + (c.pvalue == void 0 ? "" : ", P-value: " + c.pvalue)
|
|
323
|
-
);
|
|
324
|
-
}
|
|
325
|
-
}
|
|
326
|
-
function loadPlot(plot, obj) {
|
|
327
|
-
plot.button.text("Loading...").attr("disabled", 1);
|
|
328
|
-
const par = {
|
|
329
|
-
genome: obj.genome.name,
|
|
330
|
-
dslabel: obj.mds.label,
|
|
331
|
-
type: plot.type,
|
|
332
|
-
samplerule: plot.samplerule
|
|
333
|
-
};
|
|
334
|
-
dofetch("mdssurvivalplot", par).then((data) => {
|
|
335
|
-
if (data.error) throw data.error;
|
|
336
|
-
if (!data.samplesets) throw "samplesets[] missing";
|
|
337
|
-
plot.samplesets = data.samplesets;
|
|
338
|
-
plot.pvalue = data.pvalue;
|
|
339
|
-
doPlot(plot, obj);
|
|
340
|
-
if (plot.samplerule.set && plot.samplerule.set.mutation) {
|
|
341
|
-
if (plot.mutation_count.cnv) plot.mutation_count.cnv.html("(n=" + data.count_cnv + ") ");
|
|
342
|
-
if (plot.mutation_count.loh) plot.mutation_count.loh.html("(n=" + data.count_loh + ") ");
|
|
343
|
-
if (plot.mutation_count.snvindel) plot.mutation_count.snvindel.html("(n=" + data.count_snvindel + ") ");
|
|
344
|
-
if (plot.mutation_count.sv) plot.mutation_count.sv.html("(n=" + data.count_sv + ") ");
|
|
345
|
-
if (plot.mutation_count.fusion) plot.mutation_count.fusion.html("(n=" + data.count_fusion + ") ");
|
|
346
|
-
if (plot.mutation_count.itd) plot.mutation_count.itd.html("(n=" + data.count_itd + ") ");
|
|
347
|
-
}
|
|
348
|
-
}).catch((e) => {
|
|
349
|
-
obj.sayerror(e);
|
|
350
|
-
}).then(() => {
|
|
351
|
-
plot.button.text("Update plot").attr("disabled", null);
|
|
352
|
-
});
|
|
353
|
-
}
|
|
354
|
-
function show_dividerules(p, div) {
|
|
355
|
-
if (!p.samplerule.set) return;
|
|
356
|
-
const st = p.samplerule.set;
|
|
357
|
-
if (st.geneexpression) {
|
|
358
|
-
if (!st.bymedian && !st.byquartile) {
|
|
359
|
-
st.bymedian = 1;
|
|
360
|
-
}
|
|
361
|
-
const row = div.append("div").style("margin-bottom", "10px");
|
|
362
|
-
row.append("span").style("opacity", 0.5).html("Divide samples by " + st.gene + " expression with ");
|
|
363
|
-
const s = row.append("select").on("change", (event) => {
|
|
364
|
-
const o = event.target.options[event.target.selectedIndex];
|
|
365
|
-
if (o.median) {
|
|
366
|
-
p.samplerule.set.bymedian = 1;
|
|
367
|
-
delete p.samplerule.set.byquartile;
|
|
368
|
-
span_quartilecompare.style("display", "none");
|
|
369
|
-
} else if (o.quartile) {
|
|
370
|
-
p.samplerule.set.byquartile = 1;
|
|
371
|
-
delete p.samplerule.set.bymedian;
|
|
372
|
-
span_quartilecompare.style("display", "inline");
|
|
373
|
-
}
|
|
374
|
-
});
|
|
375
|
-
s.append("option").text("median (group=2)").property("median", 1);
|
|
376
|
-
s.append("option").text("quartile (group=4)").property("quartile", 1);
|
|
377
|
-
