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8414x 8414x 8414x 8414x 8414x 51614x 51614x 51596x 51596x 51613x 51613x 51614x 8414x 8414x 8414x 8414x 8414x 20x 20x 20x 20x 20x 20x 20x 20x 20x 20x 20x 20x 20x 20x 20x 20x 20x 20x 20x 2x 2x 1x 1x 1x 1x 1x 2x | /**
* The pictures the Analysis drawer puts under a result.
*
* Every one of them is drawn **through a `CanvasRenderingContext2D` and through
* nothing else** — no DOM nodes, no SVG, no chart library. That is not a
* preference about how to draw a chart; it is the single decision that gives
* §18.7 its promise of a true vector figure. `ui/vector.ts` implements the same
* context interface and emits PDF operators, so a function that takes a context
* and a box already knows how to write itself onto paper, and the export path
* has nothing to reimplement. The corollary is a hard constraint the whole file
* lives under: only the members enumerated in `VectorTarget` may be touched.
* `putImageData` and `createImageData` are not among them, which is why a matrix
* here is a grid of filled rectangles rather than a raster — the opposite of the
* choice `render/heatmap.ts` makes, and right for the opposite reason: a pileup
* is tens of cells on a side, and tens of cells are paths. The one exception is
* a **list**, the metaplot's per-feature heatmap: thousands of rows read as a
* density, which is a picture and not a grid, so it is coloured on a canvas of
* its own and placed with `drawImage` — a member the page does have, and one it
* writes as a single image the viewer interpolates (see `drawListImage`).
*
* The three drawing functions are pure: a context, an output, a box and a
* palette in, marks out. Nothing here owns a canvas, reads the clock or knows
* what a devicePixelRatio is. The two figure wrappers below own the canvas, the
* resizing and the redraw, and hand the *same* draw function to the export — so
* the figure in the PDF is the figure that was on screen by construction rather
* than by care.
*/
import type {
CurveOutput,
CurveSeries,
MarginProfile,
MatrixMargins,
MatrixOutput,
MatrixSegment,
ProfileOutput,
TableOutput,
} from '../analysis/types'
import {
COLORMAP_SIZE,
DEFAULT_COLORMAP,
applyColormap,
colormapIndex,
isColormap,
} from '../render/colormaps'
import { cellText } from '../figures/tableFigure'
import { figurePaper } from './canvasPalette'
import { el, fmt, trimNumber } from './dom'
import { axisNumber, resolutionLabel } from '../units'
import { scaleFont, subscribeTextScale } from './textScale'
import { parseFont } from './vector'
// ---------------------------------------------------------------------------
// The palette
// ---------------------------------------------------------------------------
export interface PlotTheme {
ink: string
muted: string
grid: string
background: string
series: string[]
font: string
}
/**
* Okabe–Ito, which is the categorical set designed against a colour-vision
* deficiency model rather than measured for lightness afterwards (§7.2 takes the
* same line about the colormaps).
*
* Ordered by how well each holds against white paper, which is why the yellow is
* last: it is the one member of the set that a printed figure loses, and a
* result with eight series has already asked more of a legend than a legend can
* give. Black sits seventh rather than being dropped — against seven hues it
* reads as a series, and this is a figure, not a UI.
*/
const SERIES_COLOURS: readonly string[] = [
'#0072B2',
'#D55E00',
'#009E73',
'#CC79A7',
'#E69F00',
'#56B4E9',
'#000000',
'#F0E442',
]
/** The size every mark in these plots is derived from, before the text scale. */
const PLOT_FONT = '11px system-ui, sans-serif'
/**
* The colours a plot borrows from the stylesheet, read off the node it is
* mounted in.
*
* Read rather than decided, which is the same arrangement `readCanvasPalette`
* keeps for the map and for the same reason: the *stylesheet* knows whether a
* given box follows the theme. In the drawer it does not — `.analysis-figure`
* re-declares the light palette exactly as `.content` does, because a plot in
* there is a figure that leaves the app as a PNG or a PDF — so a figure comes
* out ink on white in either theme while a plot mounted anywhere else follows
* the theme like the rest of the furniture. Both behaviours fall out of asking
* the host, and neither is written down twice.
*
* The fallbacks are the light values, because a canvas asked before it is in the
* document has no computed custom properties and the palette it is about to be
* mounted into is the light one. A plot that came out invisible would be the
* worse failure.
*/
export function plotTheme(host: HTMLElement): PlotTheme {
const style = getComputedStyle(host)
const pick = (name: string, fallback: string): string => {
const value = style.getPropertyValue(name).trim()
return value === '' ? fallback : value
}
return {
ink: pick('--text', '#16181d'),
muted: pick('--text-dim', '#5b6169'),
grid: pick('--border', '#dcdfe3'),
background: pick('--bg', '#ffffff'),
// A copy: the constant is shared by every plot on screen and a caller that
// recoloured one series would recolour all of them.
series: [...SERIES_COLOURS],
font: scaleFont(PLOT_FONT),
}
}
// ---------------------------------------------------------------------------
// Geometry
// ---------------------------------------------------------------------------
interface PlotBox {
width: number
height: number
}
interface Rect {
x: number
y: number
width: number
height: number
}
/**
* Line widths, in CSS pixels, and deliberately not `1 / dpr`.
*
* The renderers in `render/` write `Math.max(1 / dpr, 0.75)` because each of
* them owns a canvas whose transform it set, so `1 / dpr` is one device pixel
* and the floor keeps it from vanishing on a high-density screen. These
* functions own no canvas and are handed a context that may be a `VectorPage`,
* where a "device pixel" is a PDF unit and the figure will be rasterised at
* whatever the printer runs at. So the widths are stated in the units the layout
* is in, with the same 0.75 floor those callers arrived at — about half a point
* at 300 dpi, which is a thin rule rather than a missing one.
*/
const RULE_WIDTH = 0.75
const FRAME_WIDTH = 1
/**
* A gridline: solid and thinner than any rule, being a guide for the eye rather
* than a mark of anything (§18.13) — the charts' own (`option.GRID_WIDTH`).
*/
const GRID_WIDTH = 0.5
const SERIES_WIDTH = 1.6
/** Tick marks, drawn outward from the frame. */
const TICK_LENGTH = 4
/** A band is a range, not a second line; it must not read as one. */
const BAND_ALPHA = 0.18
/** Below this the plot area is smaller than its own axis labels. */
const MIN_PLOT_SIDE = 24
function fontSizeOf(font: string): number {
return parseFont(font).size
}
/** The same font with a heading's weight, for the axis titles. */
function boldOf(font: string): string {
return parseFont(font).bold ? font : `600 ${font}`
}
function paintBackground(ctx: CanvasRenderingContext2D, box: PlotBox, theme: PlotTheme): void {
// Painted rather than cleared: `VectorPage.clearRect` is a no-op, since a page
// is written in order and there is nothing behind it, so a figure that relied
// on the clear would have no ground of its own in the PDF.
ctx.fillStyle = theme.background
ctx.fillRect(0, 0, box.width, box.height)
}
function drawEmpty(
ctx: CanvasRenderingContext2D,
box: PlotBox,
theme: PlotTheme,
message: string,
): void {
ctx.fillStyle = theme.muted
ctx.font = theme.font
ctx.textAlign = 'center'
ctx.textBaseline = 'middle'
ctx.fillText(message, box.width / 2, box.height / 2)
}
// ---------------------------------------------------------------------------
// Axes
// ---------------------------------------------------------------------------
interface Span {
lo: number
hi: number
}
interface Axis {
readonly log: boolean
/** Domain in *drawing* space, which is log10 units on a log axis. */
readonly lo: number
readonly hi: number
/** Fraction along the axis, or `NaN` where the value has no place on it. */
fraction(value: number): number
}
/**
* Where a curve was drawn, and on what axes — the figure's answer to "what is
* under this pixel".
*
* Returned by {@link drawCurve} rather than recomputed by the caller, and that
* is the whole point: the margins are decided by the widths of the tick labels
* and the height of the legend, so anything that measured them from outside
* would be an approximation that drifts every time a label changes. A marquee
* has to land on the number the reader is pointing at, and a rectangle that is
* eight pixels out is a rectangle that selects the wrong range.
*
* `lo` and `hi` are in **drawing space** — log10 units on a log axis — because
* that is the space the pixel mapping is linear in.
*/
export interface CurveLayout {
plot: Rect
x: { log: boolean; lo: number; hi: number }
y: { log: boolean; lo: number; hi: number }
}
/**
* A data value in the space the axis is linear in, or `NaN` if it has none.
*
* The `NaN` for a non-positive value on a log axis is the whole point of this
* function existing. `Math.log10(0)` is `-Infinity` and `Math.log10(-1)` is
* `NaN`, and either one, folded into a minimum, drags the axis to negative
* infinity and collapses every curve onto a single line at the top of the plot.
* A contact-probability curve starts at a separation of zero, so this is not a
* corner case: it is what P(s) does to a log axis on the first point of the
* first series, every time. The point is **dropped**, exactly as `NaN` is
* dropped from a sum everywhere else in this codebase.
*/
function drawSpace(value: number, log: boolean): number {
if (!Number.isFinite(value)) return Number.NaN
if (!log) return value
return value > 0 ? Math.log10(value) : Number.NaN
}
function makeAxis(log: boolean, span: Span): Axis {
const width = span.hi - span.lo
return {
log,
lo: span.lo,
hi: span.hi,
fraction(value: number): number {
const at = drawSpace(value, log)
return Number.isNaN(at) ? Number.NaN : (at - span.lo) / width
},
}
}
/**
* Room around the data, in drawing space.
*
* The y axis gets a little: a maximum drawn exactly on the frame is a maximum a
* reader cannot see. The x axis gets none — a P(s) runs from its first
* separation to its last, and padding it would put white space where the data's
* own limits are the information.
*/
function padSpan(span: Span, fraction: number): Span {
const width = span.hi - span.lo
if (!(width > 0)) {
// A single distinct value would divide by zero. Half a unit either side puts
// the line across the middle of the plot instead of along its edge.
const pad = Math.max(Math.abs(span.lo) * 0.05, 0.5)
return { lo: span.lo - pad, hi: span.hi + pad }
}
return { lo: span.lo - width * fraction, hi: span.hi + width * fraction }
}
function trimZeros(text: string): string {
return text.includes('.') ? text.replace(/\.?0+$/, '') : text
}
/** Through `units.axisNumber`, which is where an axis tick's magnitude is spelled. */
function exponentLabel(value: number): string {
return axisNumber(value)
}
/**
* A tick's number, with as many places as its own step justifies and no more.
