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* A karyotype, drawn along its lane (§8.22).
*
* The chromosome is **one shape**, and the bands are colours inside it. That is
* the whole difference from every other feature lane, where each row of the
* file is a box of its own: here the rows tile one outline, and the outline is
* what says *chromosome* — rounded at a telomere, pinched to a waist at the
* centromere, narrowed along a stalk. So each sequence in view is traced once,
* as a polygon along its top edge and back along its bottom, the bands are
* filled inside it as plain rectangles clipped to it, and it is edged once in
* the plot's ink. A centromere's triangles are not drawn as triangles: they are
* what the rectangles of two `acen` bands look like inside a waist.
*
* ## The stains
*
* Physical, and the same in both themes. A Giemsa band is dark or light on a
* metaphase spread, and a reader who knows ideograms reads `gpos100` as black:
* turning the ramp over for a dark page would draw every G-light band dark.
* `gposN` is N % of the way from the unstained colour to the darkest one — how
* UCSC and IGV read the number — the centromere is the red every ideogram gives
* it, `gvar` is hatched because it is *variable* rather than a darkness, and a
* stalk is a paler, narrower stretch of the outline.
*
* ## One axis
*
* The bands are drawn where they are, on the lane's own axis (§8.4) — this is
* not IGV's whole-chromosome thumbnail with the window boxed in red, which
* would be a second coordinate system beside the one every other lane shares.
* Zoomed out, the lane is the ideogram; zoomed in, it is the bands under the
* window, named, which is what the caption under the lane's name says too.
*/
import { iscnName, stainOf } from '../annotations/cytoband'
import type { FeatureSet } from '../annotations/types'
import type { FeatureLayout, FeaturePaint, FeaturePlacement } from './features'
import {
OUTLINE_WIDTH,
laneCurve,
laneLine,
laneMove,
laneRect,
laneText,
type LaneFrame,
} from './lane'
/** The unstained colour, `gneg` — and the light end of the `gposN` ramp. */
const UNSTAINED: readonly [number, number, number] = [247, 247, 245]
/** The darkest stain, `gpos100`. Not quite black, so an outline still shows on it. */
const DARKEST: readonly [number, number, number] = [26, 26, 28]
/** The centromere's red. */
export const ACEN_COLOUR = '#b3322b'
/** Variable heterochromatin's ground, and the hatching over it. */
export const GVAR_COLOUR = '#cfd6e3'
const GVAR_HATCH = '#76819a'
/** A stalk's grey: paler than a stain, because a stalk is where there is little to stain. */
export const STALK_COLOUR = '#b7bbc2'
/**
* How much of the body's half-height a stalk keeps, and how much the
* centromere's waist does.
*
* A half for the stalk, which is how much narrower an acrocentric's stalk is
* drawn in every ideogram. A fifth at the waist rather than nothing: pinched to
* a point the outline is two shapes touching, and its edge crosses itself there.
*/
const STALK_WAIST = 0.5
const CENTROMERE_WAIST = 0.2
/**
* The narrowest a centromere is drawn, in pixels.
*
* A human centromere is megabases and draws itself. A yeast CEN is 118 bases —
* a hairline at any zoom where the chromosome is on screen — so it is widened
* to this, centred on itself, for the reason a variant is widened to three
* pixels (§8.14): a mark too narrow to see is not a mark. The bands either side
* are drawn under it where it overlaps them.
*/
const CENTROMERE_MIN_PX = 6
/** The tallest the body is drawn, however thick the lane. */
const MAX_BODY = 22
/** The colour a stain is drawn in. */
export function stainColour(stain: string): string {
if (stain === 'acen') return ACEN_COLOUR
if (stain === 'gvar') return GVAR_COLOUR
if (stain === 'stalk') return STALK_COLOUR
let darkness = 0
if (stain.startsWith('gpos')) {
const rest = stain.slice(4)
const value = rest === '' ? 100 : Number(rest)
darkness = Number.isFinite(value) ? Math.max(0, Math.min(100, value)) / 100 : 1
}
const mix = (at: number): number => Math.round(UNSTAINED[at] + (DARKEST[at] - UNSTAINED[at]) * darkness)
return `rgb(${mix(0)}, ${mix(1)}, ${mix(2)})`
}
/** Whether text on a band of this stain should be light rather than dark. */
function darkBand(stain: string): boolean {
if (stain === 'acen') return true
if (!stain.startsWith('gpos')) return false
const rest = stain.slice(4)
const value = rest === '' ? 100 : Number(rest)
return !Number.isFinite(value) || value >= 50
}
/** The stains a key lists, in the order UCSC's own legend gives them. */
export const STAIN_ORDER: readonly string[] = [
'gneg',
'gpos25',
'gpos33',
'gpos50',
'gpos66',
'gpos75',
'gpos100',
'gpos',
'acen',
'gvar',
'stalk',
]
/** What a key calls a stain: the file's word, with what it means. */
export function stainLabel(stain: string): string {
if (stain === 'gneg') return 'gneg · unstained'
if (stain === 'acen') return 'acen · centromere'
if (stain === 'gvar') return 'gvar · variable'
if (stain === 'stalk') return 'stalk'
if (stain === 'gpos') return 'gpos · stained'
return stain
}
/**
* One sequence's run of placed bands, and what the outline needs to know about
* where the chromosome itself begins and ends.
*/
interface Run {
placements: FeaturePlacement[]
/** Whether the chromosome's first base, and its last, are among the bands in view. */
startsHere: boolean
endsHere: boolean
}
/**
* The placements, cut into one run per sequence.
*
* A layout lists every window's features in axis order, one window after the
* next, so a new sequence is a placement whose band belongs to another contig
* than the one before it — or the same contig drawn again, as a circle across
* its junction is, which begins again at an along before the last one's end.
*/
function runsOf(set: FeatureSet, layout: FeatureLayout): Run[] {
const runs: Run[] = []
let current: FeaturePlacement[] = []
let contig = -1
let lastAlong = Number.NEGATIVE_INFINITY
const close = (): void => {
if (current.length === 0) return
const first = current[0].index
const last = current[current.length - 1].index
const c = set.contig[first]
runs.push({
placements: current,
// The file's first band of the sequence, starting at its first base; and
// its last band, which ends where the sequence does if anything does.
startsHere: first === set.contigAt[c] && set.start[first] === 0,
endsHere: last === set.contigAt[c + 1] - 1,
})
current = []
}
for (const placement of layout.placements) {
const c = set.contig[placement.index]
if (c !== contig || placement.along0 < lastAlong - 0.5) {
close()
contig = c
}
current.push(placement)
lastAlong = placement.along1
}
close()
return runs
}
/** One vertex of a run's outline: where along, and how far from the midline. */
interface Vertex {
along: number
half: number
}
/**
* A run's top edge, left to right, as vertices of the half-height.
*
* Every band contributes its two ends at the body's half-height, a stalk its
* two ends at the stalk's, and a run of `acen` bands a waist: full at the run's
* ends, pinched at the centromere — where the first band whose name is on the q
* arm begins, or the middle of the run where the names do not say.
*/
function edgeOf(
set: FeatureSet,
run: Run,
half: number,
): { edge: Vertex[]; centromeres: Array<{ from: number; to: number; index: number }> } {
const out: Vertex[] = []
const centromeres: Array<{ from: number; to: number; index: number }> = []
const bands = run.placements
for (let k = 0; k < bands.length; k++) {
const placement = bands[k]
const stain = stainOf(set.detail[placement.index])
if (stain === 'acen') {
// The whole run of centromeric bands, handled at once.
let end = k
while (end + 1 < bands.length && stainOf(set.detail[bands[end + 1].index]) === 'acen') end++
let from = placement.along0
let to = bands[end].along1
let pinch = (from + to) / 2
for (let j = k; j <= end; j++) {
if (set.name[bands[j].index].startsWith('q')) {
pinch = bands[j].along0
break
}
}
// Widened to be seen, and centred on itself (see CENTROMERE_MIN_PX) —
// taking back whatever of the edge before it the widened waist now
// covers, so the waist is as wide on the p side as on the q side.
if (to - from < CENTROMERE_MIN_PX) {
from = pinch - CENTROMERE_MIN_PX / 2
to = pinch + CENTROMERE_MIN_PX / 2
while (out.length > 0 && out[out.length - 1].along > from) out.pop()
}
out.push({ along: from, half }, { along: pinch, half: half * CENTROMERE_WAIST }, { along: to, half })
centromeres.push({ from, to, index: placement.index })
k = end
continue
}
const at = stain === 'stalk' ? half * STALK_WAIST : half
out.push({ along: placement.along0, half: at }, { along: placement.along1, half: at })
}
// In order, and never backwards: a centromere widened past its neighbours
// would otherwise fold the edge over itself.
let furthest = Number.NEGATIVE_INFINITY
const kept: Vertex[] = []
for (const vertex of out) {
if (vertex.along < furthest) continue
kept.push(vertex)
furthest = vertex.along
}
return { edge: kept, centromeres }
}
/**
* Trace one run's outline: along the top from the near end, round the far
* telomere if it is in view, back along the bottom, round the near one.
*
* `centre` is the midline, in across-coordinates, and the telomeres are the
* body's own half-height round — capped by half the run's length, so a
* chromosome a few pixels long at genome zoom is a pill rather than a knot.
*/
function tracePath(
ctx: CanvasRenderingContext2D,
frame: LaneFrame,
edge: Vertex[],
centre: number,
run: Run,
): void {
if (edge.length === 0) return
const first = edge[0]
const last = edge[edge.length - 1]
const length = last.along - first.along
const capOf = (vertex: Vertex, here: boolean): number =>
here ? Math.max(0, Math.min(vertex.half, length / 2)) : 0
const nearCap = capOf(first, run.startsHere)
const farCap = capOf(last, run.endsHere)
// The top edge, left to right, with each cap's straight part removed from
// the vertices it would otherwise run through.
laneMove(ctx, frame, first.along + nearCap, centre - first.half)
for (const vertex of edge) {
const along = Math.min(Math.max(vertex.along, first.along + nearCap), last.along - farCap)
laneLine(ctx, frame, along, centre - vertex.half)
}
if (farCap > 0) {
laneCurve(ctx, frame, last.along, centre - last.half, last.along, centre)
laneCurve(ctx, frame, last.along, centre + last.half, last.along - farCap, centre + last.half)
} else {
laneLine(ctx, frame, last.along, centre - last.half)
laneLine(ctx, frame, last.along, centre + last.half)
}
for (let k = edge.length - 1; k >= 0; k--) {
const vertex = edge[k]
const along = Math.min(Math.max(vertex.along, first.along + nearCap), last.along - farCap)
laneLine(ctx, frame, along, centre + vertex.half)
}
if (nearCap > 0) {
laneCurve(ctx, frame, first.along, centre + first.half, first.along, centre)
laneCurve(ctx, frame, first.along, centre - first.half, first.along + nearCap, centre - first.half)
} else {
laneLine(ctx, frame, first.along, centre + first.half)
laneLine(ctx, frame, first.along, centre - first.half)
}
ctx.closePath()
}
/** How tall the chromosome is drawn in a lane this thick, in pixels. */
export function ideogramBody(thickness: number): number {
return Math.max(4, Math.min(MAX_BODY, thickness - 6))
}
/**
* Draw an ideogram's bands (§8.22).
*
* Every placement is drawn, whatever `layout.dense` says: the collapse to a
* density is for features that overlap, and bands tile — a genome's worth of
* them at a pixel apiece is still the karyotype, which is what a reader zoomed
* out that far is looking at.
*/
export function drawIdeogram(
ctx: CanvasRenderingContext2D,
frame: LaneFrame,
set: FeatureSet,
layout: FeatureLayout,
paint: FeaturePaint,
): void {
if (layout.placements.length === 0) return
const body = ideogramBody(frame.thickness)
const half = body / 2
const centre = frame.thickness / 2
const colourOf = (index: number): string =>
paint.colourOf === undefined ? stainColour(stainOf(set.detail[index])) : paint.colourOf(index)
ctx.save()
ctx.globalAlpha = paint.opacity
const runs = runsOf(set, layout)
for (const run of runs) {
const { edge, centromeres } = edgeOf(set, run, half)
if (edge.length === 0) continue
// The bands, inside the outline.
ctx.save()
ctx.beginPath()
tracePath(ctx, frame, edge, centre, run)
ctx.clip()
const byInk = new Map<string, FeaturePlacement[]>()
for (const placement of run.placements) {
const ink = colourOf(placement.index)
const held = byInk.get(ink)
if (held === undefined) byInk.set(ink, [placement])
else held.push(placement)
}
for (const [ink, placements] of byInk) {
ctx.fillStyle = ink
ctx.beginPath()
for (const placement of placements) {
const [x, y, w, h] = laneRect(frame, placement.along0, placement.along1, centre - half, centre + half)
ctx.rect(x, y, w, h)
}
ctx.fill()
}
// A centromere across the width it is drawn at, which for a yeast CEN is
// wider than its bands: the waist has to be red where it is a waist.