const span_quartilecompare = row.append("span").style("margin-left", "10px");
|
|
378
|
-
span_quartilecompare.append("span").html("Compare each quartile against ").style("opacity", 0.5);
|
|
379
|
-
{
|
|
380
|
-
const s2 = span_quartilecompare.append("select").on("change", (event) => {
|
|
381
|
-
delete p.samplerule.set.against1st;
|
|
382
|
-
delete p.samplerule.set.against4th;
|
|
383
|
-
switch (event.target.selectedIndex) {
|
|
384
|
-
case 0:
|
|
385
|
-
break;
|
|
386
|
-
case 1:
|
|
387
|
-
p.samplerule.set.against1st = 1;
|
|
388
|
-
break;
|
|
389
|
-
case 2:
|
|
390
|
-
p.samplerule.set.against4th = 1;
|
|
391
|
-
break;
|
|
392
|
-
}
|
|
393
|
-
});
|
|
394
|
-
s2.append("option").text("none");
|
|
395
|
-
s2.append("option").text("first quartile");
|
|
396
|
-
s2.append("option").text("fourth quartile");
|
|
397
|
-
if (st.against1st) {
|
|
398
|
-
s2.node().selectedIndex = 1;
|
|
399
|
-
} else if (s2.against4th) {
|
|
400
|
-
s2.node().selectedIndex = 2;
|
|
401
|
-
}
|
|
402
|
-
}
|
|
403
|
-
if (st.bymedian) {
|
|
404
|
-
s.node().selectedIndex = 0;
|
|
405
|
-
span_quartilecompare.style("display", "none");
|
|
406
|
-
} else if (st.byquartile) {
|
|
407
|
-
s.node().selectedIndex = 1;
|
|
408
|
-
span_quartilecompare.style("display", "inline");
|
|
409
|
-
}
|
|
410
|
-
}
|
|
411
|
-
if (st.mutation) {
|
|
412
|
-
p.mutation_count = {};
|
|
413
|
-
if (st.snvindel) {
|
|
414
|
-
const row = div.append("div").style("margin-bottom", "20px");
|
|
415
|
-
p.mutation_count.snvindel = row.append("span");
|
|
416
|
-
if (st.snvindel.name) {
|
|
417
|
-
row.append("span").html("SNV/indel ");
|
|
418
|
-
const s = row.append("select");
|
|
419
|
-
s.append("option").text(st.snvindel.name).property("named", 1);
|
|
420
|
-
s.append("option").text("any mutation at " + st.chr + ":" + st.start);
|
|
421
|
-
} else {
|
|
422
|
-
row.append("span").text("SNV/indel at " + st.chr + ":" + (st.start == st.stop ? st.start : st.start + "-" + st.stop));
|
|
423
|
-
}
|
|
424
|
-
}
|
|
425
|
-
if (st.cnv) {
|
|
426
|
-
const row = div.append("div").style("margin-bottom", "20px");
|
|
427
|
-
p.mutation_count.cnv = row.append("span");
|
|
428
|
-
row.append("span").html(
|
|
429
|
-
"Copy number variation over " + st.chr + ":" + st.start + "-" + st.stop + ' <span style="font-size:.7em">' + bplen(st.stop - st.start) + "</span> "
|
|
430
|
-
);
|
|
431
|
-
}
|
|
432
|
-
if (st.loh) {
|
|
433
|
-
const row = div.append("div").style("margin-bottom", "20px");
|
|
434
|
-
p.mutation_count.loh = row.append("span");
|
|
435
|
-
row.append("span").html(
|
|
436
|
-
"LOH over " + st.chr + ":" + st.start + "-" + st.stop + ' <span style="font-size:.7em">' + bplen(st.stop - st.start) + "</span> "
|
|
437
|
-
);
|
|
438
|
-
}
|
|
439
|
-
if (st.sv) {
|
|