*
* `step` rather than the value decides the precision, so a ladder of 0.25, 0.50,
* 0.75 keeps its trailing zeros aligned instead of reading 0.25, 0.5, 0.75.
*/
function formatTick(value: number, step: number): string {
if (!Number.isFinite(value)) return ''
if (value === 0) return '0'
const abs = Math.abs(value)
if (abs < 1e-4 || abs >= 1e6) return exponentLabel(value)
const places = Math.min(6, Math.max(0, -Math.floor(Math.log10(Math.abs(step)))))
return trimZeros(value.toFixed(places))
}
/** The 1-2-5 ladder over `[lo, hi]`, the same rung set `chooseBpStep` climbs. */
function linearTicks(lo: number, hi: number, maxTicks: number): number[] {
const raw = (hi - lo) / Math.max(1, maxTicks)
if (!(raw > 0)) return []
const magnitude = 10 ** Math.floor(Math.log10(raw))
const norm = raw / magnitude
const step = (norm <= 1 ? 1 : norm <= 2 ? 2 : norm <= 5 ? 5 : 10) * magnitude
const first = Math.ceil(lo / step)
const out: number[] = []
// Indexed off `first` rather than accumulated: `v += 0.1` twenty times lands
// a whole ulp away from `2`, and the last tick then falls outside the domain
// and is dropped — the one tick a reader most wants, the axis maximum.
for (let i = 0; ; i++) {
const value = (first + i) * step
if (value > hi + step * 1e-9) break
out.push(value === 0 ? 0 : value)
if (out.length > maxTicks + 2) break
}
return out
}
/**
* Decades within a log domain, with the 2…9 subdivisions where they still read.
*
* `lo` and `hi` are log10. Minor ticks are dropped past six decades, where they
* stop being a subdivision and become a grey smear along the axis.
*/
function decadeTicks(
lo: number,
hi: number,
maxTicks: number,
): { major: number[]; minor: number[] } {
const first = Math.ceil(lo - 1e-9)
const last = Math.floor(hi + 1e-9)
const decades: number[] = []
for (let d = first; d <= last; d++) decades.push(d)
const stride = Math.max(1, Math.ceil(decades.length / Math.max(1, maxTicks)))
const major = decades.filter((_, index) => index % stride === 0).map((d) => 10 ** d)
const minor: number[] = []
if (stride === 1 && decades.length <= 6) {
for (let d = first - 1; d <= last; d++) {
for (let m = 2; m <= 9; m++) {
const value = m * 10 ** d
const at = Math.log10(value)
if (at > lo && at < hi) minor.push(value)
}
}
}
return { major, minor }
}
interface AxisTicks {
major: Array<{ value: number; label: string }>
minor: number[]
}
function axisTicks(axis: Axis, maxTicks: number): AxisTicks {
const label = (values: number[]): AxisTicks => {
const step = values.length > 1 ? values[1] - values[0] : axis.hi - axis.lo
return { major: values.map((value) => ({ value, label: formatTick(value, step) })), minor: [] }
}
if (!axis.log) return label(linearTicks(axis.lo, axis.hi, maxTicks))
const { major, minor } = decadeTicks(axis.lo, axis.hi, maxTicks)
if (major.length >= 2) {
return { major: major.map((value) => ({ value, label: formatTick(value, value) })), minor }
}
// Less than two decades in view — a zoomed-in P(s), a saddle strength over one
// order of magnitude. Decades alone would label such an axis once or not at
// all, so it is labelled on the 1-2-5 ladder in data units instead. The axis
// is still logarithmic; only its labels stop being powers of ten.
return label(linearTicks(10 ** axis.lo, 10 ** axis.hi, maxTicks))
}
// ---------------------------------------------------------------------------
// Curves
// ---------------------------------------------------------------------------
/**
* The x and y domains, over every series and every band edge at once.
*
* Paired rather than scanned axis by axis: a point whose x has no place on a log
* axis contributes no y either, which is what stops the dropped first point of a
* P(s) — separation zero, and by far the largest count in the series — from
* setting the top of a y axis it is not drawn on.
*/
function curveDomains(output: CurveOutput): { x: Span; y: Span } | null {
const xLog = output.xScale === 'log'
const yLog = output.yScale === 'log'
const asked = { x: askedSpan(output.xDomain, xLog), y: askedSpan(output.yDomain, yLog) }
const x: Span = { lo: Number.POSITIVE_INFINITY, hi: Number.NEGATIVE_INFINITY }
const y: Span = { lo: Number.POSITIVE_INFINITY, hi: Number.NEGATIVE_INFINITY }
for (const series of output.series) {
const columns = [series.y, series.low, series.high]
for (let i = 0; i < series.x.length; i++) {
const at = drawSpace(series.x[i], xLog)
if (Number.isNaN(at)) continue
// **The y fit is over the x window, not over the series.** With a window
// asked for, the points outside it are not on the picture, and letting
// them set the ordinate is how a P(s) zoomed to 4 kb–1 Mb still came out
// with its whole height spent on the near-diagonal spike sitting off the
// left edge. Auto means "fit what is shown".
const inside = asked.x === null || (at >= asked.x.lo && at <= asked.x.hi)
let seen = false
for (const column of columns) {
if (column === undefined || i >= column.length) continue
const value = drawSpace(column[i], yLog)
if (Number.isNaN(value)) continue
seen = true
if (!inside) continue
if (value < y.lo) y.lo = value
if (value > y.hi) y.hi = value
}
if (!seen) continue
if (at < x.lo) x.lo = at
if (at > x.hi) x.hi = at
}
}
// A window an axis cannot be fitted in — nothing inside the x window, so no y
// to draw against — is `null`, and the figure says "nothing to plot". Widening
// back out to the whole series instead would answer a question nobody asked
// and look exactly like a figure that had not been asked one.
const xSpan = asked.x ?? (x.lo <= x.hi ? padSpan(x, 0) : null)
const ySpan = asked.y ?? (y.lo <= y.hi ? padSpan(y, 0.05) : null)
if (xSpan === null || ySpan === null) return null
return { x: xSpan, y: ySpan }
}
/**
* An explicit axis window in drawing space, or `null` for "fit the data".
*
* Either bound may be absent or unusable — a reader clears one box, or asks for
* zero on a log axis — and the answer is to fall back to the data for *that*
* axis rather than to refuse the pair. Reversed bounds are sorted rather than
* rejected: a marquee dragged right to left is the same rectangle.
*/
function askedSpan(domain: readonly [number, number] | undefined, log: boolean): Span | null {
if (domain === undefined) return null
const lo = drawSpace(domain[0], log)
const hi = drawSpace(domain[1], log)
if (Number.isNaN(lo) || Number.isNaN(hi) || lo === hi) return null
return { lo: Math.min(lo, hi), hi: Math.max(lo, hi) }
}
function seriesColour(series: CurveSeries, index: number, theme: PlotTheme): string {
return series.colour ?? theme.series[index % theme.series.length]
}
/**
* Every series' colour fixed against the list it belongs to, once.
*
* {@link seriesColour} colours by **position**, which is right when it is handed
* the whole figure and wrong the moment anything filters the list first. Hiding
* a series in the drawer's figures used to do exactly that: with series
* `A, B, C` and `A` switched off, `B` took `A`'s colour and `C` took `B`'s — the
* lines, their confidence bands and their legend swatches all stepping one place
* up the palette. It was silent, it survived into the PNG and the PDF, and its
* most visible form was alt-click *isolate*, which hides everything but one
* series and so always redrew that series in the first palette entry, whichever
* one the reader had picked out.
*
* So the colour is resolved here, against the full, unfiltered list, and stamped
* onto the series before anything is allowed to drop entries. `colour` already
* wins over the palette everywhere it is read, so nothing downstream changes:
* what a filtered list gets is a list of series that already know what colour
* they are.
*
* **A series that carries its own colour keeps it**, sentinels included — the
* `colour: 'none'` of the legend's "+N more" entry names no series and must go
* on naming none. And the *index* is the only thing this reads, so a task that
* left its colours off still gets one palette entry per line in list order,
* which is what `analysis/combine.ts` relies on to give four maps four colours.
*
* No theme is needed, and that is a fact about the palette rather than an
* oversight: `plotTheme` reads ink, grid and background off the host but hands
* back the *same* Okabe–Ito series list either way, because a figure is a figure
* in light and dark alike. Should the categorical palette ever come to depend on
* the host, this function is where the theme has to arrive.
*/
export function resolveSeriesColours(series: readonly CurveSeries[]): CurveSeries[] {
return series.map((entry, index) =>
entry.colour === undefined
? { ...entry, colour: SERIES_COLOURS[index % SERIES_COLOURS.length] }
: entry,
)
}
function legendText(series: CurveSeries): string {
return series.n === undefined || !Number.isFinite(series.n)
? series.name
: `${series.name} (n = ${fmt.int(series.n)})`
}
/**
* How many lines of legend a figure will give up to naming its series.
*
* Three, and past that it says how many it did not name. **The curves are all
* drawn either way** — this is a cap on the *names*, not on the data, and the
* distinction is the whole of why it is here rather than in the task: P(s) over
* a metagenome is four thousand sequences and every one of them is a real
* answer, but four thousand legend entries is a legend taller than the screen
* pushing the picture off the bottom of it. What the reader loses is a lookup
* they could not have used at that size anyway; what they keep is the shape of
* four thousand curves, which is the thing they ran it for.
*/
const LEGEND_LINES = 3
/**
* The legend, wrapped into lines above the plot.
*
* Above rather than floating inside the frame at a corner, which is what a
* chart library would do: a legend over the data hides whichever series happens
* to reach that corner, and on a drawer 300 pixels wide there is no corner that
* is reliably empty. Measured here so the caller can subtract its height before
* it lays the plot out — the legend takes room from the picture rather than
* covering it.
