@sjcrh/proteinpaint-client 2.166.0 → 2.167.0
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-VLW5XJ4O.js +1364 -0
- package/dist/AIProjectAdmin-X3TBCRPR.js +780 -0
- package/dist/AppHeader-YA7FCKVM.js +813 -0
- package/dist/BoxPlot-PAZYARCX.js +44 -0
- package/dist/CorrelationVolcano-S35GWKV5.js +616 -0
- package/dist/DifferentialAnalysis-DTDFAUXT.js +237 -0
- package/dist/Disco-OE6YY3MH.js +3089 -0
- package/dist/Disco.UI-2CCWETSM.js +238 -0
- package/dist/DziViewer-OHPZOH72.js +16328 -0
- package/dist/GB-LIHKHJ32.js +1099 -0
- package/dist/HicApp-6AYCPCW6.js +2218 -0
- package/dist/NumBinaryEditor-ONJB4DKM.js +259 -0
- package/dist/NumBinaryEditor.unit.spec-Y6DGBAIB.js +277 -0
- package/dist/NumContEditor-6WGAI3PH.js +98 -0
- package/dist/NumContEditor.unit.spec-6LT5MALH.js +160 -0
- package/dist/NumCustomBinEditor-K4OD7SWD.js +29 -0
- package/dist/NumCustomBinEditor.unit.spec-O6QYV6Q4.js +275 -0
- package/dist/NumDiscreteEditor-AFLINO62.js +145 -0
- package/dist/NumDiscreteEditor.unit.spec-3VWWSS24.js +193 -0
- package/dist/NumRegularBinEditor-IRKC5SVF.js +29 -0
- package/dist/NumRegularBinEditor.unit.spec-2ZTI7HR2.js +220 -0
- package/dist/NumSplineEditor-DBW6XE4N.js +181 -0
- package/dist/NumSplineEditor.unit.spec-645ZQXXL.js +190 -0
- package/dist/NumericDensity-27SM2P45.js +29 -0
- package/dist/NumericDensity.unit.spec-DM7PPSMV.js +212 -0
- package/dist/NumericHandler-KFQ2OSUR.js +30 -0
- package/dist/NumericHandler.unit.spec-RNXGCYH7.js +210 -0
- package/dist/SC-SUUATZYR.js +714 -0
- package/dist/Volcano-DEKTKEEZ.js +1018 -0
- package/dist/WSIViewer-SWX4OXHY.js +46959 -0
- package/dist/WsiSamplesPlot-OCVLBBBD.js +153 -0
- package/dist/adSandbox-VGHHJWLL.js +29 -0
- package/dist/alphaGenome-YOJWFJCS.js +170 -0
- package/dist/app-3TXV35H5.js +28 -0
- package/dist/app-NUTP544R.js +54 -0
- package/dist/app.js +16 -16
- package/dist/bam-LXDFDUBH.js +842 -0
- package/dist/barchart-P4BTYT5K.js +48 -0
- package/dist/barchart.data-6WIS5D4I.js +30 -0
- package/dist/barchart.events-V4ANDWUH.js +44 -0
- package/dist/barchart.integration.spec-QU3Y3YHM.js +1600 -0
- package/dist/bars.renderer-4N4QOUNI.js +12 -0
- package/dist/bars.settings-SDU7PZOS.js +10 -0
- package/dist/block-OGJAZG3E.js +6291 -0
- package/dist/block.init-SNZKGO2G.js +29 -0
- package/dist/block.mds.expressionrank-WYV55X5Y.js +350 -0
- package/dist/block.mds.geneboxplot-2LVYSSSU.js +819 -0
- package/dist/block.mds.junction-YY3P64U5.js +1536 -0
- package/dist/block.mds.svcnv-JFNOLZX3.js +6792 -0
- package/dist/block.svg-JBR6OYAD.js +155 -0
- package/dist/block.tk.aicheck-2XDMLOND.js +274 -0
- package/dist/block.tk.ase-TC3NY65S.js +356 -0
- package/dist/block.tk.bam-YA32442V.js +1897 -0
- package/dist/block.tk.bedgraphdot-TRNM4O4F.js +375 -0
- package/dist/block.tk.bigwig.ui-6JJG42M3.js +202 -0
- package/dist/block.tk.hicstraw-HEQXBJZN.js +814 -0
- package/dist/block.tk.junction-7LWL3N6V.js +2355 -0
- package/dist/block.tk.junction.textmatrixui-6CTLQ2M7.js +190 -0
- package/dist/block.tk.ld-SG4ZJ5VB.js +90 -0
- package/dist/block.tk.menu-FNKM5H5D.js +1020 -0
- package/dist/block.tk.pgv-KNLGEASZ.js +935 -0
- package/dist/brainImaging-RO5P7ZR6.js +417 -0
- package/dist/chat-JS4NIRVH.js +142 -0
- package/dist/chat-JS4NIRVH.js.map +7 -0
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- package/dist/chunk-56IFQMJK.js +413 -0
- package/dist/chunk-5GQEXGQC.js +256 -0
- package/dist/chunk-5GQEXGQC.js.map +7 -0
- package/dist/chunk-5HXU7P5T.js +276 -0
- package/dist/chunk-5KUQSXQC.js +293 -0
- package/dist/chunk-6ADTREVX.js +1968 -0
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- package/dist/geneExpClustering-GHGBONBF.js +242 -0
- package/dist/geneExpression-UGYGT6DM.js +54 -0
- package/dist/geneExpression-X6HAUFPK.js +310 -0
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- /package/dist/{summary.integration.spec-GM73ERMN.js.map → summary.integration.spec-WSI3JNTO.js.map} +0 -0
- /package/dist/{summaryInput-FD4SONTY.js.map → summaryInput-3L7CM52X.js.map} +0 -0
- /package/dist/{sunburst-3LCJTBRN.js.map → sunburst-HA7UGSXX.js.map} +0 -0
- /package/dist/{survival-A3A7IVXT.js.map → survival-2HZ446Y3.js.map} +0 -0
- /package/dist/{survival-XF72VMM6.js.map → survival-LJI5JEZZ.js.map} +0 -0
- /package/dist/{survival.integration.spec-AU7MCAQV.js.map → survival.integration.spec-7XVO2WNF.js.map} +0 -0
- /package/dist/{svgraph-BEMS4JDJ.js.map → svgraph-TRPAXTNP.js.map} +0 -0
- /package/dist/{svmr-CDEMTZPK.js.map → svmr-TJOCKTE2.js.map} +0 -0
- /package/dist/{table-WYF6QCGB.js.map → table-35RHJK4M.js.map} +0 -0
- /package/dist/{termCollection-BVQMNVY7.js.map → termCollection-JS6N5TAP.js.map} +0 -0
- /package/dist/{termInfo-JXLIVCSO.js.map → termInfo-5USFZGDB.js.map} +0 -0
- /package/dist/{tk-TGIIJYBO.js.map → tk-4ARNGTEQ.js.map} +0 -0
- /package/dist/{tp.ui-USYF67P7.js.map → tp.ui-QZEMGVEH.js.map} +0 -0