for (const centromere of centromeres) {
ctx.fillStyle = colourOf(centromere.index)
const [x, y, w, h] = laneRect(frame, centromere.from, centromere.to, centre - half, centre + half)
ctx.fillRect(x, y, w, h)
}
hatch(ctx, frame, set, run, centre, half)
ctx.restore()
// …and the outline over them, in the plot's ink.
ctx.beginPath()
tracePath(ctx, frame, edge, centre, run)
ctx.strokeStyle = paint.guideColour
ctx.lineWidth = OUTLINE_WIDTH
ctx.lineJoin = 'round'
ctx.stroke()
}
if (paint.labels) labelBands(ctx, frame, set, layout, paint, centre, body)
ctx.restore()
}
/**
* Hatch the `gvar` bands of a run: strokes at 45°, since a pattern fill is the
* one thing a vector export cannot carry (`ui/vector.ts`).
*/
function hatch(
ctx: CanvasRenderingContext2D,
frame: LaneFrame,
set: FeatureSet,
run: Run,
centre: number,
half: number,
): void {
const step = 4
ctx.beginPath()
let any = false
for (const placement of run.placements) {
if (stainOf(set.detail[placement.index]) !== 'gvar') continue
any = true
const bottom = centre + half
for (let along = placement.along0 - 2 * half; along < placement.along1; along += step) {
const from = Math.max(along, placement.along0)
const to = Math.min(along + 2 * half, placement.along1)
if (!(to > from)) continue
// A 45° stroke from the bottom edge to the top, cut to the band's ends.
laneMove(ctx, frame, from, bottom - (from - along))
laneLine(ctx, frame, to, bottom - (to - along))
}
}
if (!any) return
ctx.strokeStyle = GVAR_HATCH
ctx.lineWidth = 0.75
ctx.stroke()
}
/**
* Each band's name, inside it, where it fits and the band is not a
* centromere's — in the stain's contrasting ink, so it is read on the band
* rather than over it.
*/
function labelBands(
ctx: CanvasRenderingContext2D,
frame: LaneFrame,
set: FeatureSet,
layout: FeatureLayout,
paint: FeaturePaint,
centre: number,
body: number,
): void {
if (body < 9) return
ctx.save()
ctx.font = paint.font
ctx.textAlign = 'center'
ctx.textBaseline = 'middle'
const lo = Math.min(frame.alongFrom, frame.alongTo) + 1
const hi = Math.max(frame.alongFrom, frame.alongTo) - 1
for (const placement of layout.placements) {
const name = set.name[placement.index]
if (name === '') continue
const stain = stainOf(set.detail[placement.index])
if (stain === 'acen') continue
// The part of the band on screen, since that is where its name can be read.
const from = Math.max(placement.along0, lo)
const to = Math.min(placement.along1, hi)
const width = ctx.measureText(name).width
if (to - from < width + 6) continue
ctx.fillStyle = darkBand(stain) ? '#ffffff' : '#1c1c1e'
laneText(ctx, frame, name, (from + to) / 2, centre)
}
ctx.restore()
}
/**
* The bands the window shows, in ISCN: `Xq28`, or `Xq27.3 – q28` across two.
*
* What a reader zoomed in most wants from an ideogram lane, and the one fact
* the picture cannot carry once a band is wider than the screen. Across two
* sequences the second is named whole, since `q28` alone would be read as the
* first one's.
*/
export function ideogramCaption(set: FeatureSet, layout: FeatureLayout): string | null {
const placements = layout.placements.filter((placement) => set.name[placement.index] !== '')
if (placements.length === 0) return null
const first = placements[0].index
const last = placements[placements.length - 1].index
const firstName = iscnName(set.contigs[set.contig[first]], set.name[first])
if (first === last) return firstName
const sameContig = set.contig[first] === set.contig[last]
const lastName = sameContig ? set.name[last] : iscnName(set.contigs[set.contig[last]], set.name[last])
return `${firstName} – ${lastName}`
}
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