*/
function legendLines(
ctx: CanvasRenderingContext2D,
output: CurveOutput,
width: number,
swatch: number,
gap: number,
): CurveSeries[][] {
if (output.series.length < 2) return []
const lines: CurveSeries[][] = []
let line: CurveSeries[] = []
let used = 0
for (let i = 0; i < output.series.length; i++) {
const series = output.series[i]
const need = swatch + gap * 0.5 + ctx.measureText(legendText(series)).width + gap * 1.5
if (line.length > 0 && used + need > width) {
lines.push(line)
line = []
used = 0
// Full. The remainder is counted rather than listed, in an entry with no
// swatch — it names no one series, so a colour beside it would be a lie
// about which.
if (lines.length === LEGEND_LINES) {
const rest = output.series.length - i
lines[LEGEND_LINES - 1] = [
...lines[LEGEND_LINES - 1],
{ name: `+${fmt.int(rest)} more`, x: EMPTY_SERIES, y: EMPTY_SERIES, colour: 'none' },
]
return lines
}
}
line.push(series)
used += need
}
if (line.length > 0) lines.push(line)
return lines
}
/** The `x`/`y` of a legend entry that names no data. Shared; never written to. */
const EMPTY_SERIES = new Float64Array(0)
/**
* One series' band, as filled polygons at reduced alpha.
*
* One polygon per run of drawable points rather than one for the whole series:
* a gap in the middle of a bootstrap interval — a distance bin no feature
* reached — would otherwise be bridged by a straight edge across it, drawing a
* confidence interval over a region where there is no estimate at all.
*/
function drawBand(
ctx: CanvasRenderingContext2D,
series: CurveSeries,
x: Axis,
y: Axis,
plot: Rect,
colour: string,
): void {
const { low, high } = series
if (low === undefined || high === undefined) return
const n = Math.min(series.x.length, low.length, high.length)
ctx.save()
ctx.globalAlpha = BAND_ALPHA
ctx.fillStyle = colour
const at = (index: number): number => plot.x + x.fraction(series.x[index]) * plot.width
const up = (value: number): number => plot.y + (1 - y.fraction(value)) * plot.height
let start = -1
const flush = (end: number): void => {
if (start >= 0 && end - start >= 2) {
ctx.beginPath()
for (let i = start; i < end; i++) {
if (i === start) ctx.moveTo(at(i), up(high[i]))
else ctx.lineTo(at(i), up(high[i]))
}
for (let i = end - 1; i >= start; i--) ctx.lineTo(at(i), up(low[i]))
ctx.closePath()
ctx.fill()
}
start = -1
}
for (let i = 0; i < n; i++) {
const ok =
!Number.isNaN(x.fraction(series.x[i])) &&
!Number.isNaN(y.fraction(low[i])) &&
!Number.isNaN(y.fraction(high[i]))
if (ok) {
if (start < 0) start = i
} else {
flush(i)
}
}
flush(n)
ctx.restore()
}
function drawSeriesLine(
ctx: CanvasRenderingContext2D,
series: CurveSeries,
x: Axis,
y: Axis,
plot: Rect,
colour: string,
): void {
const n = Math.min(series.x.length, series.y.length)
ctx.strokeStyle = colour
ctx.fillStyle = colour
ctx.lineWidth = SERIES_WIDTH
ctx.lineJoin = 'round'
// A series whose x is not an ordering draws as marks and nothing else. Taken
// first, because everything below is about which *runs* of points to join, and
// the answer here is none of them.
if (series.mark === 'points') {
const radius = SERIES_WIDTH * 1.4
for (let i = 0; i < n; i++) {
const fx = x.fraction(series.x[i])
const fy = y.fraction(series.y[i])
if (Number.isNaN(fx) || Number.isNaN(fy)) continue
ctx.beginPath()
ctx.arc(
plot.x + fx * plot.width,
plot.y + (1 - fy) * plot.height,
radius,
0,
Math.PI * 2,
)
ctx.fill()
}
return
}
let start = -1
const flush = (end: number): void => {
if (start >= 0) {
if (end - start === 1) {
// A lone drawable point between two gaps strokes nothing, and dropping
// it would silently lose the only estimate in that stretch. Drawn as a
// square of the line's own width, which is what the eye reads as "one
// measurement" rather than "a very short line".
const size = SERIES_WIDTH * 1.6
ctx.fillRect(
plot.x + x.fraction(series.x[start]) * plot.width - size / 2,
plot.y + (1 - y.fraction(series.y[start])) * plot.height - size / 2,
size,
size,
)
} else if (end - start > 1) {
ctx.beginPath()
for (let i = start; i < end; i++) {
const px = plot.x + x.fraction(series.x[i]) * plot.width
const py = plot.y + (1 - y.fraction(series.y[i])) * plot.height
if (i === start) ctx.moveTo(px, py)
else ctx.lineTo(px, py)
}
ctx.stroke()
}
}
start = -1
}
for (let i = 0; i < n; i++) {
const ok = !Number.isNaN(x.fraction(series.x[i])) && !Number.isNaN(y.fraction(series.y[i]))
if (ok) {
if (start < 0) start = i
} else {
flush(i)
}
}
flush(n)
}
/**
* Draw a curve output into `box`, from its own origin.
*
* The transform is the caller's: on screen the figure wrapper has already scaled
* the context by the device pixel ratio, and on paper `VectorPage.setOrigin` has
* placed it. Touching `setTransform` here would undo either one.
*/
export function drawCurve(
ctx: CanvasRenderingContext2D,
output: CurveOutput,
box: { width: number; height: number },
theme: PlotTheme,
): CurveLayout | null {
paintBackground(ctx, box, theme)
const size = fontSizeOf(theme.font)
const line = Math.round(size * 1.35)
const gap = Math.round(size * 0.45)
ctx.font = theme.font
const domains = curveDomains(output)
if (domains === null) {
drawEmpty(ctx, box, theme, 'nothing to plot')
return null
}
const x = makeAxis(output.xScale === 'log', domains.x)
const y = makeAxis(output.yScale === 'log', domains.y)
// Tick counts come from the box rather than from the plot area, which is not
// known yet: the labels decide the margins and the margins would then decide
// the labels. Erring towards too few is the safe direction — a sparse axis
// reads, a crowded one does not.
const yTicks = axisTicks(y, Math.max(2, Math.floor(box.height / (line * 3))))
const xTicks = axisTicks(x, Math.max(2, Math.floor(box.width / (size * 7))))
let widestY = 0
for (const tick of yTicks.major) widestY = Math.max(widestY, ctx.measureText(tick.label).width)
let widestX = 0
for (const tick of xTicks.major) widestX = Math.max(widestX, ctx.measureText(tick.label).width)
const left = Math.ceil(widestY) + TICK_LENGTH + gap + (output.yLabel === '' ? 0 : line)
const right = Math.ceil(widestX / 2) + gap
// Wrapped against the plot area rather than the whole box, because that is
// where it is drawn from: measuring against the box would let the last entry
// of a line run off the right edge by the width of the y axis.
const legend = legendLines(ctx, output, Math.max(0, box.width - left - right), size * 1.6, gap)
// Half a line of headroom above the frame, because the topmost y tick label is
// centred on its own tick and a tick can land on the domain's ceiling.
const top = legend.length * line + (legend.length > 0 ? gap : 0) + Math.ceil(line / 2)
const bottom =
TICK_LENGTH + gap + line + (output.xLabel === '' ? 0 : line) + Math.round(size * 0.3)
const plot: Rect = {
x: left,
y: top,
width: box.width - left - right,
height: box.height - top - bottom,
}
if (plot.width < MIN_PLOT_SIDE || plot.height < MIN_PLOT_SIDE) {
drawEmpty(ctx, box, theme, 'too small to draw')
return null
}
// Gridlines under everything, so a line crossing one is unambiguously on top.
ctx.strokeStyle = theme.grid
ctx.lineWidth = GRID_WIDTH
ctx.beginPath()
for (const tick of yTicks.major) {
const at = y.fraction(tick.value)
if (!(at >= 0 && at <= 1)) continue
const py = plot.y + (1 - at) * plot.height
ctx.moveTo(plot.x, py)
ctx.lineTo(plot.x + plot.width, py)
}
for (const tick of xTicks.major) {
const at = x.fraction(tick.value)
if (!(at >= 0 && at <= 1)) continue
const px = plot.x + at * plot.width
ctx.moveTo(px, plot.y)
ctx.lineTo(px, plot.y + plot.height)
}
ctx.stroke()
// Clipped to the frame, which matters only once an axis window can be asked
// for: a series then runs off the edge of the plot rather than ending at it,
// and unclipped it would be drawn across the tick labels and the legend. The
// clip is a path in the PDF as much as on the canvas (`ui/vector.ts`), so the
// export is cut the same way rather than differently.
ctx.save()
ctx.beginPath()
ctx.rect(plot.x, plot.y, plot.width, plot.height)
ctx.clip()
// Every band before any line: within a series the band belongs under its own
// line, and across series it belongs under all of them — a translucent wash
// laid over a neighbour's line tints it into a colour the legend does not
// name.
output.series.forEach((series, index) => {
drawBand(ctx, series, x, y, plot, seriesColour(series, index, theme))
})
output.series.forEach((series, index) => {
drawSeriesLine(ctx, series, x, y, plot, seriesColour(series, index, theme))
})
ctx.restore()
// The frame last, so it closes over the ends of the data rather than being
// painted through by them; in the ink, as every plot's is (§18.13).
ctx.strokeStyle = theme.ink
ctx.lineWidth = FRAME_WIDTH
// The series left a round join behind, which is right for a polyline and
// wrong for a rectangle; PDF carries the join in the graphics state, so it has
// to be put back rather than assumed.
ctx.lineJoin = 'miter'
ctx.strokeRect(plot.x, plot.y, plot.width, plot.height)
ctx.strokeStyle = theme.grid
ctx.lineWidth = RULE_WIDTH
ctx.beginPath()
for (const value of xTicks.minor) {
const at = x.fraction(value)
if (!(at >= 0 && at <= 1)) continue
const px = plot.x + at * plot.width
ctx.moveTo(px, plot.y + plot.height)
ctx.lineTo(px, plot.y + plot.height + TICK_LENGTH / 2)
}
for (const value of yTicks.minor) {
const at = y.fraction(value)
if (!(at >= 0 && at <= 1)) continue
const py = plot.y + (1 - at) * plot.height
ctx.moveTo(plot.x - TICK_LENGTH / 2, py)
ctx.lineTo(plot.x, py)
}
ctx.stroke()
ctx.strokeStyle = theme.muted
ctx.fillStyle = theme.muted
ctx.font = theme.font
ctx.lineWidth = RULE_WIDTH
ctx.textAlign = 'right'
ctx.textBaseline = 'middle'
for (const tick of yTicks.major) {
const at = y.fraction(tick.value)
if (!(at >= 0 && at <= 1)) continue
const py = plot.y + (1 - at) * plot.height
ctx.beginPath()
ctx.moveTo(plot.x - TICK_LENGTH, py)
ctx.lineTo(plot.x, py)
ctx.stroke()
ctx.fillText(tick.label, plot.x - TICK_LENGTH - gap * 0.5, py)
}
ctx.textAlign = 'center'
ctx.textBaseline = 'top'
for (const tick of xTicks.major) {
const at = x.fraction(tick.value)
if (!(at >= 0 && at <= 1)) continue
const px = plot.x + at * plot.width
ctx.beginPath()
ctx.moveTo(px, plot.y + plot.height)
ctx.lineTo(px, plot.y + plot.height + TICK_LENGTH)
ctx.stroke()
// The mark stays on its value and the label steps back inside the box when
// it would hang off the end — the colourbar's rule, for the same reason:
// half of a number is not a number.