- /package/dist/{tvs.dtcnv.continuous-7SCTSFK3.js.map → tvs.dtcnv.continuous-4K7B7FXF.js.map} +0 -0
- /package/dist/{tvs.numeric-OLVW6US3.js.map → tvs.numeric-FCC2EY62.js.map} +0 -0
- /package/dist/{tvs.samplelst-BHZHCX5V.js.map → tvs.samplelst-IUSDLB6P.js.map} +0 -0
- /package/dist/{violin-OEOWVIZF.js.map → violin-I5JO56GZ.js.map} +0 -0
- /package/dist/{violin.integration.spec-AW2U3RHO.js.map → violin.integration.spec-5WVLT3DW.js.map} +0 -0
- /package/dist/{violin.interactivity-3O2UDNPQ.js.map → violin.interactivity-EFFBMTN2.js.map} +0 -0
- /package/dist/{violin.renderer-W26FA6M7.js.map → violin.renderer-Z3AIV5RH.js.map} +0 -0
- /package/dist/{vocabulary-BIQYDKVY.js.map → vocabulary-4PHACFSG.js.map} +0 -0
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import {
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axisstyle,
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bulk_badline,
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disappear2 as disappear,
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make_table_2col,
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newpane,
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newpane3,
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renderSandboxFormDiv,
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to_svg
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import {
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Menu
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category10_default
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format,
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linear,
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log,
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time,
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timeParse
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} from "./chunk-W2IWHXLL.js";
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import "./chunk-OMR2DT66.js";
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import {
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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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var showcircle = true;
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var maflogscale = true;
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var tip = new Menu();
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function maftimelineui(genomes, holder, sandbox_header) {
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let pane, inputdiv, gselect, filediv, saydiv, visualdiv;
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if (holder !== void 0) [inputdiv, gselect, filediv, saydiv, visualdiv] = renderSandboxFormDiv(holder, genomes);
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;
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[pane, inputdiv, gselect, filediv, saydiv, visualdiv] = newpane3(100, 100, genomes);
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pane.header.text("MAF timeline plot");
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}
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inputdiv.append("p").html(
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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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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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p.append("input").attr("type", "checkbox").attr("id", id).property("checked", true).style("margin-right", "5px").on("change", () => {
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maflogscale = !maflogscale;
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});
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p.append("label").attr("for", id).text("Y axis (MAF) log10 scale");
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}
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const fileui = () => {
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filediv.selectAll("*").remove();
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const butt = filediv.append("input").attr("type", "file").on("change", (event) => {
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saydiv.text("");
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const file = event.target.files[0];
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fileui();
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return;
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}
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if (file.size == 0) {
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saydiv.text("Wrong file: " + file.name);
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fileui();
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return;
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}
