-
Notifications
You must be signed in to change notification settings - Fork 29
/
Copy pathgosling-track.ts
1437 lines (1237 loc) · 57.4 KB
/
gosling-track.ts
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
import type * as PIXI from 'pixi.js';
import * as uuid from 'uuid';
import { isEqual, sampleSize, uniqBy } from 'lodash-es';
import type { ScaleLinear } from 'd3-scale';
import type {
SingleTrack,
OverlaidTrack,
Datum,
EventStyle,
GenomicPosition,
Assembly,
ValueExtent,
Range
} from '@gosling-lang/gosling-schema';
import { type MouseEventData, isPointInsideDonutSlice } from '../gosling-track/gosling-mouse-event';
import { BamDataFetcher, type TabularDataFetcher } from '@data-fetchers';
import type { Tile as _Tile, TileData, TileDataBase } from '@higlass/services';
import { LinearBrushModel } from '@gosling-lang/gosling-brush';
import { getTheme } from 'gosling-theme';
import { getTabularData } from './data-abstraction';
import type { CompleteThemeDeep } from '../../core/utils/theme';
import { drawMark, drawPostEmbellishment, drawPreEmbellishment } from '../../core/mark';
import { GoslingTrackModel } from './gosling-track-model';
import { validateTrack } from '@gosling-lang/gosling-schema';
import { shareScaleAcrossTracks } from '../../core/utils/scales';
import { resolveSuperposedTracks } from '../../core/utils/overlay';
import colorToHex from '../../core/utils/color-to-hex';
import {
aggregateCoverage,
calculateData,
concatString,
displace,
filterData,
calculateGenomicLength,
parseSubJSON,
replaceString,
splitExon,
inferSvType
} from '../../core/utils/data-transform';
import { publish } from '../../api/pubsub';
import { getRelativeGenomicPosition } from '../../core/utils/assembly';
import { getTextStyle } from '../../core/utils/text-style';
import {
Is2DTrack,
IsChannelDeep,
IsMouseEventsDeep,
IsXAxis,
isTabularDataFetcher,
hasDataTransform
} from '@gosling-lang/gosling-schema';
import { HIGLASS_AXIS_SIZE } from '../../compiler/higlass-model';
import { flatArrayToPairArray } from '../../core/utils/array';
import { createPluginTrack, type PluginTrackFactory, type TrackConfig } from '../../core/utils/define-plugin-track';
// Set `true` to print in what order each function is called
export const PRINT_RENDERING_CYCLE = false;
// For using libraries, refer to https://github.com/higlass/higlass/blob/f82c0a4f7b2ab1c145091166b0457638934b15f3/app/scripts/configs/available-for-plugins.js
// `getTilePosAndDimensions()` definition: https://github.com/higlass/higlass/blob/1e1146409c7d7c7014505dd80d5af3e9357c77b6/app/scripts/Tiled1DPixiTrack.js#L133
// Refer to the following already supported graphics:
// https://github.com/higlass/higlass/blob/54f5aae61d3474f9e868621228270f0c90ef9343/app/scripts/PixiTrack.js#L115
const DEFAULT_MOUSE_EVENT_STYLE: Required<EventStyle> = {
stroke: 'black',
strokeWidth: 1,
strokeOpacity: 1,
color: 'none',
opacity: 1,
arrange: 'front'
};
interface GoslingTrackOptions {
/**
* Track ID specified by users
*/
id: string;
/**
* Track IDs that are superposed with this track, containing the id of this track itself
*/
siblingIds: string[];
spec: SingleTrack | OverlaidTrack;
theme: CompleteThemeDeep;
showMousePosition?: boolean;
}
/** Tile data used in Gosling data fetchers */
interface TabularTileData extends TileDataBase {
tabularData: Datum[];
}
/** Mutated type of `Tile` that includes Gosling's tile data, i.e., tabular tile data */
export interface Tile extends Omit<_Tile, 'tileData'> {
tileData: TileData | TabularTileData;
}
interface ProcessedTileInfo {
/** Single tile can contain multiple gosling models if multiple tracks are superposed */
goslingModels: GoslingTrackModel[];
tabularData: Datum[];
/** Flag variable that indicate that rendering of this tile should be skipped */
skipRendering: boolean;
}
/** Information about the rendered color legend */
export interface DisplayedLegend {
domain: ValueExtent;
range: Range;
}
function initProcessedTileInfo(): ProcessedTileInfo {
return { goslingModels: [], tabularData: [], skipRendering: false };
}
const config: TrackConfig<GoslingTrackOptions> = {
type: 'gosling-track',
datatype: ['multivec', 'epilogos'],
orientation: '1d-horizontal',
// @ts-expect-error missing default spec
defaultOptions: {
// TODO: Are any of these used?