const half = ctx.measureText(tick.label).width / 2
const put = Math.min(Math.max(px, half), box.width - half)
ctx.fillText(tick.label, put, plot.y + plot.height + TICK_LENGTH + gap * 0.4)
}
ctx.fillStyle = theme.ink
ctx.font = boldOf(theme.font)
if (output.xLabel !== '') {
ctx.textAlign = 'center'
ctx.textBaseline = 'bottom'
ctx.fillText(output.xLabel, plot.x + plot.width / 2, box.height - Math.round(size * 0.2))
}
if (output.yLabel !== '') {
ctx.save()
ctx.translate(Math.round(size * 0.9), plot.y + plot.height / 2)
ctx.rotate(-Math.PI / 2)
ctx.textAlign = 'center'
ctx.textBaseline = 'middle'
ctx.fillText(output.yLabel, 0, 0)
ctx.restore()
}
ctx.font = theme.font
ctx.textAlign = 'left'
ctx.textBaseline = 'middle'
const swatch = size * 1.6
legend.forEach((entries, row) => {
let at = plot.x
const py = Math.round(row * line + line / 2)
for (const series of entries) {
// `colour: 'none'` is the "+N more" entry, which names no series and
// therefore draws no swatch; everything else takes its own line's colour.
if (series.colour !== 'none') {
ctx.strokeStyle = seriesColour(series, output.series.indexOf(series), theme)
ctx.lineWidth = SERIES_WIDTH
ctx.beginPath()
ctx.moveTo(at, py)
ctx.lineTo(at + swatch, py)
ctx.stroke()
}
const text = legendText(series)
ctx.fillStyle = theme.ink
ctx.fillText(text, at + swatch + gap * 0.5, py)
at += swatch + gap * 0.5 + ctx.measureText(text).width + gap * 1.5
}
})
return { plot, x: { log: x.log, lo: x.lo, hi: x.hi }, y: { log: y.log, lo: y.lo, hi: y.hi } }
}
// ---------------------------------------------------------------------------
// Matrices
// ---------------------------------------------------------------------------
/**
* The 256 colours of a colormap as CSS strings, built once per name.
*
* The same argument `RGBA_CACHE` makes one level down: this is read once per
* cell of the matrix, and a `rgb(…)` string built inside that loop is an
* allocation per cell for a value that has 256 possibilities.
*/
const CSS_LUTS = new Map<string, string[]>()
function colourTable(name: string): string[] {
const held = CSS_LUTS.get(name)
if (held !== undefined) return held
const lut = applyColormap(name)
const table: string[] = new Array<string>(COLORMAP_SIZE)
for (let i = 0; i < COLORMAP_SIZE; i++) {
table[i] = `rgb(${lut[i * 4]}, ${lut[i * 4 + 1]}, ${lut[i * 4 + 2]})`
}
CSS_LUTS.set(name, table)
return table
}
/**
* The colour scale, symmetric about `centre` where the output declares one.
*
* That symmetry is the whole reason `MatrixOutput.centre` exists: a scale fitted
* to the data's own extremes moves its midpoint with the data, so the value that
* means "no change" — 1 for a ratio, 0 for a correlation — lands on a different
* colour in every panel, and two pileups become uncomparable by exactly the
* amount their tails differ.
*/
function matrixRange(output: MatrixOutput): { vmin: number; vmax: number } | null {
// A scale the task fixed is not a suggestion: it is there so the picture can
// be laid beside the one the tool it agrees with draws. See `MatrixOutput.range`.
if (output.range !== undefined && output.range[1] > output.range[0]) {
return { vmin: output.range[0], vmax: output.range[1] }
}
let lo = Number.POSITIVE_INFINITY
let hi = Number.NEGATIVE_INFINITY
for (const value of output.values) {
if (!Number.isFinite(value)) continue
if (value < lo) lo = value
if (value > hi) hi = value
}
if (!(lo <= hi)) return null
if (output.centre !== undefined) {
const centre = output.centre
// A constant matrix at the centre value has no half-width; one unit is a
// readable span and puts every cell on the midpoint colour, which is the
// true answer rather than a division by zero.
const half = Math.max(Math.abs(hi - centre), Math.abs(lo - centre)) || 1
return { vmin: centre - half, vmax: centre + half }
}
return { vmin: lo, vmax: hi > lo ? hi : lo + 1 }
}
/**
* A cell's side, in CSS pixels, snapped to a whole pixel where there is room.
*
* Adjacent rectangles that meet on a fractional boundary are antialiased against
* each other, and a grid of them shows a lattice of pale seams that reads as
* structure in the data. Whole-pixel cells tile exactly and have none. Below one
* pixel there is no grid to snap to and no seam to see either, so the fractional
* size stands — which is what keeps a 500-row per-feature heatmap inside its box
* instead of overflowing it by 500 rounded-up pixels.
*/
function cellSide(available: number, count: number): number {
const raw = available / Math.max(1, count)
return raw >= 1 ? Math.floor(raw) : Math.max(raw, 0)
}
/**
* **One cell size for both axes**, so a cell is a square and an `n × n` matrix
* is a square picture.
*
* The two were computed independently, each filling its own axis, which left the
* aspect of a saddle or a correlation heatmap to be decided by how wide the
* reader had dragged the drawer: the same 50 × 50 saddle was a tall rectangle in
* a narrow panel and a squat one in a wide one. That is a picture whose shape
* carries no information and reads as one whose shape does — a saddle is read by
* comparing its two corners, and a corner stretched 40% along one axis looks
* stronger than the one opposite it. A correlation heatmap over eight tracks is
* the same argument with the diagonal as the giveaway.
*
* The smaller of the two, so the picture fits either way; the slack on the other
* axis is centred rather than pooled at one end (see {@link drawMatrix}). A
* non-square matrix keeps its own aspect exactly, which is the same rule stated
* once: the cells are square, so the picture is as tall as it is many.
*
* Not every matrix wants it: see {@link matrixCells}, which is where the choice
* is made, and `MatrixOutput.aspect`, which is where it is declared.
*/
export function squareCell(
availableWidth: number,
availableHeight: number,
ncols: number,
nrows: number,
): number {
return Math.min(cellSide(availableWidth, ncols), cellSide(availableHeight, nrows))
}
/**
* The cell's width and height — square, or one that fills the box.
*
* {@link squareCell} is the rule for a matrix with the *same quantity on both
* axes*, which is nearly all of them and every one with a diagonal. The
* exception is a picture whose rows are a **list**: the metaplot's per-feature
* heatmap is three thousand features down and a thousand bins across, and
* square cells there make it a ribbon a fifth of the card wide with white on
* either side. Nothing is compared across its diagonal because it has none —
* a row is a feature and a column is a distance — so the cell may be as wide as
* the box allows, which is the block every metaplot tool draws and the shape
* that lines the picture up with the profile above it.
*/
export function matrixCells(
availableWidth: number,
availableHeight: number,
output: Pick<MatrixOutput, 'ncols' | 'nrows' | 'aspect' | 'large'>,
): { width: number; height: number } {
if (output.aspect === 'fill') {
// The whole box, unsnapped: a list is drawn as one image (see
// {@link drawListImage}), so there are no neighbouring rectangles to seam,
// and a box that whole cells left a strip of white beside is just filled.
return {
width: availableWidth / Math.max(1, output.ncols),
height: availableHeight / Math.max(1, output.nrows),
}
}
if (output.large === true) {
// Unsnapped: the painter puts each cell's edges on whole pixels instead.
const side = Math.min(availableWidth / Math.max(1, output.ncols), availableHeight / Math.max(1, output.nrows))
return { width: side, height: side }
}
const cell = squareCell(availableWidth, availableHeight, output.ncols, output.nrows)
return { width: cell, height: cell }
}
/**
* Where a list of tick labels sits along an axis of `cells` cells.
*
* One label per cell names *that cell*, so it goes at the cell's centre — a
* saddle's quantile groups, a MAG list. Any other count is a scale laid across
* the axis and its two ends are the axis's two ends — a pileup's `-100 kb`,
* `0`, `+100 kb`, which must reach the corners or they are describing a
* different window from the one drawn.
*/
function tickFractions(count: number, cells: number): number[] {
if (count <= 0) return []
if (count === 1) return [0.5]
if (count === cells) return Array.from({ length: count }, (_, i) => (i + 0.5) / count)
return Array.from({ length: count }, (_, i) => i / (count - 1))
}
/** Every k-th label, where k is what it takes for two of them not to collide. */
function labelStride(need: number, fractions: number[], length: number): number {
if (fractions.length < 2) return 1
const spacing = Math.abs(fractions[1] - fractions[0]) * length
if (!(spacing > 0)) return fractions.length
return Math.max(1, Math.ceil(need / spacing))
}
function formatStat(value: number, digits?: number): string {
if (!Number.isFinite(value)) return '—'
if (digits !== undefined) return value.toFixed(digits)
return Number.isInteger(value) ? fmt.int(value) : trimNumber(value)
}
/**
* The extent a marginal profile is drawn against, per track name (§18.8).
*
* **Its own**, and not from zero. A band three lines tall is not an axis and
* cannot be read as one; what it promises is the *shape* of the aggregate along
* the window, which is the whole reason it is there. Drawn from zero, a ChIP
* track whose aggregate runs from 45 to 92 — a signal that doubles at the
* anchor — is a line across the top of the band with a bump in it, while the
* same numbers as a metaplot curve in the same drawer are a peak twice the
* height of the baseline. Two pictures of one quantity that disagree about
* whether anything happened is the complaint this is a fix for. The range is
* printed in the key, which is what keeps a self-scaled band honest about how
* much of an effect it is showing.
*
* **One ruler per quantity, across both edges.** The same track drawn above the
* picture and beside it is one measurement, and two bands normalised apart
* would invite a reader to compare a bump on one against a bump on the other
* when the two are drawn to different scales. Two *different* tracks keep their
* own rulers, because two units have no common axis.