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const reader = new FileReader();
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reader.onload = (event2) => {
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const lines = event2.target.result.trim().split(/\r?\n/);
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const [err, header] = parseheader(lines[0].trim());
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saydiv.text("File header error: " + err);
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fileui();
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return;
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}
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const badlines = [];
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const data = {};
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let good = 0;
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for (let i = 1; i < lines.length; i++) {
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const m = parseline(i, lines[i], header, badlines, data);
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if (m) {
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good++;
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}
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}
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if (badlines.length) {
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bulk_badline(header, badlines);
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}
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fileui();
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}
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disappear(pane.pane);
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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 = pane2.body;
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}
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if (holder !== void 0) {
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visual_holder = visualdiv.html('<span style="opacity:.5;font-size:.7em">MAF TIMELINE</span> ' + file.name);
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inputdiv.selectAll("*").remove();
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saydiv.text("");
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}
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render(data, header, visual_holder);
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};
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reader.onerror = function() {
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saydiv.text("Error reading file " + file.name);
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fileui();
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return;
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};
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saydiv.text("Parsing file " + file.name + " ...");
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reader.readAsText(file, "utf8");
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});
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setTimeout(() => butt.node().focus(), 1100);
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};
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fileui();
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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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for (const i2 of lst) {
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const j = header.indexOf(i2);
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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]);
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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) {
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badlines.push([i, "missing total_readcount", lst]);
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return;
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}
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if (m.call_manual && m.call_manual == "wildtype") {
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m.maf = zerovalue;
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}
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v = Number.parseInt(m.coverage);
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if (Number.isNaN(v)) {
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badlines.push([i, "invalid total_readcount", lst]);
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return;
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}
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m.coverage = v;
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let date;
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if (m.date) {
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const f = timeParse("%m/%d/%Y");
