Press n or j to go to the next uncovered block, b, p or k for the previous block.
| 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 | 2x 2x 2x 73x 73x 73x 73x 73x 73x 73x 73x 73x 86x 86x 86x 564x 67x 497x 411x 86x 564x 564x 564x 564x 9463x 9463x 9463x 9463x 9463x 9463x 564x 86x 73x 73x 73x 73x 73x 73x 73x 73x 73x 73x 2x 122x 122x 122x 122x 122x 120x 122x 122x 122x 122x 116x 116x 2x 7x 7x 7x 7x 7x 7x 7x 7x 7x 7x 2x 4x 4x 4x 4x 4x 4x 4x 4x 2x 12x 12x 12x 12x 12x 2x 42x 42x 42x 42x 42x 42x 42x 42x 2x 65x 65x 65x 65x 65x 102x 204x 204x 102x 65x 65x 2x 21x 21x 21x 21x 21x 17x 17x 4x 4x 4x 4x 4x 2x 319x 319x 319x 319x 319x 319x 319x 2x 144x 144x 144x 144x 144x 2x 6x 6x 2x 3x 3x 2x 11x 11x 2x 8x 8x 2x 12x 12x 12x 2x 97x 97x 90x 90x 84x 97x 97x 2x 97x 97x 2x 13x 13x 13x 13x 13x 13x 13x 13x 12x 12x 12x 12x 12x 12x 12x 12x 12x 12x 12x 1x 2x 2x 2x 2x 2x 2x 2x 2x 2x 2x 2x 2x 2x 2x 13x 13x 2x 2x 21x 21x 21x 21x 2x 22x 22x 22x 22x 22x 3x 3x 3x 3x 3x 3x 3x 19x 16x 3x 22x 2x 2x 5x 5x | /**
* The map turned 45°: position along the bottom, distance from the diagonal up
* the side.
*
* A contact map is symmetric about its diagonal, and the diagonal is where all
* the signal is — so a square map spends most of its area on the far corners,
* which are empty, and draws the part anybody is reading as a thin bright band
* across the middle. Turning it puts that band along the bottom of a rectangle
* and gives the whole picture to it. Two things follow, and the second is the
* real reason to do it:
*
* 1. A domain becomes a **triangle standing on the axis**, and a loop becomes a
* **dot at the height of its own span** — both far easier to see than a
* square-cornered block and a dot off the diagonal.
* 2. The x axis is now *genomic position*, the same axis a track is drawn
* against. A coverage profile under a square map lines up with one edge of
* it; under a turned map it lines up with the picture. That is what every
* published Hi-C figure is doing, and it is what §8.4's one coordinate model
* was already built for.
*
* ---
*
* **The transform is a true rotation, and that decides the units.** A cell
* `(b1, b2)` goes to `x = (b1 + b2) / 2` and `y = (b2 - b1) / 2`, both in bins,
* both drawn at the same bases per pixel. Isometric: nothing is stretched, a
* domain's two edges meet at a right angle over its midpoint, and a base pair
* measured up the side is the same length as a base pair measured along the
* bottom.
*
* The consequence to hold on to is that **height is half of separation**. A
* contact between two bins 100 kb apart sits 50 kb above the axis. The y axis is
* therefore *labelled* in separation — which is the question a reader is asking,
* and the number this module takes and returns — while the coordinate underneath
* it is half that. Stretching the picture to make the two agree is the
* alternative and it is worse: it would put a domain's edges at 63° and make a
* base pair up the side shorter than one along the bottom, so nothing could be
* measured off the plot with one ruler.
*
* **The lattice is half-bin.** `b1 + b2` and `b2 - b1` always share parity, so
* the rotated grid is a checkerboard: half its positions have no cell. Filling
* only those and interpolating the rest is one option and it blurs; drawing each
* source cell as a diamond is another and it costs a path per cell. Instead each
* source cell fills **two adjacent columns**, which makes the output dense,
* uniform, square-celled and exact to within the half bin it is drawn at. The
* output cell is `binsize / 2` on both axes, so the block the renderer receives
* is an ordinary uniform matrix and every part of it — pooling, colouring, pan,
* zoom, clip, colourbar, export — is the same code it always was.