*/
function marginScales(
margins: MatrixMargins | undefined,
): Map<string, { lo: number; hi: number }> {
const out = new Map<string, { lo: number; hi: number }>()
for (const profile of [...(margins?.top ?? []), ...(margins?.right ?? [])]) {
const held = out.get(profile.name) ?? {
lo: Number.POSITIVE_INFINITY,
hi: Number.NEGATIVE_INFINITY,
}
for (const value of profile.values) {
if (!Number.isFinite(value)) continue
if (value < held.lo) held.lo = value
if (value > held.hi) held.hi = value
}
out.set(profile.name, held)
}
return out
}
/**
* One marginal profile, filled under a line, against an edge of the picture.
*
* Its colour comes from {@link SERIES_COLOURS}, deliberately the same list a
* curve draws from: a track above a pileup and the same track as a curve two
* blocks down the drawer are one quantity, and one colour for it in both is the
* difference between a figure a reader can follow and a page of unrelated
* pictures.
*
* Normalised against {@link marginScales}'s answer for its track. A profile with
* no variation in it draws flat on its own baseline rather than filling the
* band, which is what "no variation" looks like.
*
* `along: 'x'` runs left to right above the picture; `along: 'y'` runs top to
* bottom beside it, growing rightwards — the two edges the anchors of an
* off-diagonal pileup sit on.
*
* `NaN` is a gap and is drawn as one: the fill and the line both break, so a
* window with no coverage reads as missing rather than as zero.
*/
function drawMargin(
ctx: CanvasRenderingContext2D,
profile: MarginProfile,
fallback: string,
theme: PlotTheme,
layout: {
along: 'x' | 'y'
plot: Rect
band: number
gap: number
range?: { lo: number; hi: number }
},
): void {
const { values } = profile
let lo = layout.range?.lo ?? Number.POSITIVE_INFINITY
let hi = layout.range?.hi ?? Number.NEGATIVE_INFINITY
if (layout.range === undefined) {
for (const value of values) {
if (!Number.isFinite(value)) continue
if (value < lo) lo = value
if (value > hi) hi = value
}
}
if (!(lo <= hi)) return
const floor = lo
const span = hi - floor
const colour = profile.colour ?? fallback
const { along, plot, band, gap: pad } = layout
// Where a value of `fraction` lands, and where the baseline is: above the
// picture the band grows upwards, beside it the band grows rightwards.
const base = along === 'x' ? plot.y - pad : plot.x + plot.width + pad
const depth = (fraction: number): number =>
along === 'x' ? base - fraction * band : base + fraction * band
const across = (index: number): number =>
along === 'x'
? plot.x + ((index + 0.5) / values.length) * plot.width
: plot.y + ((index + 0.5) / values.length) * plot.height
const point = (index: number, fraction: number): [number, number] =>
along === 'x' ? [across(index), depth(fraction)] : [depth(fraction), across(index)]
// Runs of finite values, each filled and stroked on its own so a gap stays a
// gap.
let run: Array<[number, number]> = []
const flush = (): void => {
if (run.length === 0) return
if (run.length > 1) {
ctx.fillStyle = colour
ctx.globalAlpha = BAND_ALPHA
ctx.beginPath()
const last = run[run.length - 1]
// The fill is the run plus the two feet that drop it onto the band's own
// baseline, so a profile is an area under a line rather than a ribbon.
if (along === 'x') ctx.moveTo(run[0][0], base)
else ctx.moveTo(base, run[0][1])
for (const [x, y] of run) ctx.lineTo(x, y)
if (along === 'x') ctx.lineTo(last[0], base)
else ctx.lineTo(base, last[1])
ctx.closePath()
ctx.fill()
ctx.globalAlpha = 1
}
ctx.strokeStyle = colour
ctx.lineWidth = SERIES_WIDTH
ctx.beginPath()
run.forEach(([x, y], at) => (at === 0 ? ctx.moveTo(x, y) : ctx.lineTo(x, y)))
ctx.stroke()
run = []
}
for (let index = 0; index < values.length; index++) {
const value = values[index]
if (!Number.isFinite(value)) {
flush()
continue
}
run.push(point(index, span > 0 ? (value - floor) / span : 0))
}
flush()
// The band's own baseline, so a flat profile is visibly flat rather than
// absent, and so the two bands read as two plots rather than as decoration.
ctx.strokeStyle = theme.grid
ctx.lineWidth = RULE_WIDTH
ctx.beginPath()
if (along === 'x') {
ctx.moveTo(plot.x, base)
ctx.lineTo(plot.x + plot.width, base)
} else {
ctx.moveTo(base, plot.y)
ctx.lineTo(base, plot.y + plot.height)
}
ctx.stroke()
ctx.lineWidth = FRAME_WIDTH
}
/** The most a sequence's name standing under a picture may take, in font sizes; a longer one is cut short. */
const SEGMENT_NAME_ROOM = 12
/** The fewest pixels between two rules marking where sequences meet; a closer one is left out. */
const SEGMENT_RULE_GAP = 3
/** How the names of the sequences along x are written: lying down or standing up, and the room they take below the picture. */
interface SegmentNames {
upright: boolean
room: number
}
/** `text`, cut short with an ellipsis to fit `room` pixels. */
function clipText(ctx: CanvasRenderingContext2D, text: string, room: number): string {
if (ctx.measureText(text).width <= room) return text
let low = 0
let high = text.length
while (low < high) {
const mid = (low + high + 1) >> 1
if (ctx.measureText(`${text.slice(0, mid)}…`).width <= room) low = mid
else high = mid - 1
}
return low === 0 ? '' : `${text.slice(0, low)}…`
}
/**
* Which of a run of sequences' names are written: each at its sequence's
* middle, where it fits the sequence's own extent and clears the last one
* written.
*
* @param extent A name's length along the axis, in pixels.
*/
function namesWritten(
segments: readonly MatrixSegment[],
cellPx: number,
at: number,
extent: (segment: MatrixSegment, index: number) => number,
gap: number,
): boolean[] {
let last = Number.NEGATIVE_INFINITY
return segments.map((segment, index) => {
const from = at + segment.from * cellPx
const to = at + segment.to * cellPx
const size = extent(segment, index)
const middle = (from + to) / 2
if (size > to - from + gap * 2 || middle - size / 2 < last + gap) return false
last = middle + size / 2
return true
})
}
/**
* How the names along x are written. Lying down, unless standing them up
* writes more of them — two assemblies' dozens of contigs are narrower than
* their names nearly always — and then as tall as the longest, up to
* {@link SEGMENT_NAME_ROOM} font sizes.
*
* @param cellPx The widest a cell can be, before the picture's height is known.
*/
function segmentNames(ctx: CanvasRenderingContext2D, output: MatrixOutput, cellPx: number, size: number, line: number, gap: number): SegmentNames {
const segments = output.xSegments ?? []
if (segments.length === 0) return { upright: false, room: 0 }
const widths = segments.map((segment) => ctx.measureText(segment.label).width)
const count = (written: boolean[]): number => written.filter(Boolean).length
const lying = count(namesWritten(segments, cellPx, 0, (_, index) => widths[index], gap))
const standing = count(namesWritten(segments, cellPx, 0, () => line, 0))
if (standing <= lying) return { upright: false, room: line }
return { upright: true, room: Math.min(Math.max(...widths), size * SEGMENT_NAME_ROOM) }
}
/**
* The sequences laid along a matrix's axes (§28): a rule where one ends and
* the next begins, across the picture — one a few pixels from the last left
* out, where small sequences crowd — and each one's name under or beside it
* where there is room, a name wider than its sequence or than the gap to the
* last one written left for a closer look.
*/
function drawSegments(
ctx: CanvasRenderingContext2D,
output: MatrixOutput,
plot: Rect,
cell: { cellW: number; cellH: number; gap: number; line: number },
names: SegmentNames,
theme: PlotTheme,
): void {
const xs = output.xSegments ?? []
const ys = output.ySegments ?? []
if (xs.length === 0 && ys.length === 0) return
ctx.save()
ctx.strokeStyle = theme.grid
ctx.lineWidth = RULE_WIDTH
ctx.beginPath()
let lastRule = Number.NEGATIVE_INFINITY
for (const segment of xs) {
if (!(segment.from > 0)) continue
const x = Math.round(plot.x + segment.from * cell.cellW) + 0.5
if (x - lastRule < SEGMENT_RULE_GAP) continue
ctx.moveTo(x, plot.y)
ctx.lineTo(x, plot.y + plot.height)
lastRule = x
}
lastRule = Number.NEGATIVE_INFINITY
for (const segment of ys) {
if (!(segment.from > 0)) continue
const y = Math.round(plot.y + segment.from * cell.cellH) + 0.5
if (y - lastRule < SEGMENT_RULE_GAP) continue
ctx.moveTo(plot.x, y)
ctx.lineTo(plot.x + plot.width, y)
lastRule = y
}
ctx.stroke()
ctx.fillStyle = theme.muted
ctx.font = theme.font
const under = plot.y + plot.height + TICK_LENGTH + cell.gap / 2
if (names.upright) {
const written = namesWritten(xs, cell.cellW, plot.x, () => cell.line, 0)
ctx.textAlign = 'right'
ctx.textBaseline = 'middle'
xs.forEach((segment, i) => {
if (!written[i]) return
ctx.save()
ctx.translate(plot.x + ((segment.from + segment.to) / 2) * cell.cellW, under)
ctx.rotate(-Math.PI / 2)
ctx.fillText(clipText(ctx, segment.label, names.room), 0, 0)
ctx.restore()
})
} else {
const written = namesWritten(xs, cell.cellW, plot.x, (segment) => ctx.measureText(segment.label).width, cell.gap)
ctx.textAlign = 'center'
ctx.textBaseline = 'top'
xs.forEach((segment, i) => {
if (written[i]) ctx.fillText(segment.label, plot.x + ((segment.from + segment.to) / 2) * cell.cellW, under)
})
}
const beside = namesWritten(ys, cell.cellH, plot.y, () => cell.line, cell.line * 0.1)
ctx.textAlign = 'right'
ctx.textBaseline = 'middle'
ys.forEach((segment, i) => {
if (beside[i]) ctx.fillText(segment.label, plot.x - TICK_LENGTH, plot.y + ((segment.from + segment.to) / 2) * cell.cellH)
})
ctx.restore()
}
/**
* The most rows a list's image keeps: past this, neighbouring rows are averaged
* into one, which is what a picture this tall does on screen and in a PNG at
* 300 dpi anyway — four thousand features in four hundred pixels are ten to a
* pixel whatever draws them.