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date = f(m.date);
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m.Date = m.date;
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} else {
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badlines.push([i, "missing date", lst]);
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return;
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}
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if (date == null) {
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badlines.push([i, "cannot parse date", lst]);
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return;
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}
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m.date = date;
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if (!m.sample) {
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badlines.push([i, "missing sample", lst]);
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return;
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}
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data[m.patient].snv4[m.snv4].samples.push(m);
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return true;
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}
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function render(data, header, holder) {
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const table = holder.append("table").style("margin", "20px");
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const tr1 = table.append("tr");
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let td = tr1.append("td").style("vertical-align", "top").attr("rowspan", 2);
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td.append("button").text("Toggle circle visibility").on("click", () => {
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showcircle = !showcircle;
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for (const n in data) {
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if (data[n].show) {
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data[n].handle.node().click();
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break;
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}
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}
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});
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const patientholder = td.append("div").style("margin-top", "10px");
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const td1 = tr1.append("td").style("vertical-align", "top");
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const graphholder = td1.append("div").style("display", "inline-block");
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const controlholder = td1.append("div").style("display", "inline-block").style("vertical-align", "top");
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const tr2 = table.append("tr");
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const tiantable = tr2.append("td").append("table").style("border-spacing", "20px").style("border-collapse", "separate");
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const gtr1 = tiantable.append("tr");
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td = gtr1.append("td").style("vertical-align", "top");
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td.append("div").text("Shared").style("font-size", "2em");
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const graph1holder = td.append("div").style("border", "solid 1px black");
|
|
277
|
-
td = gtr1.append("td").style("vertical-align", "top");
|
|
278
|
-
td.append("div").text("Rising").style("font-size", "2em");
|
|
279
|
-
const graph2holder = td.append("div").style("border", "solid 1px black");
|
|
280
|
-
const gtr2 = tiantable.append("tr");
|
|
281
|
-
td = gtr2.append("td").style("vertical-align", "top");
|
|
282
|
-
td.append("div").text("Falling").style("font-size", "2em");
|
|
283
|
-
const graph3holder = td.append("div").style("border", "solid 1px black");
|
|
284
|
-
td = gtr2.append("td").style("vertical-align", "top");
|
|
285
|
-
td.append("div").text("R-only").style("font-size", "2em");
|
|
286
|
-
const graph4holder = td.append("div").style("border", "solid 1px black");
|
|
287
|
-
for (const patient in data) {
|
|
288
|
-
const snvlst = [];
|
|
289
|
-
const colors = ordinal(category10_default);
|
|
290
|
-
for (const x in data[patient].snv4) {
|
|
291
|
-
const snv = data[patient].snv4[x];
|
|
292
|
-
snv.show = true;
|
|
293
|
-
snv.color = colors(snv.mutationname);
|
|
294
|
-
snv.samples.sort((a, b) => a.date - b.date);
|
|
295
|
-
for (const s of snv.samples) {
|
|
296
|
-
s.color = snv.color;
|
|
297
|
-
}
|
|
298
|
-
snvlst.push(snv);
|
|
299
|
-
}
|
|
300
|
-
const div = patientholder.append("div").classed("sja_menuoption", true).style("color", "black").text(patient).on("click", () => {
|
|
301
|
-
for (const pn in data) {
|
|
302
|
-
data[pn].handle.style("color", "black");
|
|
303
|
-
data[pn].show = false;
|
|
304
|
-
}
|
|
305
|
-
data[patient].handle.style("color", "red");
|
|
306
|
-
data[patient].show = true;
|
|
307
|
-
makegraph(snvlst, header, graphholder);
|
|
308
|
-
makesubgraph(snvlst, graph1holder, graph2holder, graph3holder, graph4holder);
|
|
309
|
-
makecontrol(snvlst, header, controlholder, graphholder, graph1holder, graph2holder, graph3holder, graph4holder);
|
|
310
|
-
});
|
|
311
|
-
data[patient].handle = div;
|
|
312
|
-
}
|
|
313
|
-
for (const n in data) {
|
|
314
|
-
data[n].handle.node().click();
|
|
315
|
-
break;
|
|
316
|
-
}
|
|
317
|
-
}
|
|
318
|
-
function makesubgraph(snvlst, g1, g2, g3, g4) {
|
|
319
|
-
g1.selectAll("*").remove();
|
|
320
|
-
g2.selectAll("*").remove();
|
|
321
|
-
g3.selectAll("*").remove();
|
|
322
|
-
g4.selectAll("*").remove();
|
|
323
|
-
const l1 = [];
|
|
324
|
-
const l2 = [];
|
|
325
|
-
const l3 = [];
|
|
326
|
-
const l4 = [];
|
|
327
|
-
for (const snv of snvlst) {
|
|
328
|
-
switch (snv.subidx) {
|
|
329
|
-
case 1:
|
|
330
|
-
l1.push(snv);
|
|
331
|
-
break;
|
|
332
|
-
case 2:
|
|
333
|
-
l2.push(snv);
|
|
334
|
-
break;
|
|
335
|
-
case 3:
|
|
336
|
-
l3.push(snv);
|
|
337
|
-
break;
|
|
338
|
-
case 4:
|
|
339
|
-
l4.push(snv);
|
|
340
|
-
break;
|
|
341
|
-
}
|
|
342
|
-
}
|
|
343
|
-
if (l1.length) {
|
|
344
|
-
makegraph(l1, null, g1, true);
|
|
345
|
-
} else {
|
|
346
|
-
g1.append("div").style("padding", "60px").style("background-color", "#ededed").text("no data");
|
|
347
|
-
}
|
|
348
|
-
if (l2.length) {
|
|
349
|
-
makegraph(l2, null, g2, true);
|
|
350
|
-
} else {
|
|
351
|
-
g2.append("div").style("padding", "60px").style("background-color", "#ededed").text("no data");
|
|
352
|
-
}
|
|
353
|
-
if (l3.length) {
|
|
354
|
-
makegraph(l3, null, g3, true);
|
|
355
|
-
} else {
|
|
356
|
-
g3.append("div").style("padding", "60px").style("background-color", "#ededed").text("no data");
|
|
357
|
-
}
|
|
358
|
-
if (l4.length) {
|
|
359
|
-
makegraph(l4, null, g4, true);
|
|
360
|
-
} else {
|
|
361
|
-
g4.append("div").style("padding", "60px").style("background-color", "#ededed").text("no data");
|
|
362
|
-
}
|
|
363
|
-
}
|
|
364
|
-
function makegraph(snvlst0, header, holder, issub) {
|
|
365
|
-
holder.selectAll("*").remove();
|
|
366
|
-
const samples = [];
|
|
367
|
-
const snvlst = [];
|
|
368
|
-
for (const snv of snvlst0) {
|
|
369
|
-
if (!issub && !snv.show) continue;
|
|
370
|
-
snvlst.push(snv);
|
|
371
|
-
for (const s of snv.samples) {
|
|
372
|
-
samples.push(s);
|
|
373
|
-
}
|
|
374
|
-
}
|
|
375
|
-
if (snvlst.length == 0) return;
|
|
376
|
-
let mindate = snvlst[0].samples[0].date;
|
|
377
|
-
let maxdate = snvlst[0].samples[0].date;
|
|
378
|
-
let maxmaf = snvlst[0].samples[0].maf;
|
|
379
|
-
let maxcoverage = snvlst[0].samples[0].coverage;
|
|
380
|
-
for (const snv of snvlst) {
|
|
381
|
-
for (const s of snv.samples) {
|
|
382
|
-
mindate = Math.min(mindate, s.date);
|
|
383
|
-
maxdate = Math.max(maxdate, s.date);
|
|
384
|
-
maxmaf = Math.max(maxmaf, s.maf);
|
|
385
|
-
maxcoverage = Math.max(maxcoverage, s.coverage);
|
|
386
|
-
}
|
|
387
|
-
}
|
|
388
|
-
const svg = holder.append("svg");
|
|
389
|
-
const toppad = 30, rightpad = 200, yaxisw = 100, xaxish = 50;
|
|
390
|
-
let width = 600;
|
|
391
|
-
let height = 400;
|
|
392
|
-
let xpad, ypad, minradius;
|
|
393
|
-
const xaxisg = svg.append("g");
|
|
394
|
-
const yaxisg = svg.append("g");
|
|
395
|
-
const drag = svg.append("text").text("drag to resize").attr("class", "sja_clb").attr("text-anchor", "end").on("mousedown", (event) => {
|
|
396
|
-
event.preventDefault();
|
|
397
|
-
const x = event.clientX;
|
|
398
|
-
const y = event.clientY;
|
|
399
|
-
const w0 = width;
|
|
400
|
-
const h0 = height;
|
|
401
|
-
const body = select_default(document.body);
|
|
402
|
-
body.on("mousemove", (event2) => {
|
|
403
|
-
setsize(w0 + event2.clientX - x, h0 + event2.clientY - y);
|
|
404
|
-
}).on("mouseup", () => {
|
|
405
|
-
body.on("mousemove", null).on("mouseup", null);
|
|
406
|
-
});
|
|
407
|
-
});
|
|
408
|
-
const xscale = time().domain([mindate, maxdate]);
|
|
409
|
-
const yscale = (maflogscale ? log() : linear()).domain([zerovalue, 1]);
|
|
410
|
-
const rscale = linear().domain([1, maxcoverage]);
|
|
411
|
-
const g = svg.append("g");
|
|
412
|
-
const lines = g.selectAll().data(snvlst).enter().append("path").attr("stroke", (d) => d.color).attr("fill", "none");
|
|
413
|
-
let circles;
|
|
414
|
-
if (showcircle) {
|
|
415
|
-
circles = g.selectAll().data(samples).enter().append("circle").attr("fill", (d) => d.color).attr("fill-opacity", 0.1).on("mouseover", (event, d) => {
|
|
416
|
-
event.target.setAttribute("fill-opacity", 0.4);