*
* **The corners are empty, and that is honest.** A cell at the far left of the
* window and high up needs a partner off the left-hand end of the block, which
* was never read. Those two corner triangles come back `NaN` and draw as paper.
* Reading wider than the window would fill them and is the obvious later
* improvement; nothing here pretends they are zeros.
*/
import { LocusAxis, type Locus, type LocusSegment } from './locus'
/** The part of a read this module needs. */
export interface RotatableBlock {
nrows: number
ncols: number
values: Float32Array
rowExtent: readonly [number, number]
colExtent: readonly [number, number]
}
/**
* Which way separation grows on screen.
*
* `up` is the ordinary turned map: the diagonal along the bottom, distance
* increasing towards the top of the panel. `down` is its mirror, and exists for
* exactly one thing — the two-file comparison, whose lower-left triangle has
* nowhere to go once the square is turned. Drawn `down` beneath a first map
* drawn `up`, the pair becomes two rectangles meeting at one shared genomic
* axis, which is a better presentation of that comparison than the square was:
* the two are read against each other at every position without the eye having
* to reflect one of them through a diagonal first.
*/
export type RotateDirection = 'up' | 'down'
export interface RotateOptions {
/**
* Largest separation to keep, **in bins**, counted as `|b2 - b1|`.
*
* The reader's "how far from the diagonal am I looking", and the thing that
* makes this cheaper than the square it replaces rather than dearer: nobody
* wants the whole triangle, and a band is a fraction of the block.
*/
maxSeparation: number
direction?: RotateDirection
/**
* Draw the block's *other* triangle as a second band, mirrored beneath the
* first.
*
* The two-file comparison, and the only thing this is for. A split map holds
* one file above the matrix diagonal and the other below it
* (`render/compare.ts`), and turning that square keeps only the upper
* triangle — so the second file, which is the entire reason the picture is
* split, vanishes the moment the reader turns it. Mirrored, the pair becomes
* two bands meeting at **one shared genomic axis**: the same position is the
* same column in both, and the two are read against each other at every place
* without the eye having to reflect one of them through a diagonal first.
*
* It is the same block read twice — `[i][j]` into the first band and `[j][i]`
* into the second — so nothing has to be rotated twice and no second square
* has to be kept. The diagonal itself is drawn in both, because it is the one
* row the two files share: `blendAcrossDiagonal` gives it to the first, and a
* dashed line of alternating owners down the middle of the picture would be
* an artefact of nothing.
*/
mirror?: boolean
/**
* What the mirrored band reads, where it is not the block itself: the square
* of a **second reading** of the same file (§5.10), the same shape as the block.
*
* A split of two files is one merged square read from both sides, and its
* diagonal is the first file's in both bands. Two readings are two squares,
* and the second band's diagonal row is the second reading's own — a diagonal
* of balanced counts drawn on an O/E's ramp would be a stripe of saturated
* colour along the axis, in the one row a reader compares the two bands by.
*/
below?: Float32Array
}
/**
* A turned block, and everything needed to read a position back out of it.
*
* Shaped so the values half can be handed to the renderer as an ordinary dense
* matrix while the geometry half answers the questions only this module can:
* where a column sits on the genome, and which pair of bins a cell came from.
*/
export interface RotatedBlock {
nrows: number
ncols: number
/** Row-major, `nrows * ncols`, `NaN` where no cell of the square reaches. */
values: Float32Array
/**
* Absolute bin position of the **left edge of column 0**, in bins.
*
* The block's own first bin: column 0 is the cell where both ends are that
* bin. Columns advance by half a bin from there, which is what
* {@link BIN_FRACTION} names.
*/
originBin: number
/** Separation, in bins, of the row furthest from the axis. */
maxSeparation: number
direction: RotateDirection
/**
* First row of the mirrored band, or `undefined` for a single band.
*
* `maxSeparation + 1` whenever it is set, which is to say the row just past
* the first band's diagonal — so the two diagonals are adjacent rows and the
* shared genomic axis is the line between them. It is carried rather than
* recomputed because it is what every reader of a turned block has to branch
* on: which band a row is in decides the separation it stands for
* ({@link separationAt}), which file it came from ({@link bandAt}), and which
* way the ruler beside it runs ({@link separationCoords}).