*/
const LIST_IMAGE_ROWS = 2048
/**
* A list's cells as one image — the metaplot's per-feature heatmap (§18.8) —
* drawn into the plot, or `false` where there is no canvas to build it on and
* the caller draws rectangles as before.
*
* Its rows are a list, not a coordinate, so what a reader reads off it is a
* density — where the signal sits across thousands of features — and a grid of
* squares with a seam at every edge, each one a target for the pointer, was
* the wrong picture of that: a grid where a heatmap was wanted. So it is
* coloured once, row by row, averaging neighbours where there are more rows than
* the image keeps, and drawn with smoothing at high quality — on screen a
* bilinear stretch of eighty bins across the plot, and on a PDF page an image
* the viewer interpolates (`ui/vector.ts`). An empty cell is clear, so the
* paper shows through it.
*/
function drawListImage(
ctx: CanvasRenderingContext2D,
output: MatrixOutput,
plot: Rect,
range: { vmin: number; vmax: number },
): boolean {
if (typeof document === 'undefined') return false
const rows = Math.min(output.nrows, LIST_IMAGE_ROWS)
const scratch = document.createElement('canvas')
scratch.width = output.ncols
scratch.height = rows
const draw = scratch.getContext('2d')
if (draw === null) return false
const image = draw.createImageData(output.ncols, rows)
const lut = applyColormap(isColormap(output.colormap) ? output.colormap : DEFAULT_COLORMAP)
const scale = 1 / (range.vmax - range.vmin)
for (let row = 0; row < rows; row++) {
// The features this image row stands for: one each while they fit.
const from = Math.floor((row * output.nrows) / rows)
const to = Math.max(from + 1, Math.floor(((row + 1) * output.nrows) / rows))
for (let col = 0; col < output.ncols; col++) {
let sum = 0
let n = 0
for (let r = from; r < to; r++) {
const value = output.values[r * output.ncols + col]
if (!Number.isFinite(value)) continue
sum += value
n++
}
const at = (row * output.ncols + col) * 4
const index = n === 0 ? -1 : colormapIndex((sum / n - range.vmin) * scale)
if (index < 0) continue
image.data[at] = lut[index * 4]
image.data[at + 1] = lut[index * 4 + 1]
image.data[at + 2] = lut[index * 4 + 2]
image.data[at + 3] = 255
}
}
draw.putImageData(image, 0, 0)
ctx.save()
ctx.imageSmoothingEnabled = true
ctx.imageSmoothingQuality = 'high'
ctx.drawImage(scratch, 0, 0, output.ncols, rows, plot.x, plot.y, plot.width, plot.height)
ctx.restore()
return true
}
/**
* Draw a matrix output into `box`, from its own origin.
*
* Cells are filled rectangles rather than a raster, and that is forced rather
* than chosen: `putImageData` is not part of `VectorTarget`, so a rasterised
* pileup could not be written to a PDF page at all. It is also the right shape
* for the data — §18.7's matrices are tens to a few hundred cells on a side, and
* a few hundred rectangles in a vector figure is a figure a reader can restyle.
*/
export function drawMatrix(
ctx: CanvasRenderingContext2D,
output: MatrixOutput,
box: { width: number; height: number },
theme: PlotTheme,
): void {
paintBackground(ctx, box, theme)
const size = fontSizeOf(theme.font)
const line = Math.round(size * 1.35)
const gap = Math.round(size * 0.45)
ctx.font = theme.font
const range = matrixRange(output)
if (range === null || output.nrows < 1 || output.ncols < 1) {
drawEmpty(ctx, box, theme, 'nothing to plot')
return
}
// An unknown colormap name would throw out of `applyColormap` in the middle of
// a paint. A result drawn on the default ramp is a result the reader can see
// and question; an exception is a blank drawer.
const colours = colourTable(isColormap(output.colormap) ? output.colormap : DEFAULT_COLORMAP)
const barTicks = linearTicks(
range.vmin,
range.vmax,
Math.max(2, Math.floor(box.height / (line * 3))),
)
const barStep = barTicks.length > 1 ? barTicks[1] - barTicks[0] : range.vmax - range.vmin
let widestBar = 0
for (const value of barTicks) {
widestBar = Math.max(widestBar, ctx.measureText(formatTick(value, barStep)).width)
}
let widestY = 0
for (const label of output.yTicks) widestY = Math.max(widestY, ctx.measureText(label).width)
// Sequences along an axis name themselves where the ticks would be.
for (const segment of output.ySegments ?? []) widestY = Math.max(widestY, ctx.measureText(segment.label).width)
const xNamed = output.xTicks.length > 0 || (output.xSegments ?? []).length > 0
const barWidth = Math.round(size * 0.9)
// The marginal profiles, and the two bands they need. A band is three lines
// tall, which is enough for a shape to be a shape and little enough that the
// picture — which is the subject — keeps its size. See {@link MatrixMargins}.
const topMargins = (output.margins?.top ?? []).filter((profile) => profile.values.length > 0)
const rightMargins = (output.margins?.right ?? []).filter((profile) => profile.values.length > 0)
const band = Math.round(size * 3)
const topBand = topMargins.length > 0 ? band + gap : 0
const rightBand = rightMargins.length > 0 ? band + gap : 0
// One key line for however many profiles there are, above everything: with
// two tracks over one pileup a reader has to be told which line is which, and
// there is no room for a legend beside a band three lines tall.
const keyLine = topMargins.length + rightMargins.length > 0 ? line : 0
const left =
Math.ceil(widestY) +
(widestY > 0 ? TICK_LENGTH + gap : gap) +
(output.yLabel === '' ? 0 : line)
const right = gap * 2 + barWidth + TICK_LENGTH + Math.ceil(widestBar) + gap + rightBand
// Half a line, so the top row's tick label and the bar's `vmax` — both centred
// on the top edge — sit inside the box rather than half out of it.
const top = Math.ceil(line / 2) + keyLine + topBand
const stats = output.stats ?? []
// The row under the picture: its ticks, or its sequences' names — standing,
// where that writes more of them, as tall as they are.
const names = segmentNames(ctx, output, (box.width - left - right) / Math.max(1, output.ncols), size, line, gap)
const tickRow = names.upright ? TICK_LENGTH + gap + Math.ceil(names.room) : xNamed ? TICK_LENGTH + gap + line : gap
const bottom =
tickRow +
(output.xLabel === '' ? 0 : line) +
(stats.length > 0 ? gap + stats.length * line : 0) +
Math.round(size * 0.3)
const availableWidth = box.width - left - right
const availableHeight = box.height - top - bottom
if (availableWidth < MIN_PLOT_SIDE || availableHeight < MIN_PLOT_SIDE) {
drawEmpty(ctx, box, theme, 'too small to draw')
return
}
const cell = matrixCells(availableWidth, availableHeight, output)
const cellW = cell.width
const cellH = cell.height
const plot: Rect = {
// Centred in what is left over after the cells were snapped to whole pixels,
// so the slack is split rather than pooled against the colour bar.
x: left + Math.round((availableWidth - cellW * output.ncols) / 2),
y: top + Math.round((availableHeight - cellH * output.nrows) / 2),
width: Math.round(cellW * output.ncols),
height: Math.round(cellH * output.nrows),
}
if (!(plot.width > 0) || !(plot.height > 0)) {
drawEmpty(ctx, box, theme, 'too small to draw')
return
}
const scale = 1 / (range.vmax - range.vmin)
// A list — the metaplot's per-feature heatmap — is a picture, not a grid of
// squares: one image, smoothed where it is drawn larger than it is. Its
// frame is the picture's edge, as every plot's is (§18.13).
const listed = output.aspect === 'fill' && drawListImage(ctx, output, plot, range)
// A large picture's cells are a fraction of a pixel wider than whole: each
// one's edges rounded, so neighbours meet without a seam of half-painted
// pixels between them. Whole cells round to themselves.
const snap = output.large === true && cellW >= 1 && cellH >= 1
const edgeX = (col: number): number => (snap ? Math.round(plot.x + col * cellW) : plot.x + col * cellW)
const edgeY = (row: number): number => (snap ? Math.round(plot.y + row * cellH) : plot.y + row * cellH)
let painted = -1
for (let row = 0; row < (listed ? 0 : output.nrows); row++) {
const y0 = edgeY(row)
const h = snap ? edgeY(row + 1) - y0 : cellH
for (let col = 0; col < output.ncols; col++) {
const index = colormapIndex((output.values[row * output.ncols + col] - range.vmin) * scale)
// `-1` is matplotlib's "bad" colour, which is transparent — a `NaN` cell.
// Left unpainted rather than filled with the background, so the paper (or
// whatever the figure is composited over) shows through and a missing cell
// is visibly missing instead of being drawn at one end of the scale.
if (index < 0) continue
if (index !== painted) {
ctx.fillStyle = colours[index]
painted = index
}
const x0 = edgeX(col)
ctx.fillRect(x0, y0, snap ? edgeX(col + 1) - x0 : cellW, h)
}
}
ctx.strokeStyle = theme.ink
ctx.lineWidth = FRAME_WIDTH
ctx.lineJoin = 'miter'
ctx.strokeRect(plot.x, plot.y, plot.width, plot.height)
drawSegments(ctx, output, plot, { cellW, cellH, gap, line }, names, theme)
// The marginals, against the two edges they run along, and the one line of key
// above both. Drawn before the ticks so the axis furniture is painted over
// them rather than under.
