@sjcrh/proteinpaint-client 2.205.0 → 2.206.1
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-XWKIQYRN.js +1367 -0
- package/dist/AggMatrixInput-D3HJXDOD.js +277 -0
- package/dist/AggregateMatrix-E2JZY5N5.js +41 -0
- package/dist/AppHeader-SR6LMFTW.js +830 -0
- package/dist/BoxPlot-G2LRWABH.js +1211 -0
- package/dist/CorrelationVolcano-CCQGOSR7.js +614 -0
- package/dist/Cuminc-QB6GE5MI.js +1219 -0
- package/dist/DE-JI7E7ZXU.js +89 -0
- package/dist/DEinput-B4A5UV4P.js +499 -0
- package/dist/DM-4OAF6WPS.js +90 -0
- package/dist/DifferentialAnalysis-6JMGV5JF.js +237 -0
- package/dist/Disco-F4HZYRGX.js +3389 -0
- package/dist/Disco.UI-KCIEUVNG.js +243 -0
- package/dist/DmrPlot-5M7E7NBT.js +637 -0
- package/dist/GB-KHKZQN5I.js +1391 -0
- package/dist/GSEA-CDGWJUFE.js +851 -0
- package/dist/GeneExpInput-CQVMNIRI.js +362 -0
- package/dist/Geomap-3F6FO54H.js +84 -0
- package/dist/HicApp-R3V46WEK.js +2245 -0
- package/dist/IDCViewer-2CGUU7EW.js +10812 -0
- package/dist/NumBinaryEditor-3LF334ID.js +279 -0
- package/dist/NumBinaryEditor.unit.spec-EIR7WOOV.js +312 -0
- package/dist/NumContEditor-CJEBKLS4.js +105 -0
- package/dist/NumContEditor.unit.spec-BKF3HKHP.js +164 -0
- package/dist/NumCustomBinEditor-BQI2NVI2.js +33 -0
- package/dist/NumCustomBinEditor.unit.spec-YWQL7STR.js +397 -0
- package/dist/NumDiscreteEditor-4VYL7IOM.js +170 -0
- package/dist/NumDiscreteEditor.unit.spec-CSORXLUZ.js +233 -0
- package/dist/NumRegularBinEditor-NSPZ7ZHQ.js +33 -0
- package/dist/NumRegularBinEditor.unit.spec-77FOOCQ7.js +278 -0
- package/dist/NumSplineEditor-CWZGMWF5.js +210 -0
- package/dist/NumSplineEditor.unit.spec-E6ITDOHV.js +224 -0
- package/dist/NumericDensity-TVXZG4E5.js +33 -0
- package/dist/NumericDensity.unit.spec-O6SIEDAM.js +418 -0
- package/dist/NumericHandler-LNQG3OWJ.js +34 -0
- package/dist/NumericHandler.unit.spec-3IJCPTRH.js +214 -0
- package/dist/ProteomeInput-SIYPPLOB.js +388 -0
- package/dist/Regression-EOITDTFO.js +1416 -0
- package/dist/RunChart2-7BIEDW6G.js +749 -0
- package/dist/SC-O4BKP23M.js +1107 -0
- package/dist/Violin-G35Y5F45.js +1082 -0
- package/dist/Volcano-DZVC5GSW.js +1649 -0
- package/dist/Wsi-LKBGTHZJ.js +431 -0
- package/dist/adSandbox-URTCAPSS.js +33 -0
- package/dist/animatedBubbleChart-KFIELJWN.js +547 -0
- package/dist/app-HOYLIBGB.js +42 -0
- package/dist/app-OPA44KOA.js +32 -0
- package/dist/app.js +17 -17
- package/dist/bam-JEC3YMC3.js +876 -0
- package/dist/barchart-UQU75RJP.js +42 -0
- package/dist/barchart2-3Z62N7NL.js +309 -0
- package/dist/block-HJ6F6LXQ.js +6249 -0
- package/dist/block.init-AYWLW2HT.js +33 -0
- package/dist/block.mds.expressionrank-HLZA7FAG.js +354 -0
- package/dist/block.mds.geneboxplot-3G2QSHDL.js +823 -0
- package/dist/block.mds.junction-DX4LWDH7.js +1539 -0
- package/dist/block.mds.svcnv-JZ33BUGK.js +6796 -0
- package/dist/block.svg-63BVZVV2.js +159 -0
- package/dist/block.tk.aicheck-KSNJ3JLB.js +278 -0
- package/dist/block.tk.ase-URSPZ66D.js +360 -0
- package/dist/block.tk.bam-DZ57VTOD.js +1901 -0
- package/dist/block.tk.bedgraphdot-QCC65WUI.js +379 -0
- package/dist/block.tk.bigwig.ui-3TGOK5PM.js +206 -0
- package/dist/block.tk.hicstraw-RASPIPEB.js +818 -0
- package/dist/block.tk.junction-HLJJSANL.js +2358 -0
- package/dist/block.tk.junction.textmatrixui-LPNEDD5D.js +194 -0
- package/dist/block.tk.ld-CDGBLDE2.js +94 -0
- package/dist/block.tk.menu-O7DLZOZZ.js +1024 -0
- package/dist/block.tk.pgv-2EGZS2II.js +938 -0
- package/dist/brainImaging-I7K3QOOA.js +515 -0
- package/dist/brainRegions-DNODMT67.js +217 -0
- package/dist/brainRegions-DNODMT67.js.map +7 -0
- package/dist/bubbleHeatmap-JOFBJ3N4.js +378 -0
- package/dist/cellTypeBubbleHeatmap-PUOOUMPO.js +278 -0
- package/dist/chunk-2SQEVMAL.js +446 -0
- package/dist/chunk-3CHQGKF6.js +54 -0