*/
fold?: number
}
/**
* How much of a bin one output cell spans, on both axes.
*
* A half, and not a tuning knob: it is what the rotated lattice *is*. `b1 + b2`
* advances by one when either end moves by one bin, so the natural column width
* is half the bin size, and the same is true up the side.
*/
export const BIN_FRACTION = 0.5
/**
* Turn a square on-diagonal block into a band above its own diagonal.
*
* The caller has already established that this block *has* a diagonal — see
* {@link isTurnable}, which is the gate the toggle is greyed by. Handing an
* off-diagonal block here would produce a picture of the distance between two
* sequences that do not have one.
*/
export function rotateBlock(block: RotatableBlock, options: RotateOptions): RotatedBlock {
const n = Math.min(block.nrows, block.ncols)
const direction = options.direction ?? 'up'
// At most the block itself: a separation wider than the window has no cells
// to draw, and asking for one would allocate rows that could only be NaN.
const maxSeparation = Math.max(0, Math.min(Math.trunc(options.maxSeparation), Math.max(0, n - 1)))
const width = Math.max(1, 2 * n - 1)
const band = maxSeparation + 1
// The second band starts where the first ends, so the two diagonals are
// adjacent rows. `undefined` — not zero — where there is only one band, so
// that every reader below has one test rather than two.
const fold = options.mirror === true ? band : undefined
const height = fold === undefined ? band : band * 2
// Not filled with `NaN` up front, and that is worth a line: the loop below
// writes every cell of the band except the two corner triangles, so a blanket
// fill is a second pass over the whole array to set values that are about to
// be overwritten — and this array is the largest thing a turned map allocates.
// The corners are filled per row instead, which is exactly the part nothing
// reaches. `Float32Array` arrives zeroed, and a zero left showing would be a
// contact count of nothing rather than an absence of data, which is the one
// distinction `rotateBlock`'s header insists on.
const values = new Float32Array(width * height)
// One pass per band. The second reads the block **transposed** — the cells
// below the matrix diagonal, which under a split are the second file — and
// lays them out growing downward from the row just past the first band's
// diagonal. Everything else about the two passes is identical, which is the
// point: a mirrored map is not a second picture, it is this one read from its
// other side.
for (let pass = 0; pass < (fold === undefined ? 1 : 2); pass++) {
const transposed = pass === 1
const source = transposed ? (options.below ?? block.values) : block.values
for (let separation = 0; separation <= maxSeparation; separation++) {
// Rows are emitted in the order they are drawn, so the renderer needs no
// notion of which way up this is: `up` puts the widest separation in row 0,
// which a top-to-bottom raster then draws as an apex over an axis along the
// bottom edge.
const row = transposed
? (fold as number) + separation
: direction === 'up'
? maxSeparation - separation
: separation
const base = row * width
// A row of separation `s` reaches from column `s` to `2n - s - 1`: the
// further from the diagonal, the more of both ends needs a partner off the
// end of the block. Those are the two triangles that come back empty.
values.fill(Number.NaN, base, base + Math.min(separation, width))
values.fill(Number.NaN, base + Math.max(0, 2 * n - separation - 1), base + width)
for (let i = 0; i + separation < n; i++) {
const j = i + separation
const value = transposed ? source[j * block.ncols + i] : source[i * block.ncols + j]
// Two columns per cell, which is what makes the output dense rather than
// a checkerboard: `i + j` and `i + j + 1` are the two half-bin columns the
// cell covers, and the second is where the parity gap would otherwise be.
const x = 2 * i + separation
values[base + x] = value
if (x + 1 < width) values[base + x + 1] = value
}
}
}
return {
nrows: height,
ncols: width,
values,
originBin: block.rowExtent[0],
maxSeparation,
direction,
...(fold === undefined ? {} : { fold }),
}
}
/**
* The pair of bins a turned cell came from, or `null` off the end of the band.
*
* What the readout needs, and the reason the two-columns-per-cell rule above is
* worth stating precisely: a column is half a bin, so two adjacent columns can
* name the same pair, and which of them a pointer is over is not a fact about
* the data. The parity of `column + separation` is what picks the pair back out
* — one of the two columns hits the lattice exactly and the other is the filled
* neighbour, so the answer is the same cell either way.