//
// **A colour per name, not per profile.** The commonest case is one track
// drawn on both edges — the same aggregate along the rows and along the
// columns — and colouring by position would give the one quantity two colours
// and the key two rows, which is a legend asserting there are two of them.
const named = [...topMargins, ...rightMargins]
const order = [...new Set(named.map((profile) => profile.name))]
const colourOf = (profile: MarginProfile): string =>
profile.colour ?? SERIES_COLOURS[Math.max(0, order.indexOf(profile.name)) % SERIES_COLOURS.length]
const scales = marginScales(output.margins)
for (const profile of topMargins) {
drawMargin(ctx, profile, colourOf(profile), theme, {
along: 'x',
plot,
band,
gap,
range: scales.get(profile.name),
})
}
for (const profile of rightMargins) {
drawMargin(ctx, profile, colourOf(profile), theme, {
along: 'y',
plot,
band,
gap,
range: scales.get(profile.name),
})
}
if (keyLine > 0) {
ctx.font = theme.font
ctx.textAlign = 'left'
ctx.textBaseline = 'top'
let keyAt = gap
for (const name of order) {
const profile = named.find((one) => one.name === name)
if (profile === undefined) continue
ctx.fillStyle = colourOf(profile)
ctx.fillRect(keyAt, Math.round(size * 0.55), Math.round(size * 0.7), RULE_WIDTH * 2.5)
keyAt += Math.round(size * 0.7) + gap * 0.6
ctx.fillStyle = theme.muted
// The range the band is drawn against, beside the name. A self-scaled
// band says *what the shape is* and not how big it is, and these two
// numbers are what put the size back — without them a doubling and a
// rounding error are the same picture.
const scale = scales.get(name)
const text =
scale === undefined || !(scale.lo <= scale.hi)
? name
: `${name} ${trimNumber(scale.lo)}–${trimNumber(scale.hi)}`
ctx.fillText(text, keyAt, 0)
keyAt += ctx.measureText(text).width + gap * 1.6
}
}
ctx.fillStyle = theme.muted
ctx.strokeStyle = theme.muted
ctx.lineWidth = RULE_WIDTH
ctx.font = theme.font
// Ticks the output placed itself (`MatrixOutput.xTickAt`) are each drawn, and
// labelled in the order given where the label clears every one already
// drawn — the output lists first what it most needs read. Evenly spaced ones
// are thinned to every k-th instead.
const placed = output.xTickAt !== undefined && output.xTickAt.length === output.xTicks.length
const xFractions = placed ? (output.xTickAt as number[]) : tickFractions(output.xTicks.length, output.ncols)
let widestX = 0
for (const label of output.xTicks) widestX = Math.max(widestX, ctx.measureText(label).width)
const xStride = placed ? 1 : labelStride(widestX + gap, xFractions, plot.width)
const drawn: Array<[number, number]> = []
ctx.textAlign = 'center'
ctx.textBaseline = 'top'
output.xTicks.forEach((label, index) => {
if (index % xStride !== 0) return
const px = plot.x + xFractions[index] * plot.width
ctx.beginPath()
ctx.moveTo(px, plot.y + plot.height)
ctx.lineTo(px, plot.y + plot.height + TICK_LENGTH)
ctx.stroke()
const half = ctx.measureText(label).width / 2
const put = Math.min(Math.max(px, half), box.width - half)
if (placed && drawn.some(([left, right]) => put - half < right + gap && put + half > left - gap)) return
drawn.push([put - half, put + half])
ctx.fillText(label, put, plot.y + plot.height + TICK_LENGTH + gap * 0.4)
})
const yFractions = tickFractions(output.yTicks.length, output.nrows)
const yStride = labelStride(line, yFractions, plot.height)
ctx.textAlign = 'right'
ctx.textBaseline = 'middle'
output.yTicks.forEach((label, index) => {
if (index % yStride !== 0) return
// Row 0 is the top row, which is how a matrix is written down and how
// `render/heatmap.ts` draws one — so the fractions run *down* the axis.
const py = plot.y + yFractions[index] * plot.height
ctx.beginPath()
ctx.moveTo(plot.x - TICK_LENGTH, py)
ctx.lineTo(plot.x, py)
ctx.stroke()
ctx.fillText(label, plot.x - TICK_LENGTH - gap * 0.5, py)
})
// The colour bar, `vmin` at the bottom, matching every other vertical bar in
// this application and matplotlib's own.
// Past the right-hand band, not over it: `right` reserves both, and the bar is
// the outermost of the two.
const barX = box.width - right + gap + rightBand
for (let i = 0; i < COLORMAP_SIZE; i++) {
const y0 = plot.y + plot.height * (1 - (i + 1) / COLORMAP_SIZE)
const y1 = plot.y + plot.height * (1 - i / COLORMAP_SIZE)
ctx.fillStyle = colours[i]
ctx.fillRect(barX, y0, barWidth, y1 - y0)
}
ctx.strokeStyle = theme.ink
ctx.lineWidth = FRAME_WIDTH
ctx.strokeRect(barX, plot.y, barWidth, plot.height)
ctx.fillStyle = theme.muted
ctx.strokeStyle = theme.muted
ctx.lineWidth = RULE_WIDTH
ctx.textAlign = 'left'
ctx.textBaseline = 'middle'
for (const value of barTicks) {
const at = (value - range.vmin) * scale
if (!(at >= 0 && at <= 1)) continue
const py = plot.y + (1 - at) * plot.height
ctx.beginPath()
ctx.moveTo(barX + barWidth, py)
ctx.lineTo(barX + barWidth + TICK_LENGTH, py)
ctx.stroke()
ctx.fillText(formatTick(value, barStep), barX + barWidth + TICK_LENGTH + gap * 0.4, py)
}
ctx.fillStyle = theme.ink
ctx.font = boldOf(theme.font)
const labelBottom = plot.y + plot.height + tickRow
if (output.xLabel !== '') {
ctx.textAlign = 'center'
ctx.textBaseline = 'top'
ctx.fillText(output.xLabel, plot.x + plot.width / 2, labelBottom)
}
if (output.yLabel !== '') {
ctx.save()
ctx.translate(Math.round(size * 0.9), plot.y + plot.height / 2)
ctx.rotate(-Math.PI / 2)
ctx.textAlign = 'center'
ctx.textBaseline = 'middle'
ctx.fillText(output.yLabel, 0, 0)
ctx.restore()
}
// The numbers under the picture — P2LL, AA/BB strength, an r. One per line
// rather than a row of them: the drawer is a column three hundred pixels wide,
// and a statistic that wrapped between its label and its value would read as
// two statistics. The `hint` is not drawn; it is a tooltip, and a figure has
// nowhere to hover.
let statY = labelBottom + (output.xLabel === '' ? 0 : line) + gap
ctx.font = theme.font
ctx.textBaseline = 'top'
for (const stat of stats) {
ctx.textAlign = 'left'
ctx.fillStyle = theme.muted
ctx.fillText(stat.label, plot.x, statY)
ctx.fillStyle = theme.ink
const after = plot.x + ctx.measureText(`${stat.label} `).width
ctx.fillText(formatStat(stat.value, stat.digits), after, statY)
statY += line
}
}
// ---------------------------------------------------------------------------
// Figures: a canvas that owns itself
// ---------------------------------------------------------------------------
export interface PlotFigure {
el: HTMLElement
draw(ctx: CanvasRenderingContext2D, box: { width: number; height: number }): void
destroy(): void
/**
* Take the height of the box instead of choosing one from the width.
*
* What the dialog turns on. In the drawer a figure decides how tall it is,
* because the column it is in has no height of its own; in a dialog the
* window decides, and a figure that kept its own answer sits in the top half
* of it with the rest blank — which is what a five-thousand-row heatmap
* enlarged to see it better used to do.
*/
setFill?(on: boolean): void
}
/** The width a figure is drawn at before anything has measured its column. */
export const MIN_FIGURE_WIDTH = 240
/**
* Call `onChange` whenever the effective theme changes.
*
* Both halves are needed and neither is enough: `ThemeToggle` writes `data-theme`
* on `<html>` for an explicit light or dark choice, and *removes* it for
* "system", where the answer comes from the media query instead. A canvas is not
* restyled by CSS, so a figure that watched only one of the two would keep the
* old palette until something else made it redraw.
*/
export function watchTheme(onChange: () => void): () => void {
const media = window.matchMedia?.('(prefers-color-scheme: dark)')
const observer =
typeof MutationObserver === 'undefined' ? null : new MutationObserver(() => onChange())
observer?.observe(document.documentElement, {
attributes: true,
attributeFilter: ['data-theme'],
})
const listener = (): void => onChange()
media?.addEventListener?.('change', listener)
return () => {
observer?.disconnect()
media?.removeEventListener?.('change', listener)
}
}
/**
* A canvas in a wrapper, sized to its column and redrawn when anything it is
* drawn *from* changes.
*
* The wrapper is not decoration. A `ResizeObserver` on the canvas itself would
* observe a box this code resizes, which is the classic feedback loop; observing
* the parent, whose height is decided by the canvas and whose width is decided
* by the drawer, breaks it — and the width comparison below closes the remaining
* half of it, since setting the canvas height changes the wrapper's height and
* fires the observer again with the same width.
*
* `draw` is exposed rather than kept private because it is the same function the
* PDF export calls with a `VectorPage`'s context. There is one implementation of
* each figure, and the file the reader downloads is drawn by it.
*/
function canvasFigure<T>(
paint: (ctx: CanvasRenderingContext2D, box: PlotBox, theme: PlotTheme) => T,
heightFor: (width: number) => number,
/**
* What the last *on-screen* paint laid out, for a caller that maps pointers
* onto it.
*
* Called from {@link redraw} and never from `draw`, and the distinction is
* load-bearing rather than tidiness: `draw` is the export path, which paints
* the same figure into a PDF page eight inches wide, and a layout recorded
* from that would put the marquee somewhere the reader is not.
*/
onLayout?: (layout: T) => void,
): PlotFigure {
// The width is stated inline as well as in the class. `canvas.width` is the
// backing store in *device* pixels, and a canvas whose stylesheet never
// arrived would be drawn at that size instead — a figure twice as wide as its
// column on a retina screen. The class still carries the block display.
const canvas = el('canvas', { class: 'analysis-figure-canvas', style: { width: '100%' } })
const host = el('div', { class: 'analysis-figure-canvas-host' }, canvas)
let width = 0
let fill = false
const redraw = (): void => {
const cssWidth = Math.max(MIN_FIGURE_WIDTH, Math.round(width))
const cssHeight = fill
? Math.max(MIN_FIGURE_WIDTH, Math.round(host.clientHeight))
: heightFor(cssWidth)
const dpr = window.devicePixelRatio > 0 ? window.devicePixelRatio : 1
canvas.style.height = `${cssHeight}px`
const wantWidth = Math.max(1, Math.round(cssWidth * dpr))
const wantHeight = Math.max(1, Math.round(cssHeight * dpr))
if (canvas.width !== wantWidth) canvas.width = wantWidth
if (canvas.height !== wantHeight) canvas.height = wantHeight
const ctx = canvas.getContext('2d')
if (ctx === null) return
ctx.setTransform(dpr, 0, 0, dpr, 0, 0)
ctx.clearRect(0, 0, cssWidth, cssHeight)
const layout = paint(ctx, { width: cssWidth, height: cssHeight }, plotTheme(host))
onLayout?.(layout)
}
const observer =
typeof ResizeObserver === 'undefined'
? null
: new ResizeObserver((entries) => {
const box = entries[0]?.contentRect
const next = box?.width ?? 0
// The height matters only when the *box* decides it; otherwise the
// figure sets it and observing it would be the classic feedback loop.
if (Math.abs(next - width) < 0.5 && !fill) return
width = next
redraw()
})
observer?.observe(host)
// A `ResizeObserver` delivers the initial size on `observe`, so the draw below
// would be thrown away a frame later. Without one — under a test runner, or an
// old browser — nothing else will ever ask for pixels.
if (observer === null) redraw()
const stopTheme = watchTheme(redraw)
// The text scale is the other thing a figure is drawn from that changes under
// it: `plotTheme` reads `scaleFont`, so a press of the smaller/larger control
// must reach the canvas the same way it reaches the lanes.
const stopText = subscribeTextScale(redraw)
return {
el: host,
draw(ctx: CanvasRenderingContext2D, box: { width: number; height: number }): void {
// On paper, whatever the theme where the figure is mounted (§7.2).
paint(ctx, box, plotTheme(figurePaper()))
},
setFill(on: boolean): void {
if (fill === on) return
fill = on
host.classList.toggle('analysis-figure-fill', on)
redraw()
},
destroy(): void {
observer?.disconnect()
stopTheme()
stopText()
},
}
}
/**
* Height for a curve.
*
* Taller than it was, and the two curves that made the case are the ones §18.8
* puts first: P(s) is read over three or four decades on a log-log axis, and its
* *derivative* is a shape whose whole content is a shoulder a few tenths of a
* unit deep. At the old 0.62 of the width both were about 170 px in a folded
* drawer, which is a plot with four y ticks in it — enough to see that a curve
* goes down and not enough to see how.
*
* 0.78, floored at 260 and capped at 520. The floor is what a narrow drawer
* gets, and it is the number that matters: a reader who has folded the drawer to
* see the map beside it is still reading a plot rather than a sparkline. The cap
* stops a full-width drawer on a wide screen from making one curve taller than
* the window, which would be worse than short — two figures in a run would then
* never be on screen together.
*/
function curveHeight(width: number): number {
return Math.max(260, Math.min(520, Math.round(width * 0.78)))
}
/**
* Height for a matrix, from its own aspect.
*
* The margins are estimated here — the exact ones need a context to measure the
* labels with, and the box has to be decided before there is one — so the number
* is a *request*. {@link drawMatrix} fits itself inside whatever box it is given
* and never overruns it, so an estimate that is a few pixels out costs a few
* pixels of white, not a clipped figure.
*/
function matrixHeight(output: MatrixOutput, width: number): number {
const size = fontSizeOf(scaleFont(PLOT_FONT))
const line = Math.round(size * 1.35)
// The marginal bands are furniture too: a picture asked for the height it
// needs without counting them comes back with its top band clipped, which is
// the one part of the figure a reader cannot reconstruct from the rest.
const gap = Math.round(size * 0.45)
const band = Math.round(size * 3)
const tops = output.margins?.top?.length ?? 0
const sides = output.margins?.right?.length ?? 0
// Sequences' names under the picture, taken as standing: at most a few
// pixels too many where they lie down after all.
const longest = Math.max(0, ...(output.xSegments ?? []).map((segment) => segment.label.length))
const names = longest > 0 ? TICK_LENGTH + gap + Math.min(longest * size * 0.6, size * SEGMENT_NAME_ROOM) : 0
const furniture =
Math.round(size * 0.9) +
(names > 0 ? names : output.xTicks.length > 0 ? TICK_LENGTH + line : 0) +
(output.xLabel === '' ? 0 : line) +
(output.stats?.length ?? 0) * line +
(tops > 0 ? band + gap : 0) +
(tops + sides > 0 ? line : 0)
const cells = Math.max(40, width - size * 4 - size * 6 - (sides > 0 ? band + gap : 0))
// A picture whose rows are a **list** has no aspect of its own to ask for —
// five thousand features against eighty bins would ask for sixty-four times
// its width — so it takes a generous share of the card instead, which is
// where a metaplot heatmap's few thousand rows want to be. See
// `MatrixOutput.aspect` and {@link matrixCells}.
if (output.aspect === 'fill') {
return Math.round(furniture + Math.max(260, Math.min(560, cells * 0.55)))
}
const aspect = output.ncols > 0 ? output.nrows / output.ncols : 1
// A picture read like a map asks for most of a screen; see `MatrixOutput.large`.
const most = output.large === true ? LARGE_MATRIX_SIDE : 420
return Math.round(furniture + Math.max(80, Math.min(most, cells * aspect)))
}
/** The tallest a {@link MatrixOutput.large} picture asks to be, in CSS pixels: most of a laptop's screen, the rest its names and scale. */
const LARGE_MATRIX_SIDE = 600
export function curveFigure(
output: CurveOutput,
onLayout?: (layout: CurveLayout | null) => void,
): PlotFigure {
return canvasFigure(
(ctx, box, theme) => drawCurve(ctx, output, box, theme),
curveHeight,
onLayout,
)
}
/**
* How many points a per-bin profile is drawn with.
*
* A metagenome has four million bins and a drawer is eight hundred pixels wide,
* so a line with a point per bin is four million `lineTo` calls to paint four
* hundred pixels — several seconds a frame, for a picture that cannot show what
* it drew. Above this many the bins are bucketed; below it every one is drawn.
*/
const PROFILE_POINTS = 1200
/**
* A per-bin profile as a curve, so it can be drawn where there is no lane.
*
* §18.5 is unchanged and this is not a second opinion about it: a per-bin result
* *is* a track, and wherever there is an Annotations panel it goes there and
* inherits colour, limits, edges, the tooltip and the browser by being the same
* object a bigWig is. A `.metacool` has no such panel (§8.5), and the choice
* there is not between a lane and a picture — it is between a picture and
* nothing at all, which is what a coverage run on a metagenome used to produce.
*
* **Bucketed with a band, not sampled.** Taking every thousandth bin would drop
* exactly the spikes a marginal is read for, and would drop them silently. Each
* bucket is drawn as its mean with its min–max behind it, so a spike inside one
* shows as a band reaching up to it — the picture says "something in here got
* that high" rather than quietly saying it did not. A profile short enough to
* draw whole gets no band, because there is nothing being summarised.
*
* `NaN` stays `NaN`: a bucket with no finite value in it is a gap, and
* {@link drawSeriesLine} breaks the line there rather than bridging it.
*/
export function profileCurve(output: ProfileOutput): CurveOutput {
const values = output.values
const from = output.extent[0]
const n = values.length
const buckets = n > PROFILE_POINTS ? PROFILE_POINTS : n
const width = buckets === 0 ? 1 : n / buckets
const x = new Float64Array(buckets)
const y = new Float64Array(buckets)
const low = new Float64Array(buckets)
const high = new Float64Array(buckets)
for (let b = 0; b < buckets; b++) {
const lo = Math.floor(b * width)
const hi = Math.max(lo + 1, Math.floor((b + 1) * width))
let sum = 0
let count = 0
let min = Number.POSITIVE_INFINITY
let max = Number.NEGATIVE_INFINITY
for (let i = lo; i < hi && i < n; i++) {
const value = values[i]
if (Number.isNaN(value)) continue
sum += value
count++
if (value < min) min = value
if (value > max) max = value
}
// The bucket's midpoint, in the file's own bin numbering: the axis a reader
// reads off this is the one the map's own coordinates are in.
x[b] = from + (lo + hi) / 2
y[b] = count === 0 ? Number.NaN : sum / count
low[b] = count === 0 ? Number.NaN : min
high[b] = count === 0 ? Number.NaN : max
}
const banded = buckets < n
return {
kind: 'curve',
id: output.id,
label: output.label,
series: [
{
name: output.label,
x,
y,
...(banded ? { low, high } : {}),
},
],
xLabel: `bin (${resolutionLabel(output.binsize)} each)`,
yLabel: output.unit === '' ? output.label : `${output.label} (${output.unit})`,
xScale: 'linear',
yScale: 'linear',
}
}
/** {@link profileCurve}, drawn. */
export function profileFigure(output: ProfileOutput): PlotFigure {
return curveFigure(profileCurve(output))
}
export function matrixFigure(output: MatrixOutput): PlotFigure {
return canvasFigure(
(ctx, box, theme) => drawMatrix(ctx, output, box, theme),
(width) => matrixHeight(output, width),
)
}
// ---------------------------------------------------------------------------
// Tables
// ---------------------------------------------------------------------------
export interface TableFigure {
el: HTMLElement
destroy(): void
}
/**
* A result table: a plain scrolling table, and deliberately not a
* {@link VirtualTable}.
*
* Virtualisation exists in this app for 154,468 contigs, where 154 k rows of DOM
* is several seconds of layout before anything appears. A per-feature score
* table is a few hundred rows, which is one layout pass — and the machinery is
* not free: `.tr` is `position: absolute` precisely so rows can be placed by
* transform, and every one of the virtual table's sort, filter and keyboard
* affordances would then have to mean something here. This is a *record* of what
* a task produced, checkable by eye and exportable as TSV (§18.7), so it is the
* table it looks like.
*
* The typography is the virtual table's, because a number in a result should be
* set like a number in a genomes table: `.thead`, `.td` and `.num` are all pure
* appearance and are reused. `.th` is not — it carries a pointer cursor and an
* accent hover, which are a promise to sort that this table does not keep.
*/
export function tableFigure(output: TableOutput): TableFigure {
const head = el(
'thead',
{ class: 'thead' },
el(
'tr',
{},
...output.columns.map((column) =>
el('th', {
class: column.kind === 'number' ? 'td num' : 'td',
text: column.label,
title: column.hint ?? '',
style: { fontWeight: '600', color: 'var(--text-dim)' },
}),
),
),
)
const body = el('tbody', {})
for (const row of output.rows) {
body.appendChild(
el(
'tr',
{ style: { borderTop: '1px solid var(--border)' } },
...output.columns.map((column) =>
el('td', {
class: column.kind === 'number' ? 'td num' : 'td',
text: cellText(column, row[column.key]),
}),
),
),
)
}
const table = el(
'table',
{
style: {
borderCollapse: 'collapse',
width: '100%',
// Digits of the same width, so a column of numbers can be compared by
// its shape — the one thing `.tr` gave the virtual table's rows that is
// worth carrying over by hand.
fontVariantNumeric: 'tabular-nums',
},
},
head,
body,
)
const host = el(
'div',
{ class: 'analysis-figure-scