@sjcrh/proteinpaint-client 2.198.0 → 2.200.0

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.
Files changed (1066) hide show
  1. package/dist/2dmaf-RRV3ORZR.js +1373 -0
  2. package/dist/AIProjectAdmin-DKLEFCGX.js +958 -0
  3. package/dist/AppHeader-WQ2F7HZY.js +835 -0
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  1047. /package/dist/{survival-UI74VXSM.js.map → survival-DINCIWW7.js.map} +0 -0
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@@ -1,1223 +0,0 @@
1
- import {
2
- getSeriesTip,
3
- renderAtRiskG,
4
- renderPvalues
5
- } from "./chunk-KI5KI3ZJ.js";
6
- import {
7
- schemeCategory20
8
- } from "./chunk-V2OJLJSK.js";
9
- import {
10
- DownloadMenu,
11
- PlotBase,
12
- controlsInit,
13
- defaultUiLabels,
14
- downloadChart,
15
- fillTermWrapper,
16
- getCombinedTermFilter,
17
- htmlLegend,
18
- rgb2hex,
19
- term0_term2_defaultQ
20
- } from "./chunk-5VOPABBA.js";
21
- import {
22
- Menu
23
- } from "./chunk-HYOEWQ5P.js";
24
- import {
25
- require_partjson_umd
26
- } from "./chunk-XPY6AWXO.js";
27
- import {
28
- copyMerge,
29
- getCompInit
30
- } from "./chunk-M3J4MINX.js";
31
- import {
32
- isNumericTerm
33
- } from "./chunk-I6WR4CG7.js";
34
- import {
35
- area_default,
36
- category10_default,
37
- line_default,
38
- stepAfter
39
- } from "./chunk-3XVVN66M.js";
40
- import {
41
- axisBottom,
42
- axisLeft
43
- } from "./chunk-LOZEKOES.js";
44
- import {
45
- linear,
46
- ordinal
47
- } from "./chunk-NSTL4MY2.js";
48
- import {
49
- select_default
50
- } from "./chunk-I6Y4O3RR.js";
51
- import {
52
- rgb
53
- } from "./chunk-OMR2DT66.js";
54
- import {
55
- __toESM
56
- } from "./chunk-HFNDKYVF.js";
57
-
58
- // plots/survival/survival.ts
59
- var import_partjson = __toESM(require_partjson_umd(), 1);
60
- var t0_t2_defaultQ = structuredClone(term0_term2_defaultQ);
61
- Object.assign(t0_t2_defaultQ, {
62
- numeric: {
63
- mode: "discrete",
64
- type: "custom-bin",
65
- preferredBins: "median"
66
- },
67
- geneExpression: {
68
- mode: "discrete",
69
- type: "custom-bin",
70
- preferredBins: "median"
71
- },
72
- ssGSEA: {
73
- mode: "discrete",
74
- type: "custom-bin",
75
- preferredBins: "median"
76
- },
77
- isoformExpression: {
78
- mode: "discrete",
79
- type: "custom-bin",
80
- preferredBins: "median"
81
- },
82
- dnaMethylation: {
83
- mode: "discrete",
84
- type: "custom-bin",
85
- preferredBins: "median"
86
- }
87
- });
88
- var TdbSurvival = class _TdbSurvival extends PlotBase {
89
- constructor(opts, api) {
90
- super(opts, api);
91
- this.components = {};
92
- // expected class-specific props
93
- this.configTermKeys = ["term", "term0", "term2"];
94
- this.activeMenu = false;
95
- this.legendClick = (_, __, ___) => {
96
- };
97
- this.download = () => {
98
- };
99
- this.getChartImages = () => this.getChartImages();
100
- this.loadingWait = 0;
101
- this.legendOrder = [];
102
- this.term2toColor = {};
103
- this.uniqueSeriesIds = /* @__PURE__ */ new Set();
104
- // TODO: migrate to this.view method
105
- this.render = () => {
106
- };
107
- this.getSymbol = (_) => {
108
- return "";
109
- };
110
- this.type = _TdbSurvival.type;
111
- this.settings = Object.assign({}, opts.settings);
112
- this.dom = this.getDom();
113
- this.pj = getPj(this);
114
- this.lineFxn = line_default().curve(stepAfter).x((c) => c.scaledX).y((c) => c.scaledY);
115
- this.legendRenderer = htmlLegend(this.dom.legendDiv, {
116
- settings: {
117
- legendOrientation: "vertical"
118
- },
119
- handlers: {
120
- legend: {
121
- click: (e) => this.legendClick(e.target.__data__, e.clientX, e.clientY)
122
- }
123
- }
124
- });
125
- this.hiddenRenderer = htmlLegend(this.dom.hiddenDiv, {
126
- settings: {
127
- legendOrientation: "vertical"
128
- },
129
- handlers: {
130
- legend: {
131
- click: (e) => this.legendClick(e.target.__data__, e.clientX, e.clientY)
132
- }
133
- }
134
- });
135
- }
136
- static {
137
- this.type = "survival";
138
- }
139
- getDom() {
140
- const opts = this.opts;
141
- const holder = opts.controls ? opts.holder : opts.holder.append("div");
142
- const { controls, errdiv, loadingDiv, renderedData, charts, legendDiv } = this.getStandardDomLayout(holder, opts);
143
- const dom = {
144
- loadingDiv,
145
- header: opts.header?.html("Survival Plot"),
146
- controls,
147
- holder,
148
- errdiv,
149
- renderedData,
150
- chartsDiv: charts.style("margin", "10px").style("display", "flex").style("flex-direction", "row").style("flex-wrap", "wrap").style("max-width", "100vw"),
151
- legendDiv: legendDiv.style("margin", "5px 5px 15px 5px"),
152
- hiddenDiv: renderedData.append("div").style("margin", "5px 5px 15px 5px"),
153
- tip: new Menu({ padding: "5px" }),
154
- legendTip: new Menu({ padding: "5px" })
155
- };
156
- dom.tip.onHide = () => {
157
- this.activeMenu = false;
158
- };
159
- return dom;
160
- }
161
- async init() {
162
- setInteractivity(this);
163
- setRenderers(this);
164
- await this.setControls();
165
- }
166
- async setControls() {
167
- const state = this.getState(this.app.getState());
168
- const controlLabels = state.config.controlLabels;
169
- if (!controlLabels) throw "controls labels not found";
170
- const stratDisabledMsg = this.app.vocabApi.termdbConfig?.survival?.stratificationDisabledMessage;
171
- if (this.opts.controls) {
172
- this.opts.controls.on("downloadClick.survival", this.download);
173
- } else {
174
- this.dom.holder.attr("class", "pp-termdb-plot-viz").style("display", "inline-block").style("min-width", "300px");
175
- this.components = {
176
- controls: await controlsInit({
177
- app: this.app,
178
- id: this.id,
179
- holder: this.dom.controls.style("display", "inline-block"),
180
- inputs: [
181
- {
182
- type: "term",
183
- configKey: "term2",
184
- chartType: "survival",
185
- usecase: { target: "survival", detail: "term2" },
186
- title: controlLabels.term2.title || controlLabels.term2.label,
187
- label: controlLabels.term2.label,
188
- vocabApi: this.app.vocabApi,
189
- numericEditMenuVersion: ["discrete"],
190
- defaultQ4fillTW: t0_t2_defaultQ,
191
- disabledMessage: stratDisabledMsg
192
- },
193
- {
194
- type: "term",
195
- configKey: "term0",
196
- chartType: "survival",
197
- usecase: { target: "survival", detail: "term0" },
198
- title: controlLabels.term0.title || controlLabels.term0.label,
199
- label: controlLabels.term0.label,
200
- vocabApi: this.app.vocabApi,
201
- numericEditMenuVersion: ["discrete"],
202
- defaultQ4fillTW: t0_t2_defaultQ,
203
- disabledMessage: stratDisabledMsg
204
- },
205
- {
206
- label: "Chart width",
207
- type: "number",
208
- chartType: "survival",
209
- settingsKey: "svgw",
210
- title: "The internal width of the chart plot"
211
- },
212
- {
213
- label: "Chart height",
214
- type: "number",
215
- chartType: "survival",
216
- settingsKey: "svgh",
217
- title: "The internal height of the chart plot"
218
- },
219
- {
220
- label: "95% Confidence Interval",
221
- boxLabel: "Visible",
222
- type: "checkbox",
223
- chartType: "survival",
224
- settingsKey: "ciVisible",
225
- title: "Display the 95% confidence interval"
226
- },
227
- {
228
- label: "Median Survival",
229
- boxLabel: "Visible",
230
- type: "checkbox",
231
- chartType: "survival",
232
- settingsKey: "medianSurvivalVisible",
233
- title: "Display dashed lines indicating the median survival time (50% probability)"
234
- },
235
- {
236
- label: "Censored Symbol",
237
- type: "radio",
238
- chartType: "survival",
239
- settingsKey: "symbol",
240
- options: [
241
- { label: "Tick", value: "vtick" },
242
- { label: "X", value: "x" }
243
- ],
244
- title: "Symbol for displaying censored samples"
245
- },
246
- {
247
- label: "Survival Time Visualized",
248
- type: "number",
249
- chartType: "survival",
250
- settingsKey: "maxTimeToEvent",
251
- title: "The maximum time-to-event to be displayed in the survival plot, affects only the visual representation and does not impact other analyses. All available data is still used to compute p-values. If this value is left empty or set to 0, no cutoff will be applied."
252
- },
253
- {
254
- label: "Time Unit",
255
- type: "radio",
256
- chartType: "survival",
257
- settingsKey: "timeUnit",
258
- options: [
259
- { label: "years", value: "years" },
260
- { label: "months", value: "months" },
261
- { label: "weeks", value: "weeks" },
262
- { label: "days", value: "days" }
263
- ],
264
- title: `The unit to display in the x-axis title, like 'years'`
265
- },
266
- {
267
- label: "X-axis ticks",
268
- type: "text",
269
- chartType: "survival",
270
- settingsKey: "xTickValues",
271
- title: `Option to customize the x-axis tick values, enter as comma-separated values. Will be ignored if empty`,
272
- processInput: (value) => value ? value.split(",").map(Number) : []
273
- },
274
- {
275
- label: "At-risk counts",
276
- boxLabel: "Visible",
277
- type: "checkbox",
278
- chartType: "survival",
279
- settingsKey: "atRiskVisible",
280
- title: "Display the at-risk counts"
281
- },
282
- //{label: 'At-risk label offset', type: 'numeric', chartType: 'survival', settingsKey: 'atRiskLabelOffset'},
283
- {
284
- label: "Default color",
285
- type: "color",
286
- chartType: "survival",
287
- settingsKey: "defaultColor",
288
- title: "Default plot color"
289
- }
290
- ]
291
- })
292
- };
293
- this.components.controls.on("downloadClick.survival", this.download);
294
- }
295
- }
296
- getState(appState) {
297
- const config = appState.plots.find((p) => p.id === this.id);
298
- if (!config) {
299
- throw `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`;
300
- }
301
- const parentConfig = appState.plots.find((p) => p.id === this.parentId);
302
- const termfilter = getCombinedTermFilter(appState, config.filter || parentConfig?.filter);
303
- return {
304
- isVisible: config.term.term.type == "survival" || config.term2?.term.type == "survival",
305
- genome: this.app.vocabApi.vocab.genome,
306
- dslabel: this.app.vocabApi.vocab.dslabel,
307
- activeCohort: appState.activeCohort,
308
- termfilter,
309
- config: {
310
- // NOTE: will create mutable copies of tw terms in async main() below
311
- term: config.term,
312
- term0: config.term0 || null,
313
- term2: config.term2 || null,
314
- controlLabels: config.controlLabels,
315
- settings: config.settings.survival
316
- },
317
- termdbConfig: appState.termdbConfig
318
- };
319
- }
320
- async main() {
321
- if (!this.state.isVisible) {
322
- this.dom.holder.style("display", "none");
323
- return;
324
- }
325
- let data;
326
- try {
327
- this.state.config = await this.getMutableConfig();
328
- this.maySetSandboxHeader();
329
- this.toggleLoadingDiv();
330
- Object.assign(this.settings, this.state.config.settings);
331
- this.settings.defaultHidden = this.getDefaultHidden();
332
- this.settings.hidden = this.settings.customHidden || this.settings.defaultHidden;
333
- this.settings.xTitleLabel = this.getXtitleLabel();
334
- const reqOpts = this.getDataRequestOpts();
335
- data = await this.app.vocabApi.getNestedChartSeriesData(reqOpts, this.api?.getAbortSignal());
336
- } catch (e) {
337
- if (this.app.isAbortError(e)) return;
338
- this.toggleLoadingDiv("none", "none");
339
- throw e;
340
- }
341
- this.serverData = data;
342
- this.toggleLoadingDiv("none");
343
- this.app.vocabApi.syncTermData(this.state.config, data);
344
- this.currData = this.processData(data);
345
- this.refs = data.refs;
346
- this.pj.refresh({ data: this.currData });
347
- this.setTerm2Color(this.pj.tree.charts);
348
- this.symbol = this.getSymbol(7);
349
- this.render();
350
- }
351
- maySetSandboxHeader() {
352
- if (!this.dom.header) return;
353
- const { term, term2 } = this.state.config;
354
- const mainTerm = term.term.name;
355
- if (term2?.type) {
356
- this.dom.header.html(`${term2.getTitleText?.() || term2.term.name} vs ${mainTerm}`);
357
- } else {
358
- this.dom.header.html(`${mainTerm} plot`);
359
- }
360
- }
361
- // creates an opts object for the vocabApi.getNestedChartsData()
362
- getDataRequestOpts() {
363
- const c = this.state.config;
364
- const opts = {
365
- chartType: "survival",
366
- term: c.term,
367
- filter: this.state.termfilter.filter,
368
- filter0: this.state.termfilter.filter0
369
- };
370
- if (c.term2) {
371
- opts.term2 = c.term2;
372
- }
373
- if (c.term0) opts.term0 = c.term0;
374
- return opts;
375
- }
376
- getDefaultHidden() {
377
- const hidden = [];
378
- const term2 = this.state.config.term2;
379
- if (!term2) return hidden;
380
- const hiddenValues = term2.q.hiddenValues;
381
- if (hiddenValues && Object.keys(hiddenValues).length) {
382
- for (const k in hiddenValues) {
383
- hidden.push(term2.term.values[k].label);
384
- }
385
- }
386
- return hidden;
387
- }
388
- getXtitleLabel() {
389
- const termNum = this.state.config.term.term.type == "survival" ? "term" : "term2";
390
- const xUnit = this.settings.timeUnit ? this.settings.timeUnit : this.state.config[termNum].term.unit;
391
- const xTitleLabel = `Time to Event (${xUnit})`;
392
- return xTitleLabel;
393
- }
394
- processData(data) {
395
- this.uniqueSeriesIds = /* @__PURE__ */ new Set();
396
- this.msg = "";
397
- const rows = [];
398
- const estKeys = ["survival", "lower", "upper"];
399
- for (const d of data.case) {
400
- const obj = {};
401
- data.keys.forEach((k, i) => {
402
- obj[k] = estKeys.includes(k) ? Number(d[i]) : d[i];
403
- });
404
- obj.time = obj.time * this.getTimeFactor();
405
- rows.push(obj);
406
- this.uniqueSeriesIds.add(obj.seriesId);
407
- }
408
- this.tests = {};
409
- if (data.tests) {
410
- for (const chartId in data.tests) {
411
- const chartTests = data.tests[chartId];
412
- this.tests[chartId] = [];
413
- for (const test of chartTests) {
414
- if (this.settings.hidden.includes(test.series1) || this.settings.hidden.includes(test.series2)) continue;
415
- this.tests[chartId].push({
416
- pvalue: { id: "pvalue", text: test.pvalue },
417
- series1: { id: test.series1 },
418
- series2: { id: test.series2 }
419
- });
420
- }
421
- if (!this.tests[chartId].length) delete this.tests[chartId];
422
- }
423
- }
424
- if (data.refs.byTermId) {
425
- const byTermId = data.refs.byTermId;
426
- const msg = byTermId[this.state.config.term.term.id]?.survMsg;
427
- if (msg) {
428
- this.msg = msg;
429
- }
430
- }
431
- return rows;
432
- }
433
- // time factor that converts survival data from default time unit to the current time unit.
434
- getTimeFactor() {
435
- const numUnitInOneYear = this.settings.numUnitInOneYear || 1;
436
- const timeUnit = this.settings.timeUnit || "years";
437
- switch (timeUnit) {
438
- case "years":
439
- return 1 / numUnitInOneYear * 1;
440
- case "months":
441
- return 1 / numUnitInOneYear * 12;
442
- case "weeks":
443
- return 1 / numUnitInOneYear * 52;
444
- case "days":
445
- return 1 / numUnitInOneYear * 365.25;
446
- default:
447
- throw "unknown time Unit for survival data";
448
- }
449
- }
450
- setTerm2Color(charts) {
451
- if (!charts) return;
452
- const config = this.state.config;
453
- const t2values = copyMerge({}, config.term2?.term?.values || {}, config.term2?.values || {});
454
- const values = this.refs.bins[2] && [this.refs.bins[2]] || Object.values(t2values);
455
- let t2groups;
456
- if (config.term2?.q.type == "predefined-groupset" || config.term2?.q.type == "custom-groupset") {
457
- const groupset = config.term2.q.type == "predefined-groupset" ? config.term2.term.groupsetting.lst[config.term2.q.predefined_groupset_idx] : config.term2.q.customset;
458
- if (!groupset) throw "groupset is missing";
459
- t2groups = groupset.groups;
460
- }
461
- this.term2toColor = {};
462
- this.colorScale = this.uniqueSeriesIds.size < 11 ? ordinal(category10_default) : ordinal(schemeCategory20);
463
- const legendItems = [];
464
- for (const chart of charts) {
465
- for (const series of chart.serieses) {
466
- let color;
467
- const v = values.find(
468
- (v2) => v2.seriesId === series.seriesId || v2.key === series.seriesId || v2.name === series.seriesId || v2.label === series.seriesId
469
- );
470
- color = v?.color;
471
- if (!color && t2groups?.length) {
472
- const group = t2groups.find((g) => g.name == series.seriesId);
473
- color = group?.color;
474
- if (color === "#D3D3D3" && group?.filter?.lst?.find((f) => f?.type === "tvs" && f.tvs.genotype == "wt"))
475
- color = "rgb(105,105,105)";
476
- }
477
- const orig = color || (series.seriesId == "" ? this.settings.defaultColor : this.colorScale(series.seriesId));
478
- const _rgb = rgb(orig);
479
- const adjusted = _rgb.toString();
480
- const c = { orig, rgb: _rgb, adjusted, hex: rgb2hex(adjusted) };
481
- this.term2toColor[series.seriesId] = c;
482
- if (!legendItems.find((d) => d.seriesId == series.seriesId)) {
483
- legendItems.push({
484
- key: series.seriesId,
485
- seriesId: series.seriesId,
486
- text: series.seriesLabel,
487
- color: this.term2toColor[series.seriesId].adjusted,
488
- isHidden: this.settings.hidden.includes(series.seriesId)
489
- });
490
- }
491
- }
492
- }
493
- if (this.refs.orderedKeys) {
494
- const s = this.refs.orderedKeys.series;
495
- legendItems.sort((a, b) => s.indexOf(a.seriesId) - s.indexOf(b.seriesId));
496
- }
497
- if (!this.legendOrder.length) {
498
- this.legendOrder = legendItems.map((item) => item.seriesId);
499
- } else {
500
- legendItems.sort((a, b) => this.legendOrder.indexOf(a.seriesId) - this.legendOrder.indexOf(b.seriesId));
501
- }
502
- if ((config.term.term.type == "survival" || config.term2) && legendItems.length) {