*/
export function cellAt(
rotated: Pick<
RotatedBlock,
'nrows' | 'ncols' | 'maxSeparation' | 'direction' | 'originBin' | 'fold'
>,
row: number,
column: number,
): { row: number; col: number; separation: number } | null {
if (row < 0 || row >= rotated.nrows || column < 0 || column >= rotated.ncols) return null
const separation = separationAt(rotated, row)
// `i + j` for this cell: the lattice point at or just left of the column.
const sum = (column + separation) % 2 === 0 ? column : column - 1
const i = (sum - separation) / 2
const j = i + separation
if (!Number.isInteger(i) || i < 0) return null
return { row: i, col: j, separation }
}
/**
* The two loci a cell names, whichever way the block it is in is drawn.
*
* The pointer's counterpart of {@link turnedPlace}, and the piece that was
* missing. A mark is placed at a *pair* of loci — one per axis, which is what
* makes one gesture serve a line, a crosshair and a loop — and on a turned map
* neither of the picture's own axes can answer for one: y is distance from the
* diagonal, which is not a place, and x is counted in half bins. So the cell is
* taken back to the square it was rotated out of ({@link cellAt}) and read
* against *that* block's two axes, which every other reader of a turned map
* already does — the tooltip, the readout, and the selection that opens a region.
*
* `square` is the untured block's pair. On a square map `turned` is `null`, the
* cell is already the square's, and this is two axis lookups.
*
* Half a cell is added on each axis because a click lands *inside* a cell and its
* left edge is not where the reader aimed: on a 10 kb grid that is the difference
* between a mark on the boundary of a domain and one 5 kb short of it.
*/
export function cellLoci(
square: { rows: LocusAxis | null; cols: LocusAxis | null },
turned: Pick<
RotatedBlock,
'nrows' | 'ncols' | 'maxSeparation' | 'direction' | 'originBin' | 'fold'
> | null,
cell: { row: number; col: number },
): { rows: Locus; cols: Locus } | null {
const at = turned === null ? cell : cellAt(turned, cell.row, cell.col)
if (at === null) return null
const rows = square.rows?.unitToLocus(at.row + 0.5) ?? null
const cols = square.cols?.unitToLocus(at.col + 0.5) ?? null
return rows === null || cols === null ? null : { rows, cols }
}
/**
* Where a turned cell's two anchors stand on the column axis, in matrix units.
*
* The pair of positions a contact is *between*, said in the coordinate a track
* under the map is drawn in — which is what lets a stack answer a pointer on the
* map with two hairlines rather than one. A bin fills two columns, so its middle
* is `2b + 1`; on the diagonal the two anchors are one place and the answer is
* one line.
*/
export function anchorColumns(
rotated: Pick<
RotatedBlock,
'nrows' | 'ncols' | 'maxSeparation' | 'direction' | 'originBin' | 'fold'
>,
row: number,
column: number,
): number[] | null {
const cell = cellAt(rotated, row, column)
if (cell === null) return null
return cell.separation === 0 ? [2 * cell.row + 1] : [2 * cell.row + 1, 2 * cell.col + 1]
}
/**
* The bins a run of turned columns covers, as a half-open range into the block.
*
* The inverse of the rotation for a *band* rather than for a cell, and what
* turns a drag across a turned map into a window on the genome. A column is half
* a bin, so the arithmetic is one multiplication — but the rounding is the whole
* of it, and it goes outward at both ends: a reader who drags across a feature
* means the bins their band touched, not the bins it wholly contained, and a
* band narrower than one bin is still a band. Hence the floor, the ceiling, and
* the guarantee of at least one bin in the answer.
*
* Clamped to the block, because a drag is clamped to the *plot* and the plot is
* larger than the data whenever the view is zoomed out.
*
* @param bins How many bins the square block this band was turned out of has.
*/
export function binsForColumns(columns: readonly [number, number], bins: number): [number, number] {
const n = Math.max(1, Math.trunc(bins))
const lo = Math.max(0, Math.min(n - 1, Math.floor(columns[0] * BIN_FRACTION)))
const hi = Math.max(lo + 1, Math.min(n, Math.ceil(columns[1] * BIN_FRACTION)))
return [lo, hi]
}
/**
* A point on a turned map, in the matrix units the renderer draws in.
*
* Fractional on both axes: a contact's true centre falls on the boundary
* between the two columns it fills, and a row's is half way down it.
*/
export interface TurnedPoint {
col: number
row: number
}
/**
* Where the contact under a turned cell truly sits, in matrix units.
*
* Not the centre of the cell the pointer is over, and the difference is the
* half-bin lattice: a contact fills *two* columns, so its own middle is the
* line between them — `i + j + 1` — while the cell under the pointer is one or
* the other of the two. Half a column is a quarter of a bin and invisible as a
* position, but it is the difference between a guide that meets the axis
* exactly on the bin its contact is with and one that meets it a quarter of a
* bin to the side, which at bin zoom is a line pointing next to the answer.
*/
export function turnedCentre(
rotated: Pick<RotatedBlock, 'maxSeparation' | 'direction' | 'fold'>,
row: number,
column: number,
): TurnedPoint {
const separation = separationAt(rotated, row)
const sum = (column + separation) % 2 === 0 ? column : column - 1
return { col: sum + 1, row: row + 0.5 }
}
/**
* The rays a guide follows from a point on a turned map, in matrix units.
*
* **A turned map's two directions are not its two axes**, and this is the whole
* of what that means for anything drawn through a point. A cell of the square
* is a contact between two places; turned, the set of cells sharing one of those
* places is not a column of the picture but a **45° ray**, because holding `i`
* fixed and letting the separation grow moves the contact half a bin along for
* every bin further from the diagonal. In matrix units that is exactly slope
* one: `col + row` is constant along one anchor and `col - row` along the other.
*
* So the honest guide on a turned map is a pair of rays rather than a cross —
* two lines that say *these two places*, meeting at the contact between them.
* Where they end is the caller's: a pointer on the map is between two anchors
* and reaches both edges of the band (an X, which near the axis is a V and near
* the top a ∧, because the rest is off the picture); a pointer on a track names
* one place on the axis and its rays only go outwards from it (a V).
*
* @param rows Matrix rows the rays reach — one row for a V, both edges for an X.
*/
export function anchorRays(
at: TurnedPoint,
rows: readonly number[],
): Array<{ from: TurnedPoint; to: TurnedPoint }> {
const out: Array<{ from: TurnedPoint; to: TurnedPoint }> = []
for (const row of rows) {
for (const way of [-1, 1]) {
out.push({ from: at, to: { col: at.col + way * (row - at.row), row } })
}
}
return out
}
/**
* The rays a **place** casts on a turned map: the contacts it is an anchor of.
*
* A V standing on the axis at the place and opening to the far edge of the
* band — both ways along the genome, because a place anchors everything to its
* left as well as everything to its right — and one V per band of a mirrored
* pair, whose two diagonals are the same place in two maps. What a pointer on a
* track draws across the map, and what a line the reader drew becomes there
* (§17.4): on the square both are a column, and a column of a turned picture is
* not a place but contacts between two *other* places, all but the one at the
* V's apex.
*
* @param col The place, in the turned block's column units.
*/
export function placeRays(
turned: Pick<RotatedBlock, 'maxSeparation' | 'direction' | 'fold' | 'nrows'>,
col: number,
): Array<{ from: TurnedPoint; to: TurnedPoint }> {
// The apex is the diagonal — separation zero, the bottom row of an ordinary
// turned band and the top row of the mirrored half.
const axis = rowForSeparation(turned, 0) + 0.5
if (turned.fold === undefined) {
return anchorRays({ col, row: axis }, [turned.direction === 'up' ? 0 : turned.nrows])
}
return [
...anchorRays({ col, row: axis }, [0]),
...anchorRays({ col, row: turned.fold + 0.5 }, [turned.nrows]),
]
}
/**
* The separation, in bins, that a row of the turned block stands for.
*
* Two lines on a mirrored block, meeting at the fold: the first band counts
* away from its own diagonal and the second counts away from the same diagonal
* the other way, so both bands read `0` on the two rows that touch the shared
* axis and grow outwards from there. That is what makes a mirrored pair one
* measurement rather than two pictures — a contact 100 kb apart stands the same
* height above the axis in the upper band and below it in the lower one.