|
|
417
|
-
tip.clear();
|
|
418
|
-
tip.show(event.clientX, event.clientY);
|
|
419
|
-
const lst = [];
|
|
420
|
-
for (const k in d) {
|
|
421
|
-
if (k == "color") continue;
|
|
422
|
-
if (k == "gene") {
|
|
423
|
-
lst.push({ k: "gene", v: '<span style="color:' + d.color + '">' + d.gene + "</span>" });
|
|
424
|
-
continue;
|
|
425
|
-
}
|
|
426
|
-
if (k == "date") continue;
|
|
427
|
-
if (k == "url") {
|
|
428
|
-
lst.push({ k: "URL", v: "<a href=" + d.url + " target=_blank>LINK</a>" });
|
|
429
|
-
continue;
|
|
430
|
-
}
|
|
431
|
-
lst.push({ k, v: d[k] });
|
|
432
|
-
}
|
|
433
|
-
make_table_2col(tip.d, lst);
|
|
434
|
-
}).on("mouseout", (event) => {
|
|
435
|
-
event.target.setAttribute("fill-opacity", 0.1);
|
|
436
|
-
});
|
|
437
|
-
}
|
|
438
|
-
const legend = svg.append("g");
|
|
439
|
-
const setsize = (w, h) => {
|
|
440
|
-
width = w;
|
|
441
|
-
height = h;
|
|
442
|
-
minradius = 2;
|
|
443
|
-
const maxradius = Math.max(width, height) / 30;
|
|
444
|
-
xpad = maxradius;
|
|
445
|
-
ypad = maxradius;
|
|
446
|
-
rscale.range([Math.pow(minradius, 2), Math.pow(maxradius, 2)]);
|
|
447
|
-
xscale.range([0, width]);
|
|
448
|
-
yscale.range([height, 0]);
|
|
449
|
-
svg.attr("width", yaxisw + xpad + width + rightpad).attr("height", toppad + height + ypad + xaxish);
|
|
450
|
-
xaxisg.attr("transform", "translate(" + (yaxisw + xpad) + "," + (toppad + height + ypad) + ")");
|
|
451
|
-
yaxisg.attr("transform", "translate(" + yaxisw + "," + toppad + ")");
|
|
452
|
-
drag.attr("x", yaxisw + xpad + width).attr("y", toppad + height + ypad + xaxish - 4);
|
|
453
|
-
axisstyle({
|
|
454
|
-
axis: xaxisg.call(axisBottom().scale(xscale)),
|
|
455
|
-
showline: true,
|
|
456
|
-
color: "black",
|
|
457
|
-
fontsize: Math.max(12, Math.min(20, width / 100))
|
|
458
|
-
});
|
|
459
|
-
axisstyle({
|
|
460
|
-
axis: yaxisg.call(
|
|
461
|
-
axisLeft().scale(yscale).tickValues([1, 0.1, 0.01, 1e-3, 1e-4, zerovalue]).tickFormat(format(" "))
|
|
462
|
-
),
|
|
463
|
-
showline: true,
|
|
464
|
-
color: "black",
|
|
465
|
-
fontsize: Math.max(12, Math.min(20, height / 100))
|
|
466
|
-
});
|
|
467
|
-
g.attr("transform", "translate(" + (yaxisw + xpad) + "," + toppad + ")");
|
|
468
|
-
lines.attr("d", (d) => {
|
|
469
|
-
const lst = [];
|
|
470
|
-
for (let i = 0; i < d.samples.length; i++) {
|
|
471
|
-
const s = d.samples[i];
|
|
472
|
-
lst.push((i == 0 ? "M" : "L") + " " + xscale(s.date) + " " + yscale(s.maf));
|
|
473
|
-
}
|
|
474
|
-
return lst.join(" ");
|
|
475
|
-
});
|
|
476
|
-
if (showcircle) {
|
|
477
|
-
circles.attr("cx", (d) => xscale(d.date)).attr("cy", (d) => yscale(d.maf)).attr("r", (d) => Math.sqrt(rscale(d.coverage)));
|
|
478
|
-
}
|
|
479
|
-
legend.attr("transform", "translate(" + (yaxisw + xpad + width + maxradius + 5) + "," + toppad + ")");
|
|
480
|
-
legend.selectAll("*").remove();
|
|
481
|
-
let y = minradius;
|
|
482
|
-
if (showcircle) {
|
|
483
|
-
legend.append("circle").attr("r", minradius).attr("cx", minradius).attr("cy", y).attr("fill", "#ccc");
|
|
484
|
-
legend.append("text").text(1).attr("x", minradius * 2 + 10).attr("y", y).attr("font-size", 10).attr("dominant-baseline", "central");
|
|
485
|
-
y += 5 + minradius + maxradius;
|
|
486
|
-
legend.append("circle").attr("r", maxradius).attr("cx", maxradius).attr("cy", y).attr("fill", "#ccc");
|
|
487
|
-
legend.append("text").text(maxcoverage).attr("x", maxradius * 2 + 10).attr("y", y).attr("font-size", 15).attr("dominant-baseline", "central");
|
|
488
|
-
y += 15 + maxradius;
|
|
489
|
-
}
|
|
490
|
-
const fontsize = 12;
|
|
491
|
-
for (const snv of snvlst) {
|
|
492
|
-
legend.append("line").attr("x2", 30).attr("y1", y).attr("y2", y).attr("stroke", snv.color);
|
|
493
|
-
if (showcircle) {
|
|
494
|
-
legend.append("circle").attr("cx", 15).attr("cy", y).attr("r", 8).attr("fill", snv.color).attr("fill-opacity", 0.1);
|
|
495
|
-
}
|
|
496
|
-
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) => {
|
|
497
|
-
event.target.setAttribute("font-weight", "bold");
|
|
498
|
-
lines.filter((d) => d.mutationname == snv.mutationname).attr("stroke-width", 3);
|
|
499
|
-
}).on("mouseout", (event) => {
|
|
500
|
-
event.target.setAttribute("font-weight", "normal");
|
|
501
|
-
lines.filter((d) => d.mutationname == snv.mutationname).attr("stroke-width", 1);
|
|
502
|
-
});
|
|
503
|
-
y += fontsize + 10;
|
|
504
|
-
}
|
|
505
|
-
};
|
|
506
|
-
setsize(width, height);
|
|
507
|
-
holder.append("div").style("text-align", "right").append("button").text("SVG").on("click", () => {
|
|
508
|
-
to_svg(svg.node(), "maf-timeline");
|
|
509
|
-
});
|
|
510
|
-
}
|
|
511
|
-
function makecontrol(snvlst, header, holder, graphholder, g1, g2, g3, g4) {
|
|
512
|
-
holder.selectAll("*").remove();
|
|
513
|
-
const table = holder.append("table");
|
|
514
|
-
for (const snv of snvlst) {
|
|
515
|
-
const tr = table.append("tr");
|
|
516
|
-
const td1 = tr.append("td");
|
|
517
|
-
td1.text(snv.gene).style("color", snv.color);
|
|
518
|
-
const td2 = tr.append("td");
|
|
519
|
-
const checkbox = td2.append("input").attr("type", "checkbox").style("zoom", "150%").property("checked", snv.show);
|
|
520
|
-
snv.checkbox = checkbox;
|
|
521
|
-
checkbox.on("change", (event) => {
|
|
522
|
-
snv.show = event.target.checked;
|
|
523
|
-
makegraph(snvlst, header, graphholder);
|
|
524
|
-
});
|
|
525
|
-
const butt = td2.append("button").style("margin-left", "5px").text("Only").on("click", () => {
|
|
526
|
-
for (const s2 of snvlst) {
|
|
527
|
-
s2.show = false;
|
|
528
|
-
s2.checkbox.property("checked", false);
|
|
529
|
-
}
|
|
530
|
-
snv.show = true;
|
|
531
|
-
snv.checkbox.property("checked", true);
|
|
532
|
-
makegraph(snvlst, header, graphholder);
|
|
533
|
-
});
|
|
534
|
-
let cname = Math.random();
|
|
535
|
-
const td11 = tr.append("td");
|
|
536
|
-
const c1 = td11.append("input").attr("type", "checkbox").attr("id", cname).on("change", (event) => cchange(1, event.target));
|
|
537
|
-
td11.append("label").html(" shared").attr("for", cname);
|
|
538
|
-
cname = Math.random();
|
|
539
|
-
const td22 = tr.append("td");
|
|
540
|
-
const c2 = td22.append("input").attr("type", "checkbox").attr("id", cname).on("change", (event) => cchange(2, event.target));
|
|
541
|
-
td22.append("label").html(" rising").attr("for", cname);
|
|
542
|
-
cname = Math.random();
|
|
543
|
-
const td33 = tr.append("td");
|
|
544
|
-
const c3 = td33.append("input").attr("type", "checkbox").attr("id", cname).on("change", (event) => cchange(3, event.target));
|
|
545
|
-
td33.append("label").html(" falling").attr("for", cname);
|
|
546
|
-
cname = Math.random();
|
|
547
|
-
const td44 = tr.append("td");
|
|
548
|
-
const c4 = td44.append("input").attr("type", "checkbox").attr("id", cname).on("change", (event) => cchange(4, event.target));
|
|
549
|
-
td44.append("label").html(" R-only").attr("for", cname);
|
|
550
|
-
if (snv.subidx == 1) c1.property("checked", true);
|
|
551
|
-
if (snv.subidx == 2) c2.property("checked", true);
|
|
552
|
-
if (snv.subidx == 3) c3.property("checked", true);
|
|
553
|
-
if (snv.subidx == 4) c4.property("checked", true);
|
|
554
|
-
const cchange = (which, check) => {
|
|
555
|
-
if (!check.checked) {
|
|
556
|
-
snv.subidx = -1;
|
|
557
|
-
} else {
|
|
558
|
-
snv.subidx = which;
|
|
559
|
-
if (which == 1) {
|
|
560
|
-
c2.property("checked", false);
|
|
561
|
-
c3.property("checked", false);
|
|
562
|
-
c4.property("checked", false);
|
|
563
|
-
} else if (which == 2) {
|
|
564
|
-
c1.property("checked", false);
|
|
565
|
-
c3.property("checked", false);
|
|
566
|
-
c4.property("checked", false);
|
|
567
|
-
} else if (which == 3) {
|
|
568
|
-
c1.property("checked", false);
|
|
569
|
-
c2.property("checked", false);
|
|
570
|
-
c4.property("checked", false);
|
|
571
|
-
} else {
|
|
572
|
-
c1.property("checked", false);
|
|
573
|
-
c2.property("checked", false);
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|
574
|
-
c3.property("checked", false);
|
|
575
|
-
}
|
|
576
|
-
}
|
|
577
|
-
makesubgraph(snvlst, g1, g2, g3, g4);
|
|
578
|
-
};
|
|
579
|
-
}
|
|
580
|
-
}
|
|
581
|
-
export {
|
|
582
|
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maftimelineui as default
|
|
583
|
-
};
|
|
584
|
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//# sourceMappingURL=maftimeline-GHKDDWYR.js.map
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package/dist/matrix-FWDLHZYR.js
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import {
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Matrix,
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componentInit,
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makeChartBtnMenu,
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matrixInit
|
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6
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} from "./chunk-KACWSU3U.js";
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import "./chunk-NRYOB7WU.js";
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import {
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getPlotConfig,
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setComputedConfig
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} from "./chunk-DA5VGV5L.js";
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import "./chunk-UOMRXQNW.js";
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import "./chunk-GBWRKJAH.js";
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import "./chunk-IPAGDFO4.js";
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import "./chunk-BP2F2GRB.js";
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import "./chunk-OS46MR72.js";
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24