- package/dist/chunk-3FVFG3YR.js +134 -0
- package/dist/chunk-3PJZWZRS.js +70 -0
- package/dist/chunk-3W76UZR2.js +2853 -0
- package/dist/chunk-4DXQJGJ7.js +31 -0
- package/dist/chunk-4F57QD3H.js +42 -0
- package/dist/chunk-4FO3INHF.js +158 -0
- package/dist/chunk-4OLM3KSB.js +2708 -0
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- package/dist/chunk-ILEXRHF7.js +367 -0
- package/dist/chunk-ILEXRHF7.js.map +7 -0
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- package/dist/chunk-M4XXKTH2.js +339 -0
- package/dist/chunk-N7DVQTPC.js +119 -0
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- package/dist/chunk-OQBGN6FW.js +1233 -0
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- package/dist/chunk-OVPEMVXT.js +397 -0
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- package/dist/chunk-PBUV4CPQ.js +302 -0
- package/dist/chunk-QABGFKK3.js +129 -0
- package/dist/chunk-QGBHBSGS.js +123 -0
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- package/dist/chunk-RF3GQYZJ.js +1275 -0
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- package/dist/chunk-WPEOBBLH.js +379 -0
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- package/dist/chunk-XDLCPJCK.js +24164 -0
- package/dist/chunk-XDLCPJCK.js.map +7 -0
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- package/dist/chunk-YY5WQQ3J.js +194 -0
- package/dist/chunk-Z2ZITHT4.js +4195 -0
- package/dist/cohort-75OBZ5EL.js +70 -0
- package/dist/condition-XSIDDH5P.js +327 -0
- package/dist/controls-UVEY3Z57.js +34 -0
- package/dist/controls.config-M325HV4N.js +34 -0
- package/dist/correlation-HVQDCYQJ.js +95 -0
- package/dist/customdata.inputui-KMCJ4UFU.js +284 -0
- package/dist/dataDownload-MJNMZPR6.js +329 -0
- package/dist/databrowser.ui-O7KNP5RH.js +425 -0
- package/dist/dictionary-LLGX2XNU.js +113 -0
- package/dist/dnaMethylation-MXRMFWGM.js +33 -0
- package/dist/dnaMethylation.integration.spec-GNF4AW32.js +198 -0
- package/dist/dofetch-F5XSHQIS.js +48 -0
- package/dist/e2pca-TNDATCU2.js +344 -0
- package/dist/ep-GH62BQS5.js +1249 -0
- package/dist/expclust.gdc.spec-3XBBPTZX.js +302 -0
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- package/dist/gb-76QWZ2UI.js +81 -0
- package/dist/geneExpClustering-7EEK4LBZ.js +244 -0
- package/dist/geneExpression-4J2JRTUQ.js +33 -0
- package/dist/geneExpression-FXQ4L2J2.js +310 -0
- package/dist/geneExpression.unit.spec-JRLUIYIU.js +99 -0
- package/dist/geneORA-MQ3DRAFK.js +273 -0
- package/dist/geneRanking-LK5CSUYP.js +548 -0
- package/dist/geneVariant-HMOFSHIN.js +36 -0
- package/dist/geneVariant-IKM4MJZN.js +286 -0
- package/dist/geneVariant.integration.spec-ZIYVXRSQ.js +388 -0
- package/dist/genefusion.ui-UFSDMLZS.js +303 -0
- package/dist/geneset-IK43N3JG.js +203 -0
- package/dist/genomeBrowser.spec-GYBHE7HU.js +276 -0
- package/dist/grin2-K7OGPM66.js +1137 -0
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- package/dist/hierCluster-2Y6D73N4.js +55 -0
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- package/dist/hierCluster.integration.spec-FTWZHMSN.js +483 -0
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- package/dist/imagePlot-DBMZYBSO.js +156 -0
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- package/dist/isoformExpression-HN3MNBKH.js +35 -0
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- package/dist/lollipop-FBATR5JC.js +166 -0
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- package/dist/multivalue-EG2OGEET.js +83 -0
- package/dist/numericDictTermCluster-5AKP6ICC.js +63 -0
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- package/dist/proteinView-67EGJJCL.js +1357 -0
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- /package/dist/{summarizeCnvGeneexp-P4AFZMKD.js.map → summarizeCnvGeneexp-RBFYEF4F.js.map} +0 -0