*/
export function separationAt(
rotated: Pick<RotatedBlock, 'maxSeparation' | 'direction' | 'fold'>,
row: number,
): number {
const fold = rotated.fold
if (fold !== undefined && row >= fold) return row - fold
return rotated.direction === 'up' ? rotated.maxSeparation - row : row
}
/**
* The row that draws a given separation. Inverse of {@link separationAt}.
*
* The **first** band's row on a mirrored block, because a separation is drawn
* twice there and the callers that ask this are placing one thing: a mark is a
* claim about the genome rather than about a file, and drawing it in both bands
* would say the reader had drawn two.
*/
export function rowForSeparation(
rotated: Pick<RotatedBlock, 'maxSeparation' | 'direction'>,
separation: number,
): number {
return rotated.direction === 'up' ? rotated.maxSeparation - separation : separation
}
/**
* Which band of a mirrored pair a row is in — `0` for the first, `1` for the
* band beneath it, and always `0` where there is only one.
*
* The one question a mirrored map adds to every reading of a cell: the two
* bands are two *files*, so the number under the pointer, the derived value
* beside it and the name it should be given all depend on which side of the
* shared axis the pointer is.
*/
export function bandAt(rotated: Pick<RotatedBlock, 'fold'>, row: number): 0 | 1 {
return rotated.fold !== undefined && row >= rotated.fold ? 1 : 0
}
/**
* The absolute bin position at the centre of a turned column.
*
* Fractional by construction — a column is half a bin — and returned that way
* rather than rounded, because the axis under a turned map is a genomic ruler
* and rounding it would make every second tick land on the wrong side of a bin
* boundary.
*/
export function positionAt(rotated: Pick<RotatedBlock, 'originBin'>, column: number): number {
return rotated.originBin + (column + 0.5) * BIN_FRACTION
}
/**
* The separation a band of `rows` pixels can show, given how tall a cell is.
*
* The arithmetic behind "the box keeps its height and the distance follows the
* zoom": the panel's height in cells is fixed by the layout, a cell is half a
* bin *of height* and therefore a whole bin *of separation*, and so the deepest
* contact on screen is the row count in bins.
*/
export function separationForRows(rows: number): number {
return Math.max(0, Math.trunc(rows))
}
/**
* How far a band of `rows` reaches from the diagonal, in base pairs.
*
* The same identity as {@link separationForRows} with the bin size put back in:
* a row is a whole bin of separation, so a band of `rows` rows reaches
* `rows × binsize`. Written down rather than open-coded because it is what a
* **deck** shares — a distance rather than a row count, exactly as the
* navigation lock's currency is base pairs rather than cells, so panels of
* unequal resolution reach the same place instead of the same number of bins
* (`panels/lock.ts`, `panels/PanelDeck.ts`'s `syncTurnReach`).
*/
export function reachForRows(rows: number, binsize: number): number {
return Math.max(0, Math.trunc(rows)) * (binsize > 0 ? binsize : 1)
}
/**
* The inverse: the rows a panel of this bin size needs to reach `bp`.
*
* At least one, on {@link turnDepthFor}'s rule — a band of no rows is a picture
* with no picture in it — and rounded rather than floored, because the two
* panels this exists to keep in step are converting the *same* distance through
* different bin sizes and a floor on both sides loses up to a bin on each.
*/
export function rowsForReach(bp: number, binsize: number): number {
const per = binsize > 0 ? binsize : 1
return Math.max(1, Math.round(bp / per))
}
/**
* Whether a block can be turned at all.
*
* Three conditions, and each of them is the same condition looked at from a
* different side: **the block must have a diagonal**. Distance from it is the
* whole of the y axis, so a block that does not have one has no picture to make.
*
* - the two axes must cover the same bins, or the block is a rectangle between
* two different stretches of the genome;
* - it must be one sequence, because a boundary between two of them is a
* discontinuity in the x axis and the "distance" across it is not a distance;
* - it must be at bin level, because above that a cell is a whole sequence and
* the separation between two of them is a count of sequences, not a length.
*
* The toggle is greyed rather than hidden where this is false, so that a reader
* looking at a whole metagenome can see the control exists and learn what it
* wants from them.
*/
export function isTurnable(block: {
level: 'bin' | 'contig' | 'genome'
rowExtent: readonly [number, number]
colExtent: readonly [number, number]
rowGroups?: ReadonlyArray<{ label?: string }>
/** Set where the block was read round a circle — see `worker/wrap.ts`. */
wrapped?: readonly [number, number]
}): boolean {
if (block.level !== 'bin') return false
if (block.rowExtent[0] !== block.colExtent[0]) return false
if (block.rowExtent[1] !== block.colExtent[1]) return false
const groups = block.rowGroups
// One run, or none at all — a plain cooler read as a single span has no runs
// and is one sequence by construction.
if ((groups?.length ?? 1) <= 1) return true
// **Or one sequence carried twice, which is what a circle looks like** (§8.15).
// A block read across a sequence's own junction has two runs — its tail, then
// its head — and refusing it here is refusing to turn the one picture the
// declaration was made for. The test is still *one sequence*: several runs of
// several names is a whole-genome block, which has no diagonal to stand on.
if (block.wrapped === undefined || groups === undefined) return false
const first = groups[0]?.label
return first !== undefined && groups.every((group) => group.label === first)
}
/**
* The genomic axis under a turned block.
*
* Built here rather than by `locusAxisFrom` because the turned block's columns
* are half a bin, and that helper takes its scale from a bin size shared with
* the rest of the read. One segment always: {@link isTurnable} has already
* refused anything spanning more than one sequence, which is the condition that
* would need more.
*
* This is what makes a turned map worth having. §8.4 gives the heatmap and the
* lanes *one* coordinate model, so the moment the x axis becomes an ordinary
* genomic axis every track already lines up with the picture — nothing in
* `AnnotationLanes` has to learn that the map was turned.
*/
export function turnedAxis(
rotated: Pick<RotatedBlock, 'ncols' | 'originBin'>,
contig: { label: string; firstBin: number; length: number },
binsize: number,
/**
* The block's own runs, where it has more than one — which is a block read
* round a circle and nothing else (§8.15).
*
* `start` and `end` are block-local **bins**, and a turned column is half a
* bin, so a run covers twice as many columns as it does bins. `unitStart` is
* the bin the *sequence* begins at for that stretch, which on the far side of
* a junction is a whole lap further along than on the near side — and carrying
* it through is the whole of what makes the turned picture read the second
* stretch as the beginning of the sequence rather than as somewhere past its
* end.
*/
runs: ReadonlyArray<{ start: number; end: number; unitStart?: number }> = [],
): LocusAxis | null {
if (!(binsize > 0) || rotated.ncols <= 0) return null
const bpPerUnit = binsize * BIN_FRACTION
if (runs.length <= 1) {
return new LocusAxis([
{
contig: contig.label,
unitStart: 0,
unitEnd: rotated.ncols,
// Where column 0's left edge sits inside the sequence. The block may
// begin part-way into it, and the turned block inherits that offset
// unchanged.
bpStart: (rotated.originBin - contig.firstBin) * binsize,
bpPerUnit,
contigLength: contig.length,
},
])
}
const segments: LocusSegment[] = []
for (const run of runs) {
const from = Math.round(run.start / BIN_FRACTION)
const to = Math.min(rotated.ncols, Math.round(run.end / BIN_FRACTION))
if (!(to > from)) continue
const firstBin = run.unitStart ?? rotated.originBin + run.start
segments.push({
contig: contig.label,
unitStart: from,
unitEnd: to,
// `locusAxisFrom`'s arithmetic, in the turned block's own units: the
// unwrapped bin this stretch opens at, measured from where its own lap of
// the sequence begins.
bpStart: (rotated.originBin + run.start - firstBin) * binsize,
bpPerUnit,
contigLength: contig.length,
})
}
return segments.length === 0 ? null : new LocusAxis(segments)
}
/**
* The fraction of a block a turned map shows before anybody says otherwise.
*
* A whole triangle is always twice as wide as it is tall — that is what the
* half-bin lattice makes it — so turning a map and fitting it produces a
* triangle that fills the panel and touches nothing. Which is a fine picture and
* is not the one the turn is for: the reading is the band near the diagonal, and
* the far apex is the part of a contact map that has least in it.
*/
export const DEFAULT_TURN_FRACTION = 0.25
/**
* How far from the diagonal to reach, in bins, given a block and a request.
*
* `asked` is `null` until the reader drags the band's top edge, and then it is
* whatever they dragged it to — clamped here rather than at the gesture, so the
* one place that decides is the one place that knows how big the block is. A
* band cannot be deeper than the block has cells to fill, and cannot be nothing:
* zero rows is a picture with no picture in it, and a reader who drags the edge
* onto the diagonal means "as shallow as it goes", not "gone".
*
* A *fraction* rather than a distance in base pairs, deliberately: a default of
* "500 kb" is most of a bacterial chromosome and a rounding error on a human
* one, and this viewer opens on both.
*/
export function turnDepthFor(block: { nrows: number; ncols: number }, asked: number | null): number {
const span = Math.max(1, Math.min(block.nrows, block.ncols))
const wanted = asked ?? Math.ceil(span * DEFAULT_TURN_FRACTION)
return Math.max(1, Math.min(span - 1, wanted))
}
/**
* The vertical ruler of a turned map, as the same line every other ruler is.
*
* A turned map's y axis answers "how far apart", not "where", so the number
* beside a row is a *distance*: labelling it with coordinates would name places
* that are not on the picture. But it is still an affine function of the row
* index, which is all `AxisCoords` has ever been — so the turned ruler needs no
* machinery of its own, only the right two numbers.
*
* The gradient is **negative** for an ordinary turned map, and that is the whole
* of what is unusual here: separation grows towards the top of the picture while
* a row index grows towards the bottom. It is positive on the mirrored half of a
* comparison, where the two grow together.
*
* The half is the cell centre. Row `r` covers `[r, r + 1)`, and the separation
* it stands for is the one at its middle — without it every label would be off
* by half a bin, which at whole-genome zoom is invisible and at bin zoom is the
* difference between a tick on a cell and a tick between two.
*/
export function separationCoords(
rotated: Pick<RotatedBlock, 'maxSeparation' | 'direction' | 'fold'>,
binsize: number,
): { bpPerCell: number; bpAtOrigin: number; tickGapPx: number; separation: true; fold?: number } {
// `separation: true` on every one of the three: what this function returns is
// always a distance from the diagonal, and {@link AxisCoords.separation}
// records that for the callers that would otherwise read it as a place.
const gap = { tickGapPx: SEPARATION_TICK_GAP_PX, separation: true as const }
// A mirrored pair is that same line and its own reflection, meeting at the
// fold — one ruler read outwards in both directions, which is what says the
// two bands are the same measurement of two files rather than two pictures.
// The reflection is `AxisCoords.fold`'s to make; stating it here as a row
// index and letting the ruler do the arithmetic is what keeps this an affine
// line, which is all `AxisCoords` has ever been.
if (rotated.fold !== undefined) {
return {
...gap,
bpPerCell: -binsize,
bpAtOrigin: (rotated.maxSeparation + 0.5) * binsize,
fold: rotated.fold,
}
}
return rotated.direction === 'up'
? { ...gap, bpPerCell: -binsize, bpAtOrigin: (rotated.maxSeparation + 0.5) * binsize }
: { ...gap, bpPerCell: binsize, bpAtOrigin: -0.5 * binsize }
}
/**
* How much room a distance label wants above the next one, in CSS pixels.
*
* A turned band is a hundred pixels tall against a square map's five hundred,
* and the default spacing — which is the *width* of a base-pair label, because
* a horizontal ruler is what it was chosen for — fits one tick in it. A label
* read bottom to top needs its own height and some air, and this is that.
*/
const SEPARATION_TICK_GAP_PX = 26
/**
* How far from the diagonal a band of `rows` rows reaches, in base pairs.
*
* The reader's number, and the one the y axis is labelled with: a row is one bin
* of *separation* even though it is half a bin of height, which is the whole of
* what {@link rotateBlock}'s header means by height being half of distance.
*/
export function separationBp(rows: number, binsize: number): number {
return Math.max(0, rows) * binsize
}
|