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import "./chunk-N5VBIEH5.js";
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import "./chunk-FOXJTDTH.js";
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import "./chunk-SN5QKRXO.js";
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import "./chunk-V2OJLJSK.js";
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import "./chunk-UT6W4ZZL.js";
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import "./chunk-5TDKRZN5.js";
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import "./chunk-RYRCMHYR.js";
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import "./chunk-ECKWM4HB.js";
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import "./chunk-5MWX5HUZ.js";
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import "./chunk-IQIXGTQV.js";
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import "./chunk-ICNJQHQZ.js";
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import "./chunk-FYTZCTJC.js";
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import "./chunk-7NTZWOJV.js";
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import "./chunk-OMO754MK.js";
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42
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import "./chunk-RA5EXEHB.js";
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import "./chunk-PMZS3SHH.js";
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44
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import "./chunk-LOZEKOES.js";
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|
45
|
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import "./chunk-TOU7EVFQ.js";
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46
|
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import "./chunk-W2IWHXLL.js";
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import "./chunk-5OHXYXLD.js";
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import "./chunk-UJUXE42U.js";
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import "./chunk-OMR2DT66.js";
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|
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import "./chunk-NDWTN4U5.js";
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|
51
|
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import "./chunk-HFNDKYVF.js";
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|
52
|
-
export {
|
|
53
|
-
Matrix,
|
|
54
|
-
componentInit,
|
|
55
|
-
getPlotConfig,
|
|
56
|
-
makeChartBtnMenu,
|
|
57
|
-
matrixInit,
|
|
58
|
-
setComputedConfig
|
|
59
|
-
};
|
|
60
|
-
//# sourceMappingURL=matrix-FWDLHZYR.js.map
|
package/dist/matrix-YMJFP53F.js
DELETED
|
@@ -1,55 +0,0 @@
|
|
|
1
|
-
import {
|
|
2
|
-
Matrix,
|
|
3
|
-
componentInit,
|
|
4
|
-
makeChartBtnMenu,
|
|
5
|
-
matrixInit
|
|
6
|
-
} from "./chunk-KACWSU3U.js";
|
|
7
|
-
import "./chunk-NRYOB7WU.js";
|
|
8
|
-
import "./chunk-DA5VGV5L.js";
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|
9
|
-
import "./chunk-UZV3QI5M.js";
|
|
10
|
-
import "./chunk-A5TSPTYC.js";
|
|
11
|
-
import "./chunk-J2E4FALN.js";
|
|
12
|
-
import "./chunk-DPU66MZ7.js";
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|
13
|
-
import "./chunk-7P67W6NF.js";
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|
14
|
-
import "./chunk-EEX5VPJG.js";
|
|
15
|
-
import "./chunk-2MRZFUHZ.js";
|
|
16
|
-
import "./chunk-UOMRXQNW.js";
|
|
17
|
-
import "./chunk-GBWRKJAH.js";
|
|
18
|
-
import "./chunk-IPAGDFO4.js";
|
|
19
|
-
import "./chunk-BP2F2GRB.js";
|
|
20
|
-
import "./chunk-OS46MR72.js";
|
|
21
|
-
import "./chunk-N5VBIEH5.js";
|
|
22
|
-
import "./chunk-FOXJTDTH.js";
|
|
23
|
-
import "./chunk-SN5QKRXO.js";
|
|
24
|
-
import "./chunk-I2GCD26Y.js";
|
|
25
|
-
import "./chunk-4XDKCFFT.js";
|
|
26
|
-
import "./chunk-V2OJLJSK.js";
|
|
27
|
-
import "./chunk-UT6W4ZZL.js";
|
|
28
|
-
import "./chunk-HJ6L54YS.js";
|
|
29
|
-
import "./chunk-5TDKRZN5.js";
|
|
30
|
-
import "./chunk-RYRCMHYR.js";
|
|
31
|
-
import "./chunk-ECKWM4HB.js";
|
|
32
|
-
import "./chunk-NXOWHUR4.js";
|
|
33
|
-
import "./chunk-5MWX5HUZ.js";
|
|
34
|
-
import "./chunk-IQIXGTQV.js";
|
|
35
|
-
import "./chunk-ICNJQHQZ.js";
|
|
36
|
-
import "./chunk-FYTZCTJC.js";
|
|
37
|
-
import "./chunk-7NTZWOJV.js";
|
|
38
|
-
import "./chunk-OMO754MK.js";
|
|
39
|
-
import "./chunk-RA5EXEHB.js";
|
|
40
|
-
import "./chunk-PMZS3SHH.js";
|
|
41
|
-
import "./chunk-LOZEKOES.js";
|
|
42
|
-
import "./chunk-TOU7EVFQ.js";
|
|
43
|
-
import "./chunk-W2IWHXLL.js";
|
|
44
|
-
import "./chunk-5OHXYXLD.js";
|
|
45
|
-
import "./chunk-UJUXE42U.js";
|
|
46
|
-
import "./chunk-OMR2DT66.js";
|
|
47
|
-
import "./chunk-NDWTN4U5.js";
|
|
48
|
-
import "./chunk-HFNDKYVF.js";
|
|
49
|
-
export {
|
|
50
|
-
Matrix,
|
|
51
|
-
componentInit,
|
|
52
|
-
makeChartBtnMenu,
|
|
53
|
-
matrixInit
|
|
54
|
-
};
|
|
55
|
-
//# sourceMappingURL=matrix-YMJFP53F.js.map
|