- /package/dist/{summarizeGeneexpSurvival-YL2J7F4R.js.map → summarizeGeneexpSurvival-2MTLML7E.js.map} +0 -0
- /package/dist/{summarizeMutationCnv-BHBHST5F.js.map → summarizeMutationCnv-6YEOAUA6.js.map} +0 -0
- /package/dist/{summarizeMutationDiagnosis-Z7ZHTV27.js.map → summarizeMutationDiagnosis-GMGPKNVC.js.map} +0 -0
- /package/dist/{summarizeMutationSurvival-PZ4TYHT7.js.map → summarizeMutationSurvival-63LEMNOV.js.map} +0 -0
- /package/dist/{summary-ZMNPO65S.js.map → summary-TUL6Z35N.js.map} +0 -0
- /package/dist/{summary.integration.spec-DPJR2ZBE.js.map → summary.integration.spec-X22T3LB4.js.map} +0 -0
- /package/dist/{summaryInput-6JUFJZ5P.js.map → summaryInput-YBMESKTV.js.map} +0 -0
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- /package/dist/{survival-6JPKG3VA.js.map → survival-ZDWBE2JO.js.map} +0 -0
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data[m.patient].snv4[m.snv4].gene = m.gene;
|
|
209
|
-
}
|
|
210
|
-
if (!m.maf) {
|
|
211
|
-
badlines.push([i, "missing maf", lst]);
|
|
212
|
-
return;
|
|
213
|
-
}
|
|
214
|
-
let v = Number.parseFloat(m.maf);
|
|
215
|
-
if (Number.isNaN(v)) {
|
|
216
|
-
badlines.push([i, "invalid maf", lst]);
|
|
217
|
-
return;
|
|
218
|
-
}
|
|
219
|
-
if (v < zerovalue) {
|
|
220
|
-
v = zerovalue;
|
|
221
|
-
}
|
|
222
|
-
m.maf = v;
|
|
223
|
-
if (!m.coverage) {
|
|
224
|
-
badlines.push([i, "missing total_readcount", lst]);
|
|
225
|
-
return;
|
|
226
|
-
}
|
|
227
|
-
if (m.call_manual && m.call_manual == "wildtype") {
|
|
228
|
-
m.maf = zerovalue;
|
|
229
|
-
}
|
|
230
|
-
v = Number.parseInt(m.coverage);
|
|
231
|
-
if (Number.isNaN(v)) {
|
|
232
|
-
badlines.push([i, "invalid total_readcount", lst]);
|
|
233
|
-
return;
|
|
234
|
-
}
|
|
235
|
-
m.coverage = v;
|
|
236
|
-
let date;
|
|
237
|
-
if (m.date) {
|
|
238
|
-
const f = timeParse("%m/%d/%Y");
|
|
239
|
-
date = f(m.date);
|
|
240
|
-
m.Date = m.date;
|
|
241
|
-
} else {
|
|
242
|
-
badlines.push([i, "missing date", lst]);
|
|
243
|
-
return;
|
|
244
|
-
}
|
|
245
|
-
if (date == null) {
|
|
246
|
-
badlines.push([i, "cannot parse date", lst]);
|
|
247
|
-
return;
|
|
248
|
-
}
|
|
249
|
-
m.date = date;
|
|
250
|
-
if (!m.sample) {
|
|
251
|
-
badlines.push([i, "missing sample", lst]);
|
|
252
|
-
return;
|
|
253
|
-
}
|
|
254
|
-
data[m.patient].snv4[m.snv4].samples.push(m);
|
|
255
|
-
return true;
|
|
256
|
-
}
|
|
257
|
-
function render(data, header, holder) {
|
|
258
|
-
const table = holder.append("table").style("margin", "20px");
|
|
259
|
-
const tr1 = table.append("tr");
|
|
260
|
-
let td = tr1.append("td").style("vertical-align", "top").attr("rowspan", 2);
|
|
261
|
-
td.append("button").text("Toggle circle visibility").on("click", () => {
|
|
262
|
-
showcircle = !showcircle;
|
|
263
|
-
for (const n in data) {
|
|
264
|
-
if (data[n].show) {
|
|
265
|
-
data[n].handle.node().click();
|
|
266
|
-
break;
|
|
267
|
-
}
|
|
268
|
-
}
|
|
269
|
-
});
|
|
270
|
-
const patientholder = td.append("div").style("margin-top", "10px");
|
|
271
|
-
const td1 = tr1.append("td").style("vertical-align", "top");
|
|
272
|
-
const graphholder = td1.append("div").style("display", "inline-block");
|
|
273
|
-
const controlholder = td1.append("div").style("display", "inline-block").style("vertical-align", "top");
|
|
274
|
-
const tr2 = table.append("tr");
|
|
275
|
-
const tiantable = tr2.append("td").append("table").style("border-spacing", "20px").style("border-collapse", "separate");
|
|
276
|
-
const gtr1 = tiantable.append("tr");
|
|
277
|
-
td = gtr1.append("td").style("vertical-align", "top");
|
|
278
|
-
td.append("div").text("Shared").style("font-size", "2em");
|
|
279
|
-
const graph1holder = td.append("div").style("border", "solid 1px black");
|
|
280