503
- const termNum = config.term.term.type == "survival" && config.term2 ? "term2" : "term";
504
- this.legendData = [
505
- {
506
- name: config[termNum].term.name,
507
- items: legendItems.filter((s) => !s.isHidden)
508
- }
509
- ];
510
- this.hiddenData = [
511
- {
512
- name: `<span style='color:#aaa; font-weight:400'><span>Hidden categories</span><span style='font-size:0.8rem'> CLICK TO SHOW</span></span>`,
513
- items: legendItems.filter((s) => s.isHidden).map((item) => Object.assign({}, item, { isHidden: false }))
514
- }
515
- ];
516
- } else {
517
- this.legendData = [];
518
- }
519
- for (const chartId in this.tests) {
520
- const chartTests = this.tests[chartId];
521
- for (const test of chartTests) {
522
- for (const key in test) {
523
- if (key == "pvalue") {
524
- test[key].color = "#000";
525
- } else {
526
- const item = legendItems.find((item2) => item2.seriesId == test[key].id);
527
- test[key].color = item.color;
528
- test[key].text = item.text;
529
- }
530
- }
531
- }
532
- }
533
- }
534
- };
535
- var survivalInit = getCompInit(TdbSurvival);
536
- var componentInit = survivalInit;
537
- function setRenderers(self) {
538
- self.render = function() {
539
- const data = self.pj.tree.charts || [{ chartId: "No survival data" }];
540
- const chartDivs = self.dom.chartsDiv.selectAll(".pp-survival-chart").data(data, (d) => d.chartId);
541
- chartDivs.exit().remove();
542
- chartDivs.each(self.updateCharts);
543
- chartDivs.enter().each(self.addCharts);
544
- self.dom.holder.style("display", "inline-block");
545
- self.dom.chartsDiv.on("mouseover", self.mouseover).on("mouseout", self.mouseout);
546
- self.legendRenderer(self.settings.atRiskVisible ? [] : self.legendData);
547
- if (!self.hiddenData?.[0]?.items.length) self.dom.hiddenDiv.style("display", "none");
548
- else {
549
- self.dom.hiddenDiv.style("display", "");
550
- self.hiddenRenderer(self.hiddenData);
551
- }
552
- };
553
- const updateHiddenPvalues = (hiddenPvalues) => {
554
- self.app.dispatch({
555
- type: "plot_edit",
556
- id: self.id,
557
- config: {
558
- settings: {
559
- survival: {
560
- hiddenPvalues
561
- }
562
- }
563
- }
564
- });
565
- };
566
- const setActiveMenu = (bool) => self.activeMenu = bool;
567
- self.addCharts = function(chart) {
568
- const s = self.settings;
569
- setVisibleSerieses(chart, s);
570
- const div = select_default(this).append("div").attr("class", "pp-survival-chart").attr("data-testid", "sjpp-survival-plotDiv").style("opacity", chart.serieses ? 0 : 1).style("width", "fit-content").style("display", "inline-block").style("margin", s.chartMargin + "px").style("padding", "10px").style("top", 0).style("left", 0).style("text-align", "left").style("vertical-align", "top");
571
- div.append("div").style("width", s.svgw + 50 + "px").style("height", s.chartTitleDivHt + "px").style("text-align", "center").style("font-weight", "600").style("margin", "5px").append("div").attr("class", "sjpp-survival-title").attr("data-testid", "sjpp-survival-plotTitle").style("display", "inline-block").style("width", "fit-content").datum(chart).html((chart2) => chart2.chartId);
572
- if (chart.serieses) {
573
- const svg = div.append("svg").attr("class", "pp-survival-svg");
574
- renderSVG(svg, chart, s, 0);
575
- div.transition().duration(s.duration).style("opacity", 1);
576
- div.append("div").attr("class", "pp-survival-chartLegends").style("vertical-align", "top").style("margin", "10px 10px 10px 10px").style("display", "none");
577
- if (self.tests && chart.rawChartId in self.tests) {
578
- const holder = div.select(".pp-survival-chartLegends").style("display", "inline-block").append("div").style("margin-bottom", "30px");
579
- renderPvalues({
580
- title: "Group comparisons (log-rank test)",
581
- holder,
582
- plot: "survival",
583
- tests: self.tests[chart.rawChartId],
584
- s,
585
- bins: self.refs.bins,
586
- tip: self.app.tip,
587
- setActiveMenu,
588
- updateHiddenPvalues
589
- });
590
- }
591
- if (self.msg) {
592
- const fontSize = s.axisTitleFontSize ? s.axisTitleFontSize - 2 : 15;
593
- const holder = div.select(".pp-survival-chartLegends").style("display", "inline-block").append("div");
594
- holder.style("font-size", fontSize + "px").style("font-style", "italic").text(self.msg);
595
- }
596
- }
597
- };
598
- function setVisibleSerieses(chart, s) {
599
- chart.visibleSerieses = chart.serieses?.filter((series) => !s.hidden.includes(series.seriesId)) || [];
600
- const maxSeriesLabelLen = chart.visibleSerieses.reduce(
601
- (maxlen, a) => a.seriesLabel && a.seriesLabel.length > maxlen ? a.seriesLabel.length : maxlen,
602
- 0
603
- );
604
- const extraPaddingForNoOverlay = maxSeriesLabelLen === 0 ? s.atRiskNoOverlayExtraPadding : 0;
605
- chart.atRiskLabelWidth = s.atRiskVisible ? maxSeriesLabelLen * (s.axisTitleFontSize - 2) * 0.4 + s.atRiskLabelOffset + extraPaddingForNoOverlay : 0;
606
- }
607
- self.updateCharts = function(chart) {
608
- if (!chart.serieses) return;
609
- const s = self.settings;
610
- setVisibleSerieses(chart, s);
611
- const div = select_default(this);
612
- div.transition().duration(s.duration).style("width", "fit-content");
613
- div.select(".sjpp-survival-title").style("width", s.svgw + 50).style("height", s.chartTitleDivHt + "px").datum(chart.chartId).html(chart.chartId);
614
- div.selectAll(".sjpp-lock-icon").style("display", s.scale == "byChart" ? "block" : "none");
615
- div.selectAll(".sjpp-unlock-icon").style("display", s.scale == "byChart" ? "none" : "block");
616
- renderSVG(div.select("svg"), chart, s, s.duration);
617
- div.select(".pp-survival-chartLegends").style("display", "none").selectAll("*").remove();
618
- if (self.tests && chart.rawChartId in self.tests) {
619
- const holder = div.select(".pp-survival-chartLegends").style("display", "inline-block").append("div").style("margin-bottom", "30px");