// labelPosition: 'none',
// labelColor: 'black',
// labelTextOpacity: 0.4,
// trackBorderWidth: 0,
// trackBorderColor: 'black',
// backgroundColor: 'white',
// barBorder: false,
// sortLargestOnTop: true,
// axisPositionHorizontal: 'left',
theme: getTheme('light')
}
};
const factory: PluginTrackFactory<Tile, GoslingTrackOptions> = (HGC, context, options) => {
// Services
const { tileProxy } = HGC.services;
const { BarTrack } = HGC.tracks;
/* Custom loading label */
const loadingTextStyle = getTextStyle({ color: 'black', size: 12 });
/**
* The main plugin track in Gosling. This is a versetile plugin track for HiGlass which relies on GoslingTrackModel
* to keep track of mouse event and channel scales.
*/
class GoslingTrackClass extends BarTrack<Tile, typeof options> {
/* *
*
* Properties
*
* */
tileSize: number;
mRangeBrush: LinearBrushModel;
#assembly?: Assembly; // Used to get the relative genomic position
#processedTileInfo: Record<string, ProcessedTileInfo>;
firstDraw = true; // False if draw has been called once already. Used with onNewTrack API. Public because used in draw()
// Used in mark/legend.ts
gLegend? = HGC.libraries.d3Selection.select(context.svgElement).append('g');
displayedLegends: DisplayedLegend[] = []; // Store the color legends added so far so that we can avoid overlaps and redundancy
// Used in mark/text.ts
textGraphics: unknown[] = [];
textsBeingUsed = 0;
// Mouse fields
pMouseHover = new HGC.libraries.PIXI.Graphics();
pMouseSelection = new HGC.libraries.PIXI.Graphics();
#mouseDownX = 0;
#mouseDownY = 0;
#isRangeBrushActivated = false;
#gBrush = HGC.libraries.d3Selection.select(context.svgElement).append('g');
#loadingTextStyleObj = new HGC.libraries.PIXI.TextStyle(loadingTextStyle);
#loadingTextBg = new HGC.libraries.PIXI.Graphics();
#loadingText = new HGC.libraries.PIXI.Text('', loadingTextStyle);
prevVisibleAndFetchedTiles?: Tile[];
/* *
*
* Constructor
*
* */
constructor() {
super(context, options);
context.dataFetcher.track = this;
this.#processedTileInfo = {};
this.#assembly = this.options.spec.assembly;
// Add unique IDs to each of the overlaid tracks that will be rendered independently.
if ('overlay' in this.options.spec) {
this.options.spec.overlay = (this.options.spec as OverlaidTrack).overlay.map(o => {
return { ...o, _renderingId: uuid.v1() };
});
} else {
this.options.spec._renderingId = uuid.v1();
}
this.fetchedTiles = {};
this.tileSize = this.tilesetInfo?.tile_size ?? 1024;
const { valid, errorMessages } = validateTrack(this.options.spec);
if (!valid) {
console.warn('The specification of the following track is invalid', errorMessages, this.options.spec);
}
// Graphics for highlighting visual elements under the cursor
this.pMain.addChild(this.pMouseHover);
this.pMain.addChild(this.pMouseSelection);
// Enable click event
this.pMask.interactive = true;
this.mRangeBrush = new LinearBrushModel(this.#gBrush, HGC.libraries, this.options.spec.style?.brush);
this.mRangeBrush.on('brush', this.#onRangeBrush.bind(this));
this.pMask.on('mousedown', (e: PIXI.InteractionEvent) => {
const { x, y } = e.data.getLocalPosition(this.pMain);
this.#onMouseDown(x, y, e.data.originalEvent.altKey);
});
this.pMask.on('mouseup', (e: PIXI.InteractionEvent) => {
const { x, y } = e.data.getLocalPosition(this.pMain);
this.#onMouseUp(x, y);
});
this.pMask.on('mousemove', (e: PIXI.InteractionEvent) => {
const { x } = e.data.getLocalPosition(this.pMain);
this.#onMouseMove(x);
});
this.pMask.on('mouseout', this.#onMouseOut.bind(this));
this.flipText = this.options.spec.orientation === 'vertical';
// Remove a mouse graphic if created by a parent, and draw ourselves.