|
-
td = gtr1.append("td").style("vertical-align", "top");
|
|
281
|
-
td.append("div").text("Rising").style("font-size", "2em");
|
|
282
|
-
const graph2holder = td.append("div").style("border", "solid 1px black");
|
|
283
|
-
const gtr2 = tiantable.append("tr");
|
|
284
|
-
td = gtr2.append("td").style("vertical-align", "top");
|
|
285
|
-
td.append("div").text("Falling").style("font-size", "2em");
|
|
286
|
-
const graph3holder = td.append("div").style("border", "solid 1px black");
|
|
287
|
-
td = gtr2.append("td").style("vertical-align", "top");
|
|
288
|
-
td.append("div").text("R-only").style("font-size", "2em");
|
|
289
|
-
const graph4holder = td.append("div").style("border", "solid 1px black");
|
|
290
|
-
for (const patient in data) {
|
|
291
|
-
const snvlst = [];
|
|
292
|
-
const colors = ordinal(category10_default);
|
|
293
|
-
for (const x in data[patient].snv4) {
|
|
294
|
-
const snv = data[patient].snv4[x];
|
|
295
|
-
snv.show = true;
|
|
296
|
-
snv.color = colors(snv.mutationname);
|
|
297
|
-
snv.samples.sort((a, b) => a.date - b.date);
|
|
298
|
-
for (const s of snv.samples) {
|
|
299
|
-
s.color = snv.color;
|
|
300
|
-
}
|
|
301
|
-
snvlst.push(snv);
|
|
302
|
-
}
|
|
303
|
-
const div = patientholder.append("div").classed("sja_menuoption", true).style("color", "black").text(patient).on("click", () => {
|
|
304
|
-
for (const pn in data) {
|
|
305
|
-
data[pn].handle.style("color", "black");
|
|
306
|
-
data[pn].show = false;
|
|
307
|
-
}
|
|
308
|
-
data[patient].handle.style("color", "red");
|
|
309
|
-
data[patient].show = true;
|
|
310
|
-
makegraph(snvlst, header, graphholder);
|
|
311
|
-
makesubgraph(snvlst, graph1holder, graph2holder, graph3holder, graph4holder);
|
|
312
|
-
makecontrol(snvlst, header, controlholder, graphholder, graph1holder, graph2holder, graph3holder, graph4holder);
|
|
313
|
-
});
|
|
314
|
-
data[patient].handle = div;
|
|
315
|
-
}
|
|
316
|
-
for (const n in data) {
|
|
317
|
-
data[n].handle.node().click();
|
|
318
|
-
break;
|
|
319
|
-
}
|
|
320
|
-
}
|
|
321
|
-
function makesubgraph(snvlst, g1, g2, g3, g4) {
|
|
322
|
-
g1.selectAll("*").remove();
|
|
323
|
-
g2.selectAll("*").remove();
|
|
324
|
-
g3.selectAll("*").remove();
|
|
325
|
-
g4.selectAll("*").remove();
|
|
326
|
-
const l1 = [];
|
|
327
|
-
const l2 = [];
|
|
328
|
-
const l3 = [];
|
|
329
|
-
const l4 = [];
|
|
330
|
-
for (const snv of snvlst) {
|
|
331
|
-
switch (snv.subidx) {
|
|
332
|
-
case 1:
|
|
333
|
-
l1.push(snv);
|
|
334
|
-
break;
|
|
335
|
-
case 2:
|
|
336
|
-
l2.push(snv);
|
|
337
|
-
break;
|
|
338
|
-
case 3:
|
|
339
|
-
l3.push(snv);
|
|
340
|
-
break;
|
|
341
|
-
case 4:
|
|
342
|
-
l4.push(snv);
|
|
343
|
-
break;
|
|
344
|
-
}
|
|
345
|
-
}
|
|
346
|
-
if (l1.length) {
|
|
347
|
-
makegraph(l1, null, g1, true);
|
|
348
|
-
} else {
|
|
349
|
-
g1.append("div").style("padding", "60px").style("background-color", "#ededed").text("no data");
|
|
350
|
-
}
|
|
351
|
-
if (l2.length) {
|
|
352
|
-
makegraph(l2, null, g2, true);
|
|
353
|
-
} else {
|
|
354
|
-
g2.append("div").style("padding", "60px").style("background-color", "#ededed").text("no data");
|
|
355
|
-
}
|
|
356
|
-
if (l3.length) {
|
|
357
|
-
makegraph(l3, null, g3, true);
|
|
358
|
-
} else {
|
|
359
|
-
g3.append("div").style("padding", "60px").style("background-color", "#ededed").text("no data");
|
|
360
|
-
}
|
|
361
|
-
if (l4.length) {
|
|
362
|
-
makegraph(l4, null, g4, true);
|
|
363
|
-
} else {
|
|
364
|
-
g4.append("div").style("padding", "60px").style("background-color", "#ededed").text("no data");
|
|
365
|
-
}
|
|
366
|
-
}
|
|
367
|
-
function makegraph(snvlst0, header, holder, issub) {
|
|
368
|
-
holder.selectAll("*").remove();
|
|
369
|
-
const samples = [];
|
|