620
- renderPvalues({
621
- title: "Group comparisons (log-rank test)",
622
- holder,
623
- plot: "survival",
624
- tests: self.tests[chart.rawChartId],
625
- s,
626
- bins: self.refs.bins,
627
- tip: self.app.tip,
628
- setActiveMenu,
629
- updateHiddenPvalues
630
- });
631
- }
632
- if (self.msg) {
633
- const fontSize = s.axisTitleFontSize ? s.axisTitleFontSize - 2 : 15;
634
- const holder = div.select(".pp-survival-chartLegends").style("display", "inline-block").append("div");
635
- holder.style("font-size", fontSize + "px").style("font-style", "italic").text(self.msg);
636
- }
637
- };
638
- function renderSVG(svg, chart, s, duration) {
639
- chart.svg = svg;
640
- const extraHeight = s.atRiskVisible ? s.axisTitleFontSize + 4 + chart.visibleSerieses.length * 2 * (s.axisTitleFontSize + 4) : 0;
641
- svg.transition().duration(duration).attr("width", s.svgw + chart.atRiskLabelWidth).attr("height", s.svgh + extraHeight).style("overflow", "visible").style("padding-left", "5px");
642
- const [mainG, seriesesG, axisG, xAxis, yAxis, xTitle, yTitle, atRiskG, plotRect, medianSurvivalG] = getSvgSubElems(svg);
643
- const xOffset = chart.atRiskLabelWidth + s.svgPadding.left + 10;
644
- mainG.attr("transform", "translate(" + xOffset + "," + s.svgPadding.top + ")");
645
- const setSeriesDataID = (series) => {
646
- return `sjpp-survival-series-${series.seriesLabel ?? series.seriesId ?? "unknown"}`;
647
- };
648
- const serieses = seriesesG.selectAll(".sjpp-survival-series").data(chart.visibleSerieses, (d) => d && d[0] ? d[0].seriesId : "");
649
- serieses.exit().remove();
650
- serieses.attr("data-testid", setSeriesDataID).each(function(series, i) {
651
- renderSeries(select_default(this), chart, series, i, s);
652
- });
653
- serieses.enter().append("g").attr("class", "sjpp-survival-series").attr("data-testid", setSeriesDataID).each(function(series, i) {
654
- renderSeries(select_default(this), chart, series, i, s);
655
- });
656
- renderAxes(xAxis, xTitle, yAxis, yTitle, s, chart);
657
- renderMedianSurvival(medianSurvivalG, chart, s);
658
- renderAtRiskG({
659
- g: atRiskG,
660
- s,
661
- chart,
662
- order: self.legendOrder,
663
- term2toColor: self.term2toColor,
664
- onSerieClick: self.legendClick
665
- });
666
- plotRect.attr("x", 0).attr("width", s.svgw - s.svgPadding.left - s.svgPadding.right).attr("y", 0).attr("height", s.svgh - s.svgPadding.top - s.svgPadding.bottom + s.xAxisOffset);
667
- svg.seriesTip.update({
668
- xScale: chart.xScale,
669
- xTitleLabel: s.xTitleLabel,
670
- decimals: s.seriesTipDecimals,
671
- serieses: chart.visibleSerieses.map((s2) => {
672
- const seriesLabel = `${s2.seriesLabel || "Probability"}:`;
673
- const color = self.term2toColor[s2.seriesId].adjusted || "#000";
674
- return {
675
- data: s2.data.map((d) => {
676
- return {
677
- x: d.x,
678
- html: `<span style='color: ${color}'>${seriesLabel} ${(100 * d.y).toFixed(2)}% (${(100 * d.lower).toFixed(2)} - ${(100 * d.upper).toFixed(
679
- 2
680
- )})</span>`
681
- };
682
- })
683
- };
684
- })
685
- });
686
- }
687
- function getSvgSubElems(svg) {
688
- let mainG, seriesesG, axisG, xAxis, yAxis, xTitle, yTitle, atRiskG, plotRect, line, medianSurvivalG;
689
- if (!svg.select(".sjpp-survival-mainG").size()) {
690
- mainG = svg.append("g").attr("class", "sjpp-survival-mainG");
691
- seriesesG = mainG.append("g").attr("class", "sjpcb-survival-seriesesG");
692
- medianSurvivalG = mainG.append("g").attr("class", "sjpp-survival-median");
693
- axisG = mainG.append("g").attr("class", "sjpp-survival-axis");
694
- xAxis = axisG.append("g").attr("class", "sjpp-survival-x-axis");
695
- yAxis = axisG.append("g").attr("class", "sjpp-survival-y-axis");
696
- xTitle = axisG.append("g").attr("class", "sjpp-survival-x-title");
697
- yTitle = axisG.append("g").attr("class", "sjpp-survival-y-title");
698
- atRiskG = mainG.append("g").attr("class", "sjpp-survival-atrisk");
699
- line = mainG.append("line").attr("class", "sjpcb-plot-tip-line").attr("stroke", "#000").attr("stroke-width", "1px");
700
- plotRect = mainG.append("rect").attr("class", "sjpcb-plot-tip-rect").style("fill", "transparent");
701
- } else {
702
- mainG = svg.select(".sjpp-survival-mainG");
703
- seriesesG = mainG.select(".sjpcb-survival-seriesesG");
704
- medianSurvivalG = mainG.select(".sjpp-survival-median");
705
- axisG = mainG.select(".sjpp-survival-axis");
706
- xAxis = axisG.select(".sjpp-survival-x-axis");
707
- yAxis = axisG.select(".sjpp-survival-y-axis");
708
- xTitle = axisG.select(".sjpp-survival-x-title");
709
- yTitle = axisG.select(".sjpp-survival-y-title");
710
- atRiskG = mainG.select(".sjpp-survival-atrisk");
711
- plotRect = mainG.select(".sjpcb-plot-tip-rect");
712
- line = mainG.select(".sjpcb-plot-tip-line");
713
- }
714
- if (!svg.seriesTip) {
715
- svg.seriesTip = getSeriesTip(line, plotRect, self.dom.tip);
716
- }
717
- return [mainG, seriesesG, axisG, xAxis, yAxis, xTitle, yTitle, atRiskG, plotRect, medianSurvivalG];
718
- }
719
- function renderSeries(g, chart, series, i, s) {
720
- let processedData = series.data;
721
- if (s.maxTimeToEvent) {
722
- processedData = series.data.filter((d) => d.x <= s.maxTimeToEvent);
723
- }
724
- g.selectAll("path").remove();
725
- g.append("path").attr("data-testid", `sjpp-survival-ci-${series.seriesLabel ?? series.seriesId ?? "unknown"}`).attr(
726
- "d",
727
- area_default().curve(stepAfter).x((c) => c.scaledX).y0((c) => c.scaledY[1]).y1((c) => c.scaledY[2])(processedData)
728
- ).style("display", s.ciVisible ? "" : "none").style("fill", self.term2toColor[series.seriesId].adjusted).style("opacity", "0.15").style("stroke", "none");
729
- renderSubseries(
730
- s,
731
- g,
732
- processedData.map((d) => {
733
- return {
734
- seriesId: d.seriesId,
735
- x: d.x,
736
- y: d.y,
737
- scaledX: d.scaledX,
738
- scaledY: d.scaledY[0],
739
- seriesName: "survival",
740
- seriesLabel: series.seriesLabel,
741
- nevent: d.nevent,
742
- ncensor: d.ncensor,
743
- nrisk: d.nrisk
744
- };
745
- })
746
- );
747
- renderSubseries(
748
- s,
749
- g.append("g"),
750
- processedData.map((d) => {
751
- return {
752
- seriesId: d.seriesId,
753
- x: d.x,
754
- y: d.lower,
755
- scaledX: d.scaledX,
756
- scaledY: d.scaledY[1],
757
- seriesName: "lower",
758
- seriesLabel: series.seriesLabel,
759
- nevent: d.nevent,
760
- ncensor: 0,
761
- // no censor marks for lower CI
762
- nrisk: d.nrisk
763
- };
764
- })
765
- );
766
- renderSubseries(
767
- s,
768
- g.append("g"),
769
- processedData.map((d) => {
770
- return {
771
- seriesId: d.seriesId,
772
- x: d.x,
773
- y: d.upper,
774
- scaledX: d.scaledX,
775
- scaledY: d.scaledY[2],
776
- seriesName: "upper",
777
- // no censor marks for upper CI
778
- seriesLabel: series.seriesLabel,
779
- nevent: d.nevent,
780
- ncensor: 0,
781
- nrisk: d.nrisk
782
- };
783
- })
784
- );
785
- }
786
- function renderSubseries(s, g, data) {
787
- g.selectAll("g").remove();
788
- const lineData = data.filter((d, i) => i === 0 || d.nevent || i === data.length - 1);
789
- const censoredData = data.filter((d) => d.ncensor);
790
- const seriesName = data[0].seriesName;
791
- const color = self.term2toColor[data[0].seriesId].adjusted;
792
- if (seriesName == "survival") {
793
- g.append("path").attr("data-testid", `sjpp-survival-curve-${data[0].seriesLabel ?? data[0].seriesId ?? "unknown"}`).attr("d", self.lineFxn(lineData)).style("fill", "none").style("stroke", color).style("opacity", 1).style("stroke-opacity", 1);
794
- }
795
- const subg1 = g.append("g").attr("class", "sjpp-survival-censored");
796
- const censored = subg1.selectAll(".sjpp-survival-censored-x").data(censoredData, (d) => d.x);
797
- censored.exit().remove();
798
- censored.attr("transform", (c) => `translate(${c.scaledX},${c.scaledY})`).style("stroke", color).style("display", "");
799
- censored.enter().append("path").attr("class", "sjpp-survival-censored-x").attr("transform", (c) => `translate(${c.scaledX},${c.scaledY})`).attr("d", self.symbol).style("fill", "transparent").style("fill-opacity", s.fillOpacity).style("stroke", color).style("display", "");
800
- }
801
- function renderAxes(xAxis, xTitle, yAxis, yTitle, s, chart) {
802
- let xTicks;
803
- if (s.xTickValues?.length) {
804
- chart.xTickValues = s.xTickValues.filter(
805
- (v) => v === 0 || v >= chart.xMin && v <= Math.min(s.maxTimeToEvent || chart.xMax, chart.xMax)
806
- );
807
- xTicks = axisBottom(chart.xScale).tickValues(chart.xTickValues);
808
- } else {
809
- chart.xTickValues = [];
810
- xTicks = axisBottom(chart.xScale).ticks(4).tickFormat((xval) => {
811
- chart.xTickValues.push(xval);
812
- return xval;
813
- });
814
- }
815
- const pixelOffset = -0.5;
816
- xAxis.attr(
817
- "transform",
818
- `translate(${pixelOffset}, ${s.svgh - s.svgPadding.top - s.svgPadding.bottom + s.xAxisOffset + pixelOffset})`
819
- ).call(xTicks);
820
- yAxis.attr("transform", `translate(${s.yAxisOffset + pixelOffset}, ${pixelOffset})`).call(axisLeft(linear().domain(chart.yScale.domain()).range(chart.yScale.range())).ticks(5));
821
- xTitle.select("text, title").remove();
822
- xTitle.attr(
823
- "transform",
824
- "translate(" + (s.svgw - s.svgPadding.left - s.svgPadding.right) / 2 + "," + (s.svgh - s.axisTitleFontSize - 4) + ")"
825
- ).append("text").style("text-anchor", "middle").style("font-size", s.axisTitleFontSize + "px").text(s.xTitleLabel);
826
- const yTitleLabel = "Probability of Survival";
827
- yTitle.select("text, title").remove();
828
- yTitle.attr(
829
- "transform",
830
- "translate(" + (-s.svgPadding.left / 2 - s.axisTitleFontSize) + "," + (s.svgh - s.svgPadding.top - s.svgPadding.bottom) / 2 + ")rotate(-90)"
831
- ).append("text").style("text-anchor", "middle").style("font-size", s.axisTitleFontSize + "px").text(yTitleLabel);
832
- }
833
- function renderMedianSurvival(g, chart, s) {
834
- g.selectAll("*").remove();
835
- if (!s.medianSurvivalVisible) return;
836
- const yMid = chart.yScale(0.5);
837
- const yBottom = chart.yScale(0);
838
- const getMedianPoint = (series) => {
839
- const data = s.maxTimeToEvent ? series.data.filter((d) => d.x <= s.maxTimeToEvent) : series.data;
840
- return data.find((d) => d.y <= 0.5);
841
- };
842
- const medianScaledXs = [];
843
- for (const series of chart.visibleSerieses) {
844
- const medianPoint = getMedianPoint(series);
845
- if (medianPoint) medianScaledXs.push(chart.xScale(medianPoint.x));
846
- }
847
- if (!medianScaledXs.length) return;
848
- g.append("line").attr("x1", 0).attr("y1", yMid).attr("x2", Math.max(...medianScaledXs)).attr("y2", yMid).attr("stroke", "#000").attr("stroke-width", 1).attr("stroke-dasharray", "4,4");
849
- for (const scaledX of medianScaledXs) {
850
- g.append("line").attr("x1", scaledX).attr("y1", yMid).attr("x2", scaledX).attr("y2", yBottom).attr("stroke", "#000").attr("stroke-width", 1).attr("stroke-dasharray", "4,4");
851
- }
852
- }
853
- self.getSymbol = function(size) {
854
- const s = size, h = s / 2;
855
- switch (self.settings.symbol) {
856
- case "x":
857
- return `M -${h},-${h} l ${s},${s} M ${h},-${h} l -${s},${s}`;
858
- case "vtick":
859
- return `M 0,-${h} L 0,${h}`;
860
- default:
861
- throw `Unrecognized survival plot symbol='${self.settings.symbol}'`;
862
- }
863
- };
864
- }
865
- function setInteractivity(self) {
866
- self.download = function(event) {
867
- const charts = self.getChartImages();
868
- const menu = new DownloadMenu(charts, self.state.config.term.term.name);
869
- menu.show(event.clientX, event.clientY, event.target);
870
- };
871
- self.getChartImages = function() {
872
- const charts = [];