// See https://github.com/higlass/higlass/blob/38f0c4415f0595c3b9d685a754d6661dc9612f7c/app/scripts/utils/show-mouse-position.js#L28
if (this.hideMousePosition) {
this.hideMousePosition();
this.hideMousePosition = undefined;
}
if (this.options?.showMousePosition && !this.hideMousePosition) {
this.hideMousePosition = HGC.utils.showMousePosition(
this,
Is2DTrack(resolveSuperposedTracks(this.options.spec)[0]),
this.isShowGlobalMousePosition()
);
}
// We do not use HiGlass' trackNotFoundText
this.pLabel.removeChild(this.trackNotFoundText);
this.#loadingText.anchor.x = 1;
this.#loadingText.anchor.y = 1;
this.pLabel.addChild(this.#loadingTextBg);
this.pLabel.addChild(this.#loadingText);
// This improves the arc/link rendering performance
HGC.libraries.PIXI.GRAPHICS_CURVES.adaptive = this.options.spec.style?.enableSmoothPath ?? false;
if (HGC.libraries.PIXI.GRAPHICS_CURVES.adaptive) {
HGC.libraries.PIXI.GRAPHICS_CURVES.maxLength = 1;
HGC.libraries.PIXI.GRAPHICS_CURVES.maxSegments = 2048 * 10;
}
}
/* *
*
* Rendering Cycle Methods
*
* */
/**
* Draw all tiles from the bottom. Called from TiledPixiTrack constructor, so all methods called must be
* public. https://github.com/higlass/higlass/blob/387a03e877dcfa4c2cfeabc0869375b58c0b362d/app/scripts/TiledPixiTrack.js#L216
* Overrides draw() in BarTrack.
* This means some class properties can be still `undefined`.
*/
override draw() {
if (PRINT_RENDERING_CYCLE) console.warn('draw()');
this.clearMouseEventData();
this.textsBeingUsed = 0;
this.pMouseHover?.clear();
const processTilesAndDraw = () => {
// Should we force to process all tiles?
// For BAM, yes, since all tiles are stored in a single tile and visible tiles had been changed.
const isBamDataFetcher = this.dataFetcher instanceof BamDataFetcher;
// Preprocess all tiles at once so that we can share scales across tiles.
this.processAllTiles(isBamDataFetcher);
// This function calls `drawTile` on each tile.
super.draw();
// Record tiles so that we ignore loading same tiles again
this.prevVisibleAndFetchedTiles = this.visibleAndFetchedTiles();
};
if (
isTabularDataFetcher(this.dataFetcher) &&
!isEqual(this.visibleAndFetchedTiles(), this.prevVisibleAndFetchedTiles)
) {
this.updateTileAsync(this.dataFetcher as TabularDataFetcher<Datum>, processTilesAndDraw);
} else {
processTilesAndDraw();
}
// Based on the updated marks, update range selection
this.mRangeBrush?.drawBrush(true);
// Publish onNewTrack if this is the first draw
if (this.firstDraw) {
this.#publishOnNewTrack();
this.firstDraw = false;
}
}
/*
* Do whatever is necessary before rendering a new tile. This function is called from `receivedTiles()`.
* Overrides initTile in BarTrack
* (Refer to https://github.com/higlass/higlass/blob/54f5aae61d3474f9e868621228270f0c90ef9343/app/scripts/HorizontalLine1DPixiTrack.js#L50)
*/
override initTile(tile: Tile) {
if (PRINT_RENDERING_CYCLE) console.warn('initTile(tile)');
// Since `super.initTile(tile)` prints warning, we call `drawTile` ourselves without calling
// `super.initTile(tile)`.
this.drawTile(tile);
}
override updateTile(/* tile: Tile */) {} // Never mind about this function for the simplicity.
override renderTile(/* tile: Tile */) {} // Never mind about this function for the simplicity.
/**
* Display a tile upon receiving a new one or when explicitly called by a developer, e.g., calling
* `this.draw()`. Overrides drawTile in BarTrack
*/
override drawTile(tile: Tile) {
if (PRINT_RENDERING_CYCLE) console.warn('drawTile(tile)');
tile.drawnAtScale = this._xScale.copy(); // being used in `super.draw()`
const tileInfo = this.#processedTileInfo[tile.tileId];
if (!tileInfo) {
// We do not have a track model prepared to visualize
return;
}
tile.graphics?.clear();
tile.graphics?.removeChildren();
// This is only to render embellishments only once.
// TODO: Instead of rendering and removing for every tiles, render pBorder only once
this.pBackground.clear();
this.pBackground.removeChildren();
this.pBorder.clear();
this.pBorder.removeChildren();
this.displayedLegends = [];
// Because a single tile contains one track or multiple tracks overlaid, we draw marks and embellishments
// for each GoslingTrackModel
tileInfo.goslingModels.forEach((model: GoslingTrackModel) => {
// check visibility condition
const trackWidth = this.dimensions[0];
const zoomLevel = this._xScale.invert(trackWidth) - this._xScale.invert(0);
if (!model.trackVisibility({ zoomLevel })) {
return;
}
drawPreEmbellishment(HGC, this, tile, model, this.options.theme);
drawMark(HGC, this, tile, model);
drawPostEmbellishment(HGC, this, tile, model, this.options.theme);
});
this.forceDraw();
}
/**
* Render this track again using a new option when a user changed the option. Overrides rerender in BarTrack.
*/
override rerender(newOptions: GoslingTrackOptions) {
if (PRINT_RENDERING_CYCLE) console.warn('rerender(options)');
this.options = newOptions;
if (this.options.spec.layout === 'circular') {
// TODO (May-27-2022): remove the following line when we support a circular brush.
// If the spec is changed to use the circular layout, we remove the current linear brush
// because circular brush is not supported.
this.mRangeBrush.remove();
}
this.clearMouseEventData();
this.textsBeingUsed = 0;
this.processAllTiles(true);
this.draw();
this.forceDraw();
}
/**
* Clears MouseEventModel from each GoslingTrackModel. Must be a public method because it is called from draw()
*/
clearMouseEventData() {
this.visibleAndFetchedGoslingModels().forEach(model => model.getMouseEventModel().clear());
}
/**
* Collect all gosling models that correspond to the tiles that are both visible and fetched.
*/
visibleAndFetchedGoslingModels() {
return this.visibleAndFetchedTiles().flatMap(
tile => this.#processedTileInfo[tile.tileId]?.goslingModels ?? []
);
}
/**
* End of the rendering cycle. This function is called when the track is removed entirely.
*/
override remove() {
super.remove();
if (this.gLegend) {
this.gLegend.remove();
this.gLegend = undefined;
}
this.mRangeBrush.remove();
}
/*
* Rerender all tiles when track size is changed. Overrides method in TiledPixiTrack
* (Refer to https://github.com/higlass/higlass/blob/54f5aae61d3474f9e868621228270f0c90ef9343/app/scripts/PixiTrack.js#L186).
*/
override setDimensions(newDimensions: [number, number]) {
if (PRINT_RENDERING_CYCLE) console.warn('setDimensions()');
super.setDimensions(newDimensions); // This simply updates `this._xScale` and `this._yScale`
this.mRangeBrush.setSize(newDimensions[1]);
}
/**
* Record new position.
*/
override setPosition(newPosition: [number, number]) {
super.setPosition(newPosition); // This simply changes `this.position`
[this.pMain.position.x, this.pMain.position.y] = this.position;
this.mRangeBrush.setOffset(...newPosition);
}
/**
* A function to redraw this track. Typically called when an asynchronous event occurs (i.e. tiles loaded)
* (Refer to https://github.com/higlass/higlass/blob/54f5aae61d3474f9e868621228270f0c90ef9343/app/scripts/TiledPixiTrack.js#L71)
*/
forceDraw() {
this.animate();
}
/**
* Called when location or zoom level has been changed by click-and-drag interaction
* (https://github.com/higlass/higlass/blob/54f5aae61d3474f9e868621228270f0c90ef9343/app/scripts/HorizontalLine1DPixiTrack.js#L215)
* For brushing, refer to https://github.com/higlass/higlass/blob/caf230b5ee41168ea491572618612ac0cc804e5a/app/scripts/HeatmapTiledPixiTrack.js#L1493
*/
override zoomed(newXScale: ScaleLinear<number, number>, newYScale: ScaleLinear<number, number>) {
if (PRINT_RENDERING_CYCLE) console.warn('zoomed()');
const range = this.mRangeBrush.getRange();
this.mRangeBrush.updateRange(
range ? [newXScale(this._xScale.invert(range[0])), newXScale(this._xScale.invert(range[1]))] : null
);
this.xScale(newXScale);
this.yScale(newYScale);
this.refreshTiles();
this.draw();
this.forceDraw();
// Publish the new genomic axis domain
const genomicRange = newXScale
.domain()
.map(absPos => getRelativeGenomicPosition(absPos, this.#assembly, true)) as [
GenomicPosition,
GenomicPosition
];
publish('location', {
id: context.viewUid,
genomicRange: genomicRange
});
}
/* *
*
* Tile and data processing methods
*
* */
/**
* Gets all tiles and generates tabular data and GoslingTrackModels for each tile. Called by this.draw(), so
* this method must be public.
* @param force if true then tabular data gets regenerated
*/
processAllTiles(force = false) {
this.tileSize = this.tilesetInfo?.tile_size ?? 1024;
const tiles = this.visibleAndFetchedTiles();
// generated tabular data
tiles.forEach(tile => this.#generateTabularData(tile, force));
// combine tabular data to the first tile if needed
this.combineAllTilesIfNeeded();
// apply data transforms to the tabular data and generate track models
const models = tiles.flatMap(tile => this.transformDataAndCreateModels(tile));
shareScaleAcrossTracks(models);
const flatTileData = ([] as Datum[]).concat(...models.map(d => d.data()));
if (flatTileData.length !== 0) {
this.options.siblingIds.forEach(id => publish('rawData', { id, data: flatTileData }));
}
}
/**
* This is currently for testing the new way of rendering visual elements. Called by this.draw()
*/
async updateTileAsync<T extends Datum>(tabularDataFetcher: TabularDataFetcher<T>, callback: () => void) {
if (!this.tilesetInfo) return;
const tiles = this.visibleAndFetchedTiles();
const tabularData = await tabularDataFetcher.getTabularData(Object.values(tiles).map(x => x.remoteId));
const tilesetInfo = this.tilesetInfo;
tiles.forEach((tile, i) => {
if (i === 0) {
const [refTile] = HGC.utils.trackUtils.calculate1DVisibleTiles(tilesetInfo, this._xScale);
tile.tileData.zoomLevel = refTile[0];
tile.tileData.tilePos = [refTile[1], refTile[1]];
(tile.tileData as TabularTileData).tabularData = tabularData;
} else {
(tile.tileData as TabularTileData).tabularData = [];
}
});
callback();
}
/**
* Overrides method in Tiled1DPixiTrack. It is called in the constructor, `super(context, options)`.
* So be aware to use defined variables.
*/
override calculateVisibleTiles() {
if (!this.tilesetInfo) return;
if (isTabularDataFetcher(this.dataFetcher)) {
const tiles = HGC.utils.trackUtils.calculate1DVisibleTiles(this.tilesetInfo, this._xScale);
const maxTileWith =
this.tilesetInfo.max_tile_width ?? this.dataFetcher.MAX_TILE_WIDTH ?? Number.MAX_SAFE_INTEGER;
for (const tile of tiles) {
const { tileWidth } = this.getTilePosAndDimensions(tile[0], [tile[1], tile[1]]);
this.forceDraw();
if (tileWidth > maxTileWith) {
return;
}
}
this.setVisibleTiles(tiles);
} else {
if (!this.tilesetInfo) {
// if we don't know anything about this dataset, no point in trying to get tiles
return;
}
// calculate the zoom level given the scales and the data bounds
const zoomLevel = this.calculateZoomLevel();
if ('resolutions' in this.tilesetInfo) {
const sortedResolutions = this.tilesetInfo.resolutions
.map((x: number) => +x)
.sort((a: number, b: number) => b - a);
const xTiles = tileProxy.calculateTilesFromResolution(
sortedResolutions[zoomLevel],
this._xScale,
this.tilesetInfo.min_pos[0],
this.tilesetInfo.max_pos[0]
);
let yTiles: number[] | undefined;
if (Is2DTrack(resolveSuperposedTracks(this.options.spec)[0])) {
// it makes sense only when the y-axis is being used for a genomic field
yTiles = tileProxy.calculateTilesFromResolution(
sortedResolutions[zoomLevel],
this._yScale,
this.tilesetInfo.min_pos[0],
this.tilesetInfo.max_pos[0]
);
}
const tiles = GoslingTrackClass.#tilesToId(xTiles, yTiles, zoomLevel);
this.setVisibleTiles(tiles);
} else {
const xTiles = tileProxy.calculateTiles(
zoomLevel,
this.relevantScale(),
this.tilesetInfo.min_pos[0],
this.tilesetInfo.max_pos[0],
this.tilesetInfo.max_zoom,
this.tilesetInfo.max_width
);
let yTiles: number[] | undefined;
if (Is2DTrack(resolveSuperposedTracks(this.options.spec)[0])) {
// it makes sense only when the y-axis is being used for a genomic field
yTiles = tileProxy.calculateTiles(
zoomLevel,
this._yScale,
this.tilesetInfo.min_pos[1],
this.tilesetInfo.max_pos[1],
this.tilesetInfo.max_zoom,
// @ts-expect-error what is max_width1?
this.tilesetInfo.max_width1 ?? this.tilesetInfo.max_width
);
}
const tiles = GoslingTrackClass.#tilesToId(xTiles, yTiles, zoomLevel);
this.setVisibleTiles(tiles);
}
}
}
/**
* Convert tile positions to tile IDs
*/
static #tilesToId(
xTiles: number[],
yTiles: number[] | undefined,
zoomLevel: number
): [number, number][] | [number, number, number][] {
if (!yTiles) {
// this means only the `x` axis is being used
return xTiles.map(x => [zoomLevel, x]);
}
// this means both `x` and `y` axes are being used together
const tiles: [number, number, number][] = [];
xTiles.forEach(x => yTiles.forEach(y => tiles.push([zoomLevel, x, y])));
return tiles;
}
/**
* Get the tile's position in its coordinate system. Overrides method in Tiled1DPixiTrack.
*/
override getTilePosAndDimensions(zoomLevel: number, tilePos: [number, number]) {
if (!this.tilesetInfo) {
throw Error('tilesetInfo not parsed');
}
if ('resolutions' in this.tilesetInfo) {
const sortedResolutions = this.tilesetInfo.resolutions
.map((x: number) => +x)
.sort((a: number, b: number) => b - a);
// A resolution specifies the number of BP per bin
const chosenResolution = sortedResolutions[zoomLevel];
const [xTilePos, yTilePos] = tilePos;
const tileWidth = chosenResolution * this.#binsPerTile;
const tileHeight = tileWidth;
const tileX = tileWidth * xTilePos;
const tileY = tileHeight * yTilePos;
return {
tileX,
tileY,
tileWidth,
tileHeight
};
} else {
const [xTilePos, yTilePos] = tilePos;
const minX = this.tilesetInfo.min_pos[0];
const minY = this.tilesetInfo.min_pos[1];
const tileWidth = this.tilesetInfo.max_width / 2 ** zoomLevel;
const tileHeight = this.tilesetInfo.max_width / 2 ** zoomLevel;
const tileX = minX + xTilePos * tileWidth;
const tileY = minY + yTilePos * tileHeight;
return {
tileX,
tileY,
tileWidth,
tileHeight
};
}
}
get #binsPerTile() {
let maybeValue: number | undefined;
if (this.tilesetInfo) {
maybeValue =
'bins_per_dimension' in this.tilesetInfo
? this.tilesetInfo.bins_per_dimension
: this.tilesetInfo.tile_size;
}
return maybeValue ?? 256;
}
/**
* Gets the indices of the visible data a tile. Overrides method in Tiled1DPixiTrack
*/
override getIndicesOfVisibleDataInTile(tile: Tile): [number, number] {
const visible = this._xScale.range();
if (!this.tilesetInfo || !tile.tileData.tilePos || !('dense' in tile.tileData)) {
return [0, 0];
}
const { tileX, tileWidth } = this.getTilePosAndDimensions(tile.tileData.zoomLevel, tile.tileData.tilePos);
const tileXScale = HGC.libraries.d3Scale
.scaleLinear()
.domain([0, this.#binsPerTile])
.range([tileX, tileX + tileWidth]);
const start = Math.max(0, Math.round(tileXScale.invert(this._xScale.invert(visible[0]))));
const end = Math.min(
tile.tileData.dense.length,
Math.round(tileXScale.invert(this._xScale.invert(visible[1])))
);
return [start, end];
}
/**
* Overrides method in TiledPixiTrack
* @param loadedTiles
*/
override receivedTiles(loadedTiles: Record<string, Tile>) {
// https://github.com/higlass/higlass/blob/38f0c4415f0595c3b9d685a754d6661dc9612f7c/app/scripts/TiledPixiTrack.js#L637
super.receivedTiles(loadedTiles);
// some items in this.fetching are removed
isTabularDataFetcher(this.dataFetcher) && this.drawLoadingCue();
}
/**
* Overrides method in TiledPixiTrack
*/
override removeOldTiles() {
super.removeOldTiles(); // some items are added to this.fetching
isTabularDataFetcher(this.dataFetcher) && this.drawLoadingCue();
}
/**
* Combile multiple tiles into the last tile.
* This is sometimes necessary, for example, when applying a displacement algorithm to all tiles at once.
* Called by this.processAllTiles() so this method needs to be public.
*/
combineAllTilesIfNeeded() {
if (!this.shouldCombineTiles()) return;
const tiles = this.visibleAndFetchedTiles();
if (!tiles || tiles.length <= 1) {
// Does not make sense to combine tiles
return;
}
// Increase the size of tiles by length
this.tileSize = (this.tilesetInfo?.tile_size ?? 1024) * tiles.length;
let merged: Datum[] = [];
tiles.forEach((tile, i) => {
const tileInfo = this.#processedTileInfo[tile.tileId];
if (tileInfo) {
// Combine data
merged = [...merged, ...tileInfo.tabularData];
// Since we merge the data to the first one, skip rendering the rest
tileInfo.skipRendering = i !== 0;
}
});
const firstTileInfo = this.#processedTileInfo[tiles[0].tileId];
firstTileInfo.tabularData = merged;
// Remove duplicated if any. Sparse tiles can have duplications.
if (firstTileInfo.tabularData[0]?.uid) {
firstTileInfo.tabularData = uniqBy(firstTileInfo.tabularData, 'uid');
}
}
/**
* Check whether tiles should be merged. Needs to be public since called by combineAllTilesIfNeeded()
*/
shouldCombineTiles() {
const includesDisplaceTransform = hasDataTransform(this.options.spec, 'displace');
// we do not need to combine dense tiles (from multivec, vector, matrix)
const hasDenseTiles = () => {
const tiles = this.visibleAndFetchedTiles();
return tiles.length >= 1 && 'dense' in tiles[0].tileData;
};
// BAM data fetcher already combines the datasets;
const isBamDataFetcher = this.dataFetcher instanceof BamDataFetcher;
return includesDisplaceTransform && !hasDenseTiles() && !isBamDataFetcher;
}
/**
* Creates an array of SingleTracks if there are overlaid tracks
*/
#getResolvedTracks() {
const copy = structuredClone(this.options.spec);
// Brushes are drawn by another plugin track.
return resolveSuperposedTracks(copy).filter(t => t.mark !== 'brush');
}
/**
* Construct tabular data from a higlass tileset and a gosling track model.
*/
#generateTabularData(tile: Tile, force = false) {
if (this.#processedTileInfo[tile.tileId] && !force) {
// we do not need to re-construct tabular data
return;
}
if (!tile.tileData.tilePos) {
// we do not have this information ready yet, i.e., cannot calculate `tileX`
return;
}
const tileInfo = initProcessedTileInfo();
const resolvedTracks = this.#getResolvedTracks();
if (resolvedTracks.length === 0) {
// we do not have enough track to display
return [];
}
/* Create tabular data */
// The data spec is identical in all overlaid tracks, so we only need the first one.
const firstResolvedTrack = resolvedTracks[0];
if ('tabularData' in tile.tileData) {
// some data fetchers directly generates `tabularData`
tileInfo.tabularData = tile.tileData.tabularData;
} else {
// generate tabular data
const { tileX, tileY, tileWidth, tileHeight } = this.getTilePosAndDimensions(
tile.tileData.zoomLevel,
tile.tileData.tilePos
);
const sparse = 'length' in tile.tileData ? Array.from(tile.tileData) : [];
const extendedTileData = Object.assign({}, tile.tileData, {
sparse,
tileX,
tileY,
tileWidth,
tileHeight,
tileSize: this.tileSize
});
const tabularData = getTabularData(firstResolvedTrack, extendedTileData);
if (tabularData) {
tileInfo.tabularData = tabularData;
}
}
this.#processedTileInfo[tile.tileId] = tileInfo;
}
/**
* Apply data transformation to each of the overlaid tracks and generate GoslingTrackModels.
*/
transformDataAndCreateModels(tile: Tile) {
const tileInfo = this.#processedTileInfo[tile.tileId];
if (!tileInfo || tileInfo.skipRendering) {
// this probably means the tile data has been merged to another tile
// so, no need to create track models
return [];
}
// clear the array first
tileInfo.goslingModels = [];
const resolvedTracks = this.#getResolvedTracks();
resolvedTracks.forEach(resolvedSpec => {
let tabularDataTransformed = Array.from(tileInfo.tabularData);
resolvedSpec.dataTransform?.forEach(t => {
switch (t.type) {
case 'filter':
tabularDataTransformed = filterData(t, tabularDataTransformed);
break;
case 'concat':
tabularDataTransformed = concatString(t, tabularDataTransformed);
break;
case 'replace':
tabularDataTransformed = replaceString(t, tabularDataTransformed);
break;
case 'log':
tabularDataTransformed = calculateData(t, tabularDataTransformed);
break;
case 'exonSplit':
tabularDataTransformed = splitExon(t, tabularDataTransformed, resolvedSpec.assembly);
break;
case 'genomicLength':
tabularDataTransformed = calculateGenomicLength(t, tabularDataTransformed);
break;
case 'svType':
tabularDataTransformed = inferSvType(t, tabularDataTransformed);
break;
case 'coverage':
tabularDataTransformed = aggregateCoverage(t, tabularDataTransformed, this._xScale.copy());
break;
case 'subjson':
tabularDataTransformed = parseSubJSON(t, tabularDataTransformed);
break;
case 'displace':
tabularDataTransformed = displace(t, tabularDataTransformed, this._xScale.copy());
break;
}
});
// TODO: Remove the following block entirely and use the `rawData` API in the Editor (June-02-2022)
// Send data preview to the editor so that it can be shown to users.
try {
if (PubSub) {
const NUM_OF_ROWS_IN_PREVIEW = 100;
const numOrRows = tabularDataTransformed.length;
PubSub.publish('data-preview', {
id: context.viewUid,
dataConfig: JSON.stringify({ data: resolvedSpec.data }),
data:
NUM_OF_ROWS_IN_PREVIEW > numOrRows
? tabularDataTransformed
: sampleSize(tabularDataTransformed, NUM_OF_ROWS_IN_PREVIEW)
// ...
});
}
} catch (e) {
// ..
}
// Replace width and height information with the actual values for responsive encoding
const [trackWidth, trackHeight] = this.dimensions; // actual size of a track
const axisSize = IsXAxis(resolvedSpec) ? HIGLASS_AXIS_SIZE : 0; // Why the axis size must be added here?
const [w, h] = [trackWidth, trackHeight + axisSize];
const circularFactor = Math.min(w, h) / Math.min(resolvedSpec.width!, resolvedSpec.height!);
if (resolvedSpec.innerRadius) {
resolvedSpec.innerRadius = resolvedSpec.innerRadius * circularFactor;
}
if (resolvedSpec.outerRadius) {
resolvedSpec.outerRadius = resolvedSpec.outerRadius * circularFactor;
}
resolvedSpec.width = w;
resolvedSpec.height = h;
// Construct separate gosling models for individual tiles
const model = new GoslingTrackModel(resolvedSpec, tabularDataTransformed, this.options.theme);
// Add a track model to the tile object
tileInfo.goslingModels.push(model);
});
return tileInfo.goslingModels;
}
/* *
*
* Mouse methods
*
* */
#onMouseDown(mouseX: number, mouseY: number, isAltPressed: boolean) {
// Record these so that we do not triger click event when dragged.
this.#mouseDownX = mouseX;
this.#mouseDownY = mouseY;
// Determine whether to activate a range brush
const mouseEvents = this.options.spec.experimental?.mouseEvents;
const rangeSelectEnabled = !!mouseEvents || (IsMouseEventsDeep(mouseEvents) && !!mouseEvents.rangeSelect);
this.#isRangeBrushActivated = rangeSelectEnabled && isAltPressed;
this.pMouseHover.clear();
}
#onMouseMove(mouseX: number) {
if (this.options.spec.layout === 'circular') {
// TODO: We do not yet support range selection on circular tracks
return;
}
if (this.#isRangeBrushActivated) {
this.mRangeBrush.updateRange([mouseX, this.#mouseDownX]).drawBrush().visible().disable();
}
}
#onMouseUp(mouseX: number, mouseY: number) {
// `trackClick` API
this.#publishTrackEvents('trackClick', mouseX, mouseY);
const mouseEvents = this.options.spec.experimental?.mouseEvents;
const clickEnabled = !!mouseEvents || (IsMouseEventsDeep(mouseEvents) && !!mouseEvents.click);