370
|
-
const snvlst = [];
|
|
371
|
-
for (const snv of snvlst0) {
|
|
372
|
-
if (!issub && !snv.show) continue;
|
|
373
|
-
snvlst.push(snv);
|
|
374
|
-
for (const s of snv.samples) {
|
|
375
|
-
samples.push(s);
|
|
376
|
-
}
|
|
377
|
-
}
|
|
378
|
-
if (snvlst.length == 0) return;
|
|
379
|
-
let mindate = snvlst[0].samples[0].date;
|
|
380
|
-
let maxdate = snvlst[0].samples[0].date;
|
|
381
|
-
let maxmaf = snvlst[0].samples[0].maf;
|
|
382
|
-
let maxcoverage = snvlst[0].samples[0].coverage;
|
|
383
|
-
for (const snv of snvlst) {
|
|
384
|
-
for (const s of snv.samples) {
|
|
385
|
-
mindate = Math.min(mindate, s.date);
|
|
386
|
-
maxdate = Math.max(maxdate, s.date);
|
|
387
|
-
maxmaf = Math.max(maxmaf, s.maf);
|
|
388
|
-
maxcoverage = Math.max(maxcoverage, s.coverage);
|
|
389
|
-
}
|
|
390
|
-
}
|
|
391
|
-
const svg = holder.append("svg");
|
|
392
|
-
const toppad = 30, rightpad = 200, yaxisw = 100, xaxish = 50;
|
|
393
|
-
let width = 600;
|
|
394
|
-
let height = 400;
|
|
395
|
-
let xpad, ypad, minradius;
|
|
396
|
-
const xaxisg = svg.append("g");
|
|
397
|
-
const yaxisg = svg.append("g");
|
|
398
|
-
const drag = svg.append("text").text("drag to resize").attr("class", "sja_clb").attr("text-anchor", "end").on("mousedown", (event) => {
|
|
399
|
-
event.preventDefault();
|
|
400
|
-
const x = event.clientX;
|
|
401
|
-
const y = event.clientY;
|
|
402
|
-
const w0 = width;
|
|
403
|
-
const h0 = height;
|
|
404
|
-
const body = select_default(document.body);
|
|
405
|
-
body.on("mousemove", (event2) => {
|
|
406
|
-
setsize(w0 + event2.clientX - x, h0 + event2.clientY - y);
|
|
407
|
-
}).on("mouseup", () => {
|
|
408
|
-
body.on("mousemove", null).on("mouseup", null);
|
|
409
|
-
});
|
|
410
|
-
});
|
|
411
|
-
const xscale = time().domain([mindate, maxdate]);
|
|
412
|
-
const yscale = (maflogscale ? log() : linear()).domain([zerovalue, 1]);
|
|
413
|
-
const rscale = linear().domain([1, maxcoverage]);
|
|
414
|
-
const g = svg.append("g");
|
|
415
|
-
const lines = g.selectAll().data(snvlst).enter().append("path").attr("stroke", (d) => d.color).attr("fill", "none");
|
|
416
|
-
let circles;
|
|
417
|
-
if (showcircle) {
|
|
418
|
-
circles = g.selectAll().data(samples).enter().append("circle").attr("fill", (d) => d.color).attr("fill-opacity", 0.1).on("mouseover", (event, d) => {
|
|
419
|
-
event.target.setAttribute("fill-opacity", 0.4);
|
|
420
|
-
tip.clear();
|
|
421
|
-
tip.show(event.clientX, event.clientY);
|
|
422
|
-
const lst = [];
|
|
423
|
-
for (const k in d) {
|
|
424
|
-
if (k == "color") continue;
|
|
425
|
-
if (k == "gene") {
|
|
426
|
-
lst.push({ k: "gene", v: '<span style="color:' + d.color + '">' + d.gene + "</span>" });
|
|
427
|
-
continue;
|
|
428
|
-
}
|
|
429
|
-
if (k == "date") continue;
|
|
430
|
-
if (k == "url") {
|
|
431
|
-
lst.push({ k: "URL", v: "<a href=" + d.url + " target=_blank>LINK</a>" });
|
|
432
|
-
continue;
|
|
433
|
-
}
|
|
434
|
-
lst.push({ k, v: d[k] });
|
|
435
|
-
}
|
|
436
|
-
make_table_2col(tip.d, lst);
|
|
437
|
-
}).on("mouseout", (event) => {
|
|
438
|
-
event.target.setAttribute("fill-opacity", 0.1);
|
|
439
|
-
});
|
|
440
|
-
}
|
|
441
|
-
const legend = svg.append("g");
|
|
442
|
-
const setsize = (w, h) => {
|
|
443
|
-
width = w;
|
|
444
|
-
height = h;
|
|
445
|
-
minradius = 2;
|
|
446
|
-
const maxradius = Math.max(width, height) / 30;
|
|
447
|
-
xpad = maxradius;
|
|
448
|
-
ypad = maxradius;
|
|
449
|
-
rscale.range([Math.pow(minradius, 2), Math.pow(maxradius, 2)]);
|
|
450
|
-
xscale.range([0, width]);
|
|
451
|
-
yscale.range([height, 0]);
|
|
452
|
-
svg.attr("width", yaxisw + xpad + width + rightpad).attr("height", toppad + height + ypad + xaxish);
|
|
453
|
-
xaxisg.attr("transform", "translate(" + (yaxisw + xpad) + "," + (toppad + height + ypad) + ")");
|
|
454
|
-
yaxisg.attr("transform", "translate(" + yaxisw + "," + toppad + ")");
|
|
455
|
-
drag.attr("x", yaxisw + xpad + width).attr("y", toppad + height + ypad + xaxish - 4);
|
|
456
|
-
axisstyle({
|
|
457
|
-
axis: xaxisg.call(axisBottom().scale(xscale)),
|
|
458
|
-
showline: true,
|
|
459
|
-
color: "black",
|
|
460
|
-
fontsize: Math.max(12, Math.min(20, width / 100))
|
|
461
|
-
});
|
|
462
|
-
axisstyle({
|
|
463
|
-
axis: yaxisg.call(
|
|
464
|
-
axisLeft().scale(yscale).tickValues([1, 0.1, 0.01, 1e-3, 1e-4, zerovalue]).tickFormat(format(" "))
|
|
465
|
-
),
|
|
466
|
-
showline: true,
|
|
467
|
-
color: "black",
|
|
468
|
-
fontsize: Math.max(12, Math.min(20, height / 100))
|
|
469
|
-
});
|
|
470
|
-
g.attr("transform", "translate(" + (yaxisw + xpad) + "," + toppad + ")");
|
|
471
|
-
lines.attr("d", (d) => {
|
|
472
|
-
const lst = [];
|
|
473
|
-
for (let i = 0; i < d.samples.length; i++) {
|
|
474
|
-
const s = d.samples[i];
|
|
475
|
-
lst.push((i == 0 ? "M" : "L") + " " + xscale(s.date) + " " + yscale(s.maf));
|
|
476
|
-
}
|
|
477
|
-
return lst.join(" ");
|
|
478
|
-
});
|
|
479
|
-
if (showcircle) {
|
|
480
|
-
circles.attr("cx", (d) => xscale(d.date)).attr("cy", (d) => yscale(d.maf)).attr("r", (d) => Math.sqrt(rscale(d.coverage)));
|
|
481
|
-
}
|
|
482
|
-
legend.attr("transform", "translate(" + (yaxisw + xpad + width + maxradius + 5) + "," + toppad + ")");
|
|
483
|
-
legend.selectAll("*").remove();
|
|
484
|
-
let y = minradius;
|
|
485
|
-
if (showcircle) {
|
|
486
|
-
legend.append("circle").attr("r", minradius).attr("cx", minradius).attr("cy", y).attr("fill", "#ccc");
|
|
487
|
-
legend.append("text").text(1).attr("x", minradius * 2 + 10).attr("y", y).attr("font-size", 10).attr("dominant-baseline", "central");
|
|
488
|
-
y += 5 + minradius + maxradius;
|
|
489
|
-
legend.append("circle").attr("r", maxradius).attr("cx", maxradius).attr("cy", y).attr("fill", "#ccc");
|
|
490
|
-
legend.append("text").text(maxcoverage).attr("x", maxradius * 2 + 10).attr("y", y).attr("font-size", 15).attr("dominant-baseline", "central");
|
|
491
|
-
y += 15 + maxradius;
|
|
492
|
-
}
|
|
493
|
-
const fontsize = 12;
|
|
494
|
-
for (const snv of snvlst) {
|
|
495
|
-
legend.append("line").attr("x2", 30).attr("y1", y).attr("y2", y).attr("stroke", snv.color);
|
|
496
|
-
if (showcircle) {
|
|
497
|
-
legend.append("circle").attr("cx", 15).attr("cy", y).attr("r", 8).attr("fill", snv.color).attr("fill-opacity", 0.1);
|
|
498
|
-
}
|
|
499
|
-
legend.append("text").text(snv.gene).attr("dominant-baseline", "central").attr("font-size", fontsize).attr("x", 30 + 10).attr("y", y).attr("fill", snv.color).style("cursor", "default").on("mouseover", (event) => {
|
|
500
|
-
event.target.setAttribute("font-weight", "bold");
|
|
501
|
-
lines.filter((d) => d.mutationname == snv.mutationname).attr("stroke-width", 3);
|
|
502
|
-
}).on("mouseout", (event) => {
|
|
503
|
-
event.target.setAttribute("font-weight", "normal");
|
|
504
|
-
lines.filter((d) => d.mutationname == snv.mutationname).attr("stroke-width", 1);
|
|
505
|
-
});
|
|
506
|
-
y += fontsize + 10;
|
|
507
|
-
}
|
|
508
|
-
};
|
|
509
|
-
setsize(width, height);
|
|
510
|
-
holder.append("div").style("text-align", "right").append("button").text("SVG").on("click", () => {
|
|
511
|
-
to_svg(svg.node(), "maf-timeline");
|
|
512
|
-
});
|
|
513
|
-
}
|
|
514
|
-
function makecontrol(snvlst, header, holder, graphholder, g1, g2, g3, g4) {
|
|
515
|
-
holder.selectAll("*").remove();
|
|
516
|
-
const table = holder.append("table");
|
|
517
|
-
for (const snv of snvlst) {
|
|
518
|
-
const tr = table.append("tr");
|
|
519
|
-
const td1 = tr.append("td");
|
|
520
|
-
td1.text(snv.gene).style("color", snv.color);
|
|
521
|
-
const td2 = tr.append("td");
|
|
522
|
-
const checkbox = td2.append("input").attr("type", "checkbox").style("zoom", "150%").property("checked", snv.show);
|
|
523
|
-
snv.checkbox = checkbox;
|
|
524
|
-
checkbox.on("change", (event) => {
|
|
525
|
-
snv.show = event.target.checked;
|
|
526
|
-
makegraph(snvlst, header, graphholder);
|
|
527
|
-
});
|
|
528
|
-
const butt = td2.append("button").style("margin-left", "5px").text("Only").on("click", () => {
|
|
529
|
-
for (const s2 of snvlst) {
|
|
530
|
-
s2.show = false;
|
|
531
|
-
s2.checkbox.property("checked", false);
|
|
532
|
-
}
|
|
533
|
-
snv.show = true;
|
|
534
|
-
snv.checkbox.property("checked", true);
|
|
535
|
-
makegraph(snvlst, header, graphholder);
|
|
536
|
-
});
|
|
537
|
-
let cname = Math.random();
|
|
538
|
-
const td11 = tr.append("td");
|
|
539
|
-
const c1 = td11.append("input").attr("type", "checkbox").attr("id", cname).on("change", (event) => cchange(1, event.target));
|
|
540
|
-
td11.append("label").html(" shared").attr("for", cname);
|
|
541
|
-
cname = Math.random();
|
|
542
|
-
const td22 = tr.append("td");
|
|
543
|
-
const c2 = td22.append("input").attr("type", "checkbox").attr("id", cname).on("change", (event) => cchange(2, event.target));
|
|
544
|
-
td22.append("label").html(" rising").attr("for", cname);
|
|
545
|
-
cname = Math.random();
|
|
546
|
-
const td33 = tr.append("td");
|
|
547
|
-
const c3 = td33.append("input").attr("type", "checkbox").attr("id", cname).on("change", (event) => cchange(3, event.target));
|
|
548
|
-
td33.append("label").html(" falling").attr("for", cname);
|
|
549
|
-
cname = Math.random();
|
|
550
|
-
const td44 = tr.append("td");
|
|
551
|
-
const c4 = td44.append("input").attr("type", "checkbox").attr("id", cname).on("change", (event) => cchange(4, event.target));
|
|
552
|
-
td44.append("label").html(" R-only").attr("for", cname);
|
|
553
|
-
if (snv.subidx == 1) c1.property("checked", true);
|
|
554
|
-
if (snv.subidx == 2) c2.property("checked", true);
|
|
555
|
-
if (snv.subidx == 3) c3.property("checked", true);
|
|
556
|
-
if (snv.subidx == 4) c4.property("checked", true);
|
|
557
|
-
const cchange = (which, check) => {
|
|
558
|
-
if (!check.checked) {
|
|
559
|
-
snv.subidx = -1;
|
|
560
|
-
} else {
|
|
561
|
-
snv.subidx = which;
|
|
562
|
-
if (which == 1) {
|
|
563
|
-
c2.property("checked", false);
|
|
564
|
-
c3.property("checked", false);
|
|
565
|
-
c4.property("checked", false);
|
|
566
|
-
} else if (which == 2) {
|
|
567
|
-
c1.property("checked", false);
|
|
568
|
-
c3.property("checked", false);
|
|
569
|
-
c4.property("checked", false);
|
|
570
|
-
} else if (which == 3) {
|
|
571
|
-
c1.property("checked", false);
|
|
572
|
-
c2.property("checked", false);
|
|
573
|
-
c4.property("checked", false);
|
|
574
|
-
} else {
|
|
575
|
-
c1.property("checked", false);
|
|
576
|
-
c2.property("checked", false);
|
|
577
|
-
c3.property("checked", false);
|
|
578
|
-
}
|
|
579
|
-
}
|
|
580
|
-
makesubgraph(snvlst, g1, g2, g3, g4);
|
|
581
|
-
};
|
|
582
|
-
}
|
|
583
|
-
}
|
|
584
|
-
export {
|
|
585
|
-
maftimelineui as default
|
|
586
|
-
};
|
|
587
|
-
//# sourceMappingURL=maftimeline-5JV3HZLE.js.map
|
package/dist/matrix-CEVGKXSK.js
DELETED
|
@@ -1,54 +0,0 @@
|
|
|
1
|
-
import {
|
|
2
|
-
Matrix,
|
|
3
|
-
componentInit,
|
|
4
|
-
makeChartBtnMenu,
|
|
5
|
-
matrixInit
|
|
6
|
-
} from "./chunk-TBPVP3KZ.js";
|
|
7
|
-
import "./chunk-SWZAHJYP.js";
|
|
8
|
-
import "./chunk-4PPZYVWZ.js";
|
|
9
|
-
import "./chunk-GRI74AXV.js";
|
|
10
|
-
import "./chunk-SY63UUF7.js";
|
|
11
|
-
import "./chunk-JIDJBM2R.js";
|
|
12
|
-
import "./chunk-OXLBPSJ6.js";
|
|
13
|
-
import "./chunk-C2MCQZWH.js";
|
|
14
|
-
import "./chunk-DDKS3MV3.js";
|
|
15
|
-
import "./chunk-IS4VLUEX.js";
|
|
16
|
-
import "./chunk-J2DICGKC.js";
|
|
17
|
-
import "./chunk-MAVDQAZE.js";
|
|
18
|
-
import "./chunk-IB4NE4SI.js";
|
|
19
|
-
import "./chunk-E4WIMTK4.js";
|
|
20
|
-
import "./chunk-67URJYN7.js";
|
|
21
|
-
import "./chunk-V2OJLJSK.js";
|
|
22
|
-
import "./chunk-J7JDCNLU.js";
|
|
23
|
-
import "./chunk-HJ6L54YS.js";
|
|
24
|
-
import "./chunk-KV4W2ACA.js";
|
|
25
|
-
import "./chunk-N635HDJ4.js";
|
|
26
|
-
import "./chunk-T46FA72N.js";
|
|
27
|
-
import "./chunk-ELJX3QIQ.js";
|
|
28
|
-
import "./chunk-EEB5VE2A.js";
|
|
29
|
-
import "./chunk-6RRZRISL.js";
|
|
30
|
-
import "./chunk-2KM4PRQM.js";
|
|
31
|
-
import "./chunk-JYOIO5UY.js";
|
|
32
|
-
import "./chunk-YN5NY3D3.js";
|
|
33
|
-
import "./chunk-RN4BOWRH.js";
|
|
34
|
-
import "./chunk-IK2BO37K.js";
|
|
35
|
-
import "./chunk-WINIL2KN.js";
|
|
36
|
-
import "./chunk-PF4DSFDR.js";
|
|
37
|
-
import "./chunk-D6G64XPJ.js";
|
|
38
|
-
import "./chunk-W5J3LTYS.js";
|
|
39
|
-
import "./chunk-YLJOZP4P.js";
|
|
40
|
-
import "./chunk-HDTFYTEL.js";
|
|
41
|
-
import "./chunk-FXQXCOII.js";
|
|
42
|
-
import "./chunk-TLT4YIG3.js";
|
|
43
|
-
import "./chunk-5R63Q5KH.js";
|
|
44
|
-
import "./chunk-I6Y4O3RR.js";
|
|
45
|
-
import "./chunk-Q5RDQNIT.js";
|
|
46
|
-
import "./chunk-DQC5FFGV.js";
|
|
47
|
-
import "./chunk-HS5PO5ZQ.js";
|
|
48
|
-
export {
|
|
49
|
-
Matrix,
|
|
50
|
-
componentInit,
|
|
51
|
-
makeChartBtnMenu,
|
|
52
|
-
matrixInit
|
|
53
|
-
};
|
|
54
|
-
//# sourceMappingURL=matrix-CEVGKXSK.js.map
|
package/dist/matrix-EXNYXYLK.js
DELETED
|
@@ -1,59 +0,0 @@
|
|
|
1
|
-
import {
|
|
2
|
-
Matrix,
|
|
3
|
-
componentInit,
|
|
4
|
-
makeChartBtnMenu,
|
|
5
|
-
matrixInit
|
|
6
|
-
} from "./chunk-TBPVP3KZ.js";
|
|
7
|
-
import "./chunk-SWZAHJYP.js";
|
|
8
|
-
import "./chunk-4PPZYVWZ.js";
|
|
9
|
-
import {
|
|
10
|
-
getPlotConfig,
|
|
11
|
-
setComputedConfig
|
|
12
|
-
} from "./chunk-GRI74AXV.js";
|
|
13
|
-
import "./chunk-SY63UUF7.js";
|
|
14
|
-
import "./chunk-JIDJBM2R.js";
|
|
15
|
-
import "./chunk-OXLBPSJ6.js";
|
|
16
|
-
import "./chunk-C2MCQZWH.js";
|
|
17
|
-
import "./chunk-DDKS3MV3.js";
|
|
18
|
-
import "./chunk-IS4VLUEX.js";
|
|
19
|
-
import "./chunk-J2DICGKC.js";
|
|
20
|
-
import "./chunk-MAVDQAZE.js";
|
|
21
|
-
import "./chunk-IB4NE4SI.js";
|
|
22
|
-
import "./chunk-E4WIMTK4.js";
|
|
23
|
-
import "./chunk-67URJYN7.js";
|
|
24
|
-
import "./chunk-V2OJLJSK.js";
|
|
25
|
-
import "./chunk-J7JDCNLU.js";
|
|
26
|
-
import "./chunk-HJ6L54YS.js";
|
|
27
|
-
import "./chunk-KV4W2ACA.js";
|
|
28
|
-
import "./chunk-N635HDJ4.js";
|
|
29
|
-
import "./chunk-T46FA72N.js";
|
|
30
|
-
import "./chunk-ELJX3QIQ.js";
|
|
31
|
-
import "./chunk-EEB5VE2A.js";
|
|
32
|
-
import "./chunk-6RRZRISL.js";
|
|
33
|
-
import "./chunk-2KM4PRQM.js";
|
|
34
|
-
import "./chunk-JYOIO5UY.js";
|
|
35
|
-
import "./chunk-YN5NY3D3.js";
|
|
36
|
-
import "./chunk-RN4BOWRH.js";
|
|
37
|
-
import "./chunk-IK2BO37K.js";
|
|
38
|
-
import "./chunk-WINIL2KN.js";
|
|
39
|
-
import "./chunk-PF4DSFDR.js";
|
|
40
|
-
import "./chunk-D6G64XPJ.js";
|
|
41
|
-
import "./chunk-W5J3LTYS.js";
|
|
42
|
-
import "./chunk-YLJOZP4P.js";
|
|
43
|
-
import "./chunk-HDTFYTEL.js";
|
|
44
|
-
import "./chunk-FXQXCOII.js";
|
|
45
|
-
import "./chunk-TLT4YIG3.js";
|
|
46
|
-
import "./chunk-5R63Q5KH.js";
|
|
47
|
-
import "./chunk-I6Y4O3RR.js";
|
|
48
|
-
import "./chunk-Q5RDQNIT.js";
|
|
49
|
-
import "./chunk-DQC5FFGV.js";
|
|
50
|
-
import "./chunk-HS5PO5ZQ.js";
|
|
51
|
-
export {
|
|
52
|
-
Matrix,
|
|
53
|
-
componentInit,
|
|
54
|
-
getPlotConfig,
|
|
55
|
-
makeChartBtnMenu,
|
|
56
|
-
matrixInit,
|
|
57
|
-
setComputedConfig
|
|
58
|
-
};
|
|
59
|
-
//# sourceMappingURL=matrix-EXNYXYLK.js.map
|