873
- if (!self.pj.tree.charts) return charts;
874
- for (const chart of self.pj.tree.charts) {
875
- charts.push({ name: chart.chartId, svg: chart.svg });
876
- }
877
- return charts;
878
- };
879
- self.mouseover = function() {
880
- };
881
- self.mouseout = function() {
882
- if (self.activeMenu) return;
883
- self.app.tip.hide();
884
- };
885
- self.legendClick = function(d, x, y) {
886
- if (d === void 0) return;
887
- const hidden = self.settings.hidden.slice();
888
- const i = hidden.indexOf(d.seriesId);
889
- if (i == -1) {
890
- hidden.push(d.seriesId);
891
- self.showLegendItemMenu(d, hidden, x, y);
892
- } else {
893
- hidden.splice(i, 1);
894
- self.app.dispatch({
895
- type: "plot_edit",
896
- id: self.id,
897
- config: {
898
- settings: {
899
- survival: {
900
- customHidden: hidden
901
- }
902
- }
903
- }
904
- });
905
- }
906
- };
907
- self.showLegendItemMenu = function(d, hidden, x, y) {
908
- const term2 = self.state.config.term2?.term || null;
909
- const seriesLabel = term2?.values?.[d.seriesId]?.label || d.seriesId;
910
- const header = `<div style='padding-bottom:8px'><b>${seriesLabel}</b></div>`;
911
- const data = d.seriesId || d.seriesId === 0 ? d : { seriesId: d.id, dataId: d.dataId };
912
- if (!data.seriesId && !data.dataId) {
913
- if (!term2) {
914
- const label = self.dom.legendTip.clear().d.append("div").html("Edit color: ");
915
- const input = label.append("input").attr("type", "color").attr("value", self.settings.defaultColor).on("change", () => self.adjustColor(input.property("value"), d));
916
- self.dom.legendTip.show(x, y);
917
- }
918
- return;
919
- }
920
- const options = [];
921
- options.push({
922
- label: "Hide",
923
- callback: () => {
924
- menu.hide();
925
- self.app.dispatch({
926
- type: "plot_edit",
927
- id: self.id,
928
- config: {
929
- settings: {
930
- survival: {
931
- customHidden: hidden
932
- }
933
- }
934
- }
935
- });
936
- }
937
- });
938
- if (self.legendData[0]?.items.length > 1) {
939
- options.push({
940
- label: "Move&nbsp;",
941
- setInput: (holder) => {
942
- const legendIndex = self.legendOrder.indexOf(d.seriesId);
943
- if (legendIndex != 0)
944
- holder.append("button").html("up").on("click", () => {
945
- menu.hide();
946
- self.adjustLegendOrder(d, -1);
947
- });
948
- if (legendIndex < self.legendData[0]?.items.length - 1)
949
- holder.append("button").html("down").on("click", () => {
950
- menu.hide();
951
- self.adjustLegendOrder(d, 1);
952
- });
953
- }
954
- });
955
- }
956
- options.push({
957
- //label: 'Color',
958
- //callback: d => {}
959
- setInput: (holder) => {
960
- const label = holder.append("div");
961
- label.html("Edit color: ");
962
- const input = label.append("input").attr("type", "color").attr("value", self.term2toColor[d.seriesId].hex).on("change", () => self.adjustColor(input.property("value"), d));
963
- }
964
- });
965
- if (!options.length) return;
966
- const menu = self.dom.legendTip.clear();
967
- menu.d.append("div").html(header);
968
- menu.d.append("div").selectAll("div").data(options).enter().append("div").attr("class", (d2) => d2.label == "Hide" ? "sja_menuoption" : "sja_menuoption_not_interactive").on("click", (event, c) => {
969
- if (c.setInput) return;
970
- self.app.tip.hide();
971
- c.callback(d);
972
- }).each(function(d2) {
973
- const div = select_default(this);
974
- if (d2.label) div.append("div").style("display", "inline-block").html(d2.label);
975
- if (d2.setInput)
976
- d2.setInput(
977
- div.append("div").style("display", "inline-block")
978
- //.style('margin-left', '10px')
979
- );
980
- });
981
- menu.show(x, y);
982
- };
983
- self.adjustLegendOrder = (d, increment) => {
984
- const oldIndex = self.legendOrder.indexOf(d.seriesId);
985
- if (oldIndex == -1) return;
986
- let newIndex = oldIndex + increment;
987
- newIndex = Math.max(0, Math.min(self.legendOrder.length - 1, newIndex));
988
- self.legendOrder.splice(oldIndex, 1);
989
- self.legendOrder.splice(newIndex, 0, d.seriesId);
990
- self.app.dispatch({
991
- type: "app_refresh"
992
- });
993
- self.app.tip.hide();
994
- };
995
- self.adjustColor = (value, d) => {
996
- const color = rgb(value).formatHex();
997
- const t2 = self.state.config.term2;
998
- if (!t2) {
999
- self.app.dispatch({
1000
- type: "plot_edit",
1001
- id: self.id,
1002
- config: { settings: { survival: { defaultColor: color } } }
1003
- });
1004
- } else {
1005
- const term2 = structuredClone(t2);
1006
- if (!term2.values) term2.values = {};
1007
- const values = term2.values;
1008
- if (!values[d.seriesId]) values[d.seriesId] = {};
1009
- if (!("key" in values[d.seriesId])) values[d.seriesId].key = d.seriesId;
1010
- values[d.seriesId].color = color;
1011
- self.app.dispatch({
1012
- type: "plot_edit",
1013
- id: self.id,
1014
- config: {
1015
- term2
1016
- }
1017
- });
1018
- }
1019
- self.app.tip.hide();
1020
- };
1021
- self.showMenuForSelectedChart = function() {
1022
- self.dom.tip.clear();
1023
- self.activeMenu = true;
1024
- self.dom.tip.showunder(this).d.append("button").html("Download SVG").on("click", () => {
1025
- if (!self.state) return;
1026
- const chartDiv = select_default(this.closest(".pp-survival-chart"));
1027
- downloadChart(
1028
- chartDiv.select(".sjpp-survival-mainG"),
1029
- "Survival_Plot",
1030
- chartDiv.node()
1031
- // use to get computed styles
1032
- );
1033
- });
1034
- };
1035
- }
1036
- async function getPlotConfig(opts, app) {
1037
- if (!opts.term) throw "survival getPlotConfig: opts.term{} missing";
1038
- try {
1039
- await fillTermWrapper(opts.term, app.vocabApi);
1040
- if (opts.term2)
1041
- await fillTermWrapper(opts.term2, app.vocabApi, opts.term2.bins || opts.term2.q ? void 0 : t0_t2_defaultQ);
1042
- if (opts.term0)
1043
- await fillTermWrapper(opts.term0, app.vocabApi, opts.term0.bins || opts.term0.q ? void 0 : t0_t2_defaultQ);
1044
- } catch (e) {
1045
- throw `${e} [survival getPlotConfig()]`;
1046
- }
1047
- const config = {
1048
- controlLabels: Object.assign({}, defaultUiLabels, app.vocabApi.termdbConfig.uiLabels || {}),
1049
- settings: {
1050
- controls: {
1051
- term2: null,
1052
- // the previous overlay value may be displayed as a convenience for toggling
1053
- term0: null
1054
- },
1055
- survival: {
1056
- radius: 5,
1057
- ciVisible: true,
1058
- medianSurvivalVisible: false,
1059
- fill: "#fff",
1060
- stroke: "#000",
1061
- symbol: "vtick",
1062
- // 'x', 'vtick'
1063
- fillOpacity: 0,
1064
- chartMargin: 10,
1065
- svgw: 400,
1066
- svgh: 300,
1067
- numUnitInOneYear: 1,
1068
- timeUnit: "years",
1069
- atRiskVisible: true,
1070
- atRiskLabelOffset: -20,
1071
- atRiskNoOverlayExtraPadding: 30,
1072
- // Extra padding when there's no overlay term to prevent "Number at risk" text overlap
1073
- xTickValues: [],
1074
- // if undefined or empty, will be ignored
1075
- seriesTipDecimals: 1,
1076
- svgPadding: {
1077
- top: 20,
1078
- left: 55,
1079
- right: 20,
1080
- bottom: 50
1081
- },
1082
- axisTitleFontSize: 16,
1083
- xAxisOffset: 5,
1084
- yAxisOffset: -5,
1085
- hiddenPvalues: [],
1086
- defaultColor: "#2077b4"
1087
- }
1088
- }
1089
- };
1090
- const overrides = app.vocabApi.termdbConfig.survival || {};
1091
- copyMerge(config.settings.survival, overrides.settings);
1092
- return copyMerge(config, opts);
1093
- }
1094
- function getPj(self) {
1095
- const pj = new import_partjson.default({
1096
- template: {
1097
- yMin: ">=yMin()",
1098
- yMax: "<=yMax()",
1099
- charts: [
1100
- {
1101
- chartId: "@key",
1102
- rawChartId: "$chartId",
1103
- xMin: ">$time",
1104
- xMax: "<$time",
1105
- "__:xScale": "=xScale()",
1106
- "__:yScale": "=yScale()",
1107
- yMin: ">=yMin()",
1108
- yMax: "<=yMax()",
1109
- serieses: [
1110
- {
1111
- chartId: "@parent.@parent.@key",
1112
- seriesId: "@key",
1113
- "__:seriesLabel": "=seriesLabel()",
1114
- data: [
1115
- {
1116
- "__:seriesId": "@parent.@parent.seriesId",
1117
- //color: "$color",
1118
- x: "$time",
1119
- y: "$survival",
1120
- lower: "$lower",
1121
- upper: "$upper",
1122
- "_1:scaledX": "=scaledX()",
1123
- "_1:scaledY": "=scaledY()",
1124
- nevent: "$nevent",
1125
- ncensor: "$ncensor",
1126
- nrisk: "$nrisk"
1127
- },
1128
- "=timeCensored()"
1129
- ]
1130
- },
1131
- "$seriesId"
1132
- ],
1133
- "@done()": "=sortSerieses()"
1134
- },
1135
- "=chartTitle()"
1136
- ],
1137
- "@done()": "=sortCharts()"
1138
- },
1139
- "=": {
1140
- chartTitle(row) {
1141
- if (!row.chartId || row.chartId == "-") {
1142
- const termNum = self.state.config.term.term.type == "survival" ? "term" : "term2";
1143
- return self.state.config[termNum].term.name;
1144
- }
1145
- const t0 = self.state.config.term0;
1146
- if (!t0 || !t0.term.values) return row.chartId;
1147
- if (t0.q?.type == "predefined-groupset" || t0.q?.type == "custom-groupset") return row.chartId;
1148
- const value = self.state.config.term0.term.values[row.chartId];
1149
- return value && value.label ? value.label : row.chartId;
1150
- },
1151
- seriesLabel(row, context) {
1152
- const t2 = self.state.config.term2;
1153
- if (!t2) return;
1154
- const seriesId = context.self.seriesId;
1155
- if (t2?.q?.type == "predefined-groupset" || t2?.q?.type == "custom-groupset") return seriesId;
1156
- if (t2 && t2.term.values && seriesId in t2.term.values) return t2.term.values[seriesId].label;
1157
- if (isNumericTerm(t2.term)) {
1158
- return t2.term.name + " " + seriesId;
1159
- }
1160
- return seriesId;
1161
- },
1162
- timeCensored(row) {
1163
- return row.time + "-" + row.ncensor;
1164
- },
1165
- y(row, context) {
1166
- const seriesId = context.context.parent.seriesId;
1167
- return seriesId == "CI" ? [row.lower, row.upper] : row[seriesId];
1168
- },
1169
- yMin(row) {
1170
- return row.lower;
1171
- },
1172
- yMax(row) {
1173
- return row.upper;
1174
- },
1175
- xScale(_, context) {
1176
- const s = self.settings;
1177
- return linear().domain([0, Math.min(s.maxTimeToEvent || context.self.xMax, context.self.xMax)]).range([0, s.svgw - s.svgPadding.left - s.svgPadding.right]);
1178
- },
1179
- scaledX(_, context) {
1180
- return context.context.context.context.parent.xScale(context.self.x);
1181
- },
1182
- scaledY(_, context) {
1183
- const yScale = context.context.context.context.parent.yScale;
1184
- const s = context.self;
1185
- return [yScale(s.y), yScale(s.lower), yScale(s.upper)];
1186
- },
1187
- yScale() {
1188
- const s = self.settings;
1189
- const domain = [1.05, 0];
1190
- return linear().domain(domain).range([0, s.svgh - s.svgPadding.top - s.svgPadding.bottom]);
1191
- },
1192
- sortSerieses(result) {
1193
- for (const series of result.serieses) {
1194
- series.data.sort((a, b) => a.x < b.x ? -1 : 1);
1195
- }
1196
- if (self.refs.orderedKeys) {
1197
- const s = self.refs.orderedKeys.series;
1198
- result.serieses.sort((a, b) => s.indexOf(a.seriesId) - s.indexOf(b.seriesId));
1199
- }
1200
- if (self.refs.bins) {
1201
- const labelOrder = self.refs.bins.map((b) => b.label);
1202
- result.serieses.sort((a, b) => labelOrder.indexOf(a.seriesId) - labelOrder.indexOf(b.seriesId));
1203
- }
1204
- },
1205
- sortCharts(result) {
1206
- if (!self.refs.orderedKeys) return;
1207
- const c = self.refs.orderedKeys.chart;
1208
- result.charts.sort(
1209
- (a, b) => (c.indexOf(a.chartId) == -1 ? c.indexOf(a.rawChartId) : c.indexOf(a.chartId)) - (c.indexOf(b.chartId) == -1 ? c.indexOf(b.rawChartId) : c.indexOf(b.chartId))
1210
- );
1211
- }
1212
- }
1213
- });
1214
- return pj;
1215
- }
1216
-
1217
- export {
1218
- t0_t2_defaultQ,
1219
- survivalInit,
1220
- componentInit,
1221
- getPlotConfig
1222
- };
1223
- //# sourceMappingURL=chunk-AZ47Q7BX.js.map