440
|
-
const row = div.append("div").style("margin-bottom", "20px");
|
|
441
|
-
p.mutation_count.sv = row.append("span");
|
|
442
|
-
row.append("span").html("SV at " + st.chr + ":" + (st.start == st.stop ? st.start : st.start + "-" + st.stop) + " ");
|
|
443
|
-
}
|
|
444
|
-
if (st.fusion) {
|
|
445
|
-
const row = div.append("div").style("margin-bottom", "20px");
|
|
446
|
-
p.mutation_count.fusion = row.append("span");
|
|
447
|
-
row.append("span").html("Fusion at " + st.chr + ":" + (st.start == st.stop ? st.start : st.start + "-" + st.stop) + " ");
|
|
448
|
-
}
|
|
449
|
-
if (st.itd) {
|
|
450
|
-
const row = div.append("div").style("margin-bottom", "20px");
|
|
451
|
-
p.mutation_count.itd = row.append("span");
|
|
452
|
-
row.append("span").html(
|
|
453
|
-
"ITD over " + st.chr + ":" + st.start + "-" + st.stop + ' <span style="font-size:.7em">' + bplen(st.stop - st.start) + "</span> "
|
|
454
|
-
);
|
|
455
|
-
}
|
|
456
|
-
}
|
|
457
|
-
}
|
|
458
|
-
function show_sampleinput(p, div) {
|
|
459
|
-
let rendered_flag = div.selectAll("div").size();
|
|
460
|
-
if (rendered_flag) return;
|
|
461
|
-
const row = div.append("div").style("margin-bottom", "10px");
|
|
462
|
-
const samplelist_div = row.append("div").style("margin-left", "20px");
|
|
463
|
-
samplelist_div.append("div").style("vertical-align", "top").style("display", "inline-block").style("opacity", 0.5).html("Enter sample names<br>(one sample per line) ");
|
|
464
|
-
const sample_input = samplelist_div.append("textarea").style("display", "inline-block").attr("cols", "20").attr("rows", "10").on("change", () => {
|
|
465
|
-
let sampleset = p.samplerule.full.sampleset = [];
|
|
466
|
-
const str = sample_input.property("value").trim();
|
|
467
|
-
if (!str) return;
|
|
468
|
-
for (const sample of str.split("\n")) {
|
|
469
|
-
sampleset.push(sample);
|
|
470
|
-
}
|
|
471
|
-
});
|
|
472
|
-
}
|
|
473
|
-
export {
|
|
474
|
-
init
|
|
475
|
-
};
|
|
476
|
-
//# sourceMappingURL=mds.survivalplot-ETLLFDWR.js.map
|
|
@@ -1,82 +0,0 @@
|
|
|
1
|
-
import {
|
|
2
|
-
getPillNameDefault,
|
|
3
|
-
set_hiddenvalues
|
|
4
|
-
} from "./chunk-GQQ4R6BI.js";
|
|
5
|
-
import "./chunk-HJ6L54YS.js";
|
|
6
|
-
import "./chunk-XFAL46LZ.js";
|
|
7
|
-
import "./chunk-7AYGTMED.js";
|
|
8
|
-
import "./chunk-ELJX3QIQ.js";
|
|
9
|
-
import "./chunk-7BLXK3GI.js";
|
|
10
|
-
import "./chunk-VSSZJHOR.js";
|
|
11
|
-
import "./chunk-5RUVBYLK.js";
|
|
12
|
-
import "./chunk-HENLCRVM.js";
|
|
13
|
-
import "./chunk-4WF3XDQP.js";
|
|
14
|
-
import "./chunk-7UFK4GVI.js";
|
|
15
|
-
import "./chunk-4QBRVM4V.js";
|
|
16
|
-
import "./chunk-H6INPPUC.js";
|
|
17
|
-
import "./chunk-PF4DSFDR.js";
|
|
18
|
-
import "./chunk-IMYSFDE5.js";
|
|
19
|
-
import "./chunk-W5J3LTYS.js";
|
|
20
|
-
import "./chunk-4ZL6IBXM.js";
|
|
21
|
-
import "./chunk-OZVWP4ZR.js";
|
|
22
|
-
import "./chunk-FXQXCOII.js";
|
|
23
|
-
import "./chunk-TLT4YIG3.js";
|
|
24
|
-
import "./chunk-5R63Q5KH.js";
|
|
25
|
-
import "./chunk-I6Y4O3RR.js";
|
|
26
|
-
import "./chunk-Q5RDQNIT.js";
|
|
27
|
-
import "./chunk-DQC5FFGV.js";
|
|
28
|
-
import "./chunk-HFNDKYVF.js";
|
|
29
|
-
|
|
30
|
-
// termsetting/handlers/multivalue.ts
|
|
31
|
-
function getHandler(self) {
|
|
32
|
-
return {
|
|
33
|
-
getPillName(d) {
|
|
34
|
-
return getPillNameDefault(self, d);
|
|
35
|
-
},
|
|
36
|
-
getPillStatus() {
|
|
37
|
-
const hidden = Object.keys(self.q?.hiddenValues || {}).length;
|
|
38
|
-
if (hidden) return { text: `${hidden} hidden` };
|
|
39
|
-
},
|
|
40
|
-
async showEditMenu(div) {
|
|
41
|
-
await makeCategoryMenu(self, div);
|
|
42
|
-
}
|
|
43
|
-
};
|
|
44
|
-
}
|
|
45
|
-
async function makeCategoryMenu(self, div) {
|
|
46
|
-
const data = await self.vocabApi.getCategories(self.term, self.filter);
|
|
47
|
-
const lst = (data.lst || []).sort((a, b) => b.samplecount - a.samplecount);
|
|
48
|
-
const holder = div.append("div").style("padding", "10px");
|
|
49
|
-
if (!lst.length) {
|
|
50
|
-
holder.append("div").style("opacity", 0.6).text("No categories");
|
|
51
|
-
return;
|
|
52
|
-
}
|
|
53
|
-
holder.append("div").style("opacity", 0.6).style("font-size", ".8em").style("padding-bottom", "5px").text("CHECK TO SHOW CATEGORY");
|
|
54
|
-
const checkboxes = /* @__PURE__ */ new Map();
|
|
55
|
-
for (const c of lst) {
|
|
56
|
-
const row = holder.append("div");
|
|
57
|
-
const label = row.append("label");
|
|
58
|
-
const checkbox = label.append("input").attr("type", "checkbox").property("checked", !self.q.hiddenValues?.[c.key]);
|
|
59
|
-
checkboxes.set(c.key, checkbox);
|
|
60
|
-
label.append("span").text(` ${c.label || c.key} `);
|
|
61
|
-
label.append("span").style("opacity", 0.6).style("font-size", ".8em").text(`n=${c.samplecount}`);
|
|
62
|
-
}
|
|
63
|
-
holder.append("button").style("margin-top", "10px").text("Apply").on("click", () => {
|
|
64
|
-
const hiddenValues = {};
|
|
65
|
-
for (const [key, checkbox] of checkboxes) {
|
|
66
|
-
if (!checkbox.property("checked")) hiddenValues[key] = 1;
|
|
67
|
-
}
|
|
68
|
-
self.q.hiddenValues = hiddenValues;
|
|
69
|
-
self.dom.tip.hide();
|
|
70
|
-
self.api.runCallback();
|
|
71
|
-
});
|
|
72
|
-
}
|
|
73
|
-
function fillTW(tw, _vocabApi) {
|
|
74
|
-
const q = tw.q;
|
|
75
|
-
if (!q.type) q.type = "values";
|
|
76
|
-
set_hiddenvalues(q, tw.term);
|
|
77
|
-
}
|
|
78
|
-
export {
|
|
79
|
-
fillTW,
|
|
80
|
-
getHandler
|
|
81
|
-
};
|
|
82
|
-
//# sourceMappingURL=multivalue-AZPAQJQD.js.map
|
|
@@ -1,63 +0,0 @@
|
|
|
1
|
-
import {
|
|
2
|
-
NumericModes
|
|
3
|
-
} from "./chunk-7UFK4GVI.js";
|
|
4
|
-
import "./chunk-4QBRVM4V.js";
|
|
5
|
-
import "./chunk-4ZL6IBXM.js";
|
|
6
|
-
import "./chunk-OZVWP4ZR.js";
|
|
7
|
-
import "./chunk-5R63Q5KH.js";
|
|
8
|
-
import "./chunk-I6Y4O3RR.js";
|
|
9
|
-
import "./chunk-Q5RDQNIT.js";
|
|
10
|
-
import "./chunk-HFNDKYVF.js";
|
|
11
|
-
|
|
12
|
-
// plots/numericDictTermCluster.ts
|
|
13
|
-
function makeChartBtnMenu(holder, chartsInstance) {
|
|
14
|
-
chartsInstance.dom.tip.clear();
|
|
15
|
-
const menuDiv = holder.append("div");
|
|
16
|
-
const numericDictTermCluster = chartsInstance.state.termdbConfig.numericDictTermCluster;
|
|
17
|
-
if (numericDictTermCluster?.plots) {
|
|
18
|
-
for (const plot of numericDictTermCluster.plots) {
|
|
19
|
-
menuDiv.append("button").style("margin", "10px").style("padding", "10px 15px").style("border-radius", "20px").style("border-color", "#ededed").style("display", "inline-block").text(plot.name).on("click", async () => {
|
|
20
|
-
chartsInstance.dom.tip.hide();
|
|
21
|
-
const config = await chartsInstance.app.vocabApi.getNumericDictTermClusterByName(plot.name);
|
|
22
|
-
config.preBuiltPlotTitle = plot.name;
|
|
23
|
-
chartsInstance.app.dispatch({
|
|
24
|
-
type: "plot_create",
|
|
25
|
-
config
|
|
26
|
-
});
|
|
27
|
-
});
|
|
28
|
-
}
|
|
29
|
-
}
|
|
30
|
-
const chart = {
|
|
31
|
-
//use the app name defined in dataset file
|
|
32
|
-
label: numericDictTermCluster?.appName || "Numeric Dictionary Term cluster",
|
|
33
|
-
chartType: "numericDictTermCluster",
|
|
34
|
-
clickTo: chartsInstance.showTree_selectlst,
|
|
35
|
-
minTermsToSubmit: 3,
|
|
36
|
-
usecase: {
|
|
37
|
-
target: "numericDictTermCluster",
|
|
38
|
-
detail: { exclude: numericDictTermCluster?.exclude }
|
|
39
|
-
},
|
|
40
|
-
updateActionBySelectedTerms: (action, termlst) => {
|
|
41
|
-
if (!termlst?.length) throw "cannot launch clustering: no terms selected";
|
|
42
|
-
const twlst = termlst.map((term) => ({
|
|
43
|
-
term: structuredClone(term),
|
|
44
|
-
q: { mode: NumericModes.continuous }
|
|
45
|
-
}));
|
|
46
|
-
action.config.chartType = "hierCluster";
|
|
47
|
-
action.config.dataType = twlst[0].term.type || "float";
|
|
48
|
-
if (numericDictTermCluster?.appName) action.config.appName = numericDictTermCluster.appName;
|
|
49
|
-
action.config.termgroups = [
|
|
50
|
-
{
|
|
51
|
-
name: numericDictTermCluster?.settings?.termGroupName || "Numeric Dictionary Term Cluster",
|
|
52
|
-
lst: twlst,
|
|
53
|
-
type: "hierCluster"
|
|
54
|
-
}
|
|
55
|
-
];
|
|
56
|
-
}
|
|
57
|
-
};
|
|
58
|
-
chartsInstance.showTree_selectlst(chart);
|
|
59
|
-
}
|
|
60
|
-
export {
|
|
61
|
-
makeChartBtnMenu
|
|
62
|
-
};
|
|
63
|
-
//# sourceMappingURL=numericDictTermCluster-KOJODGZT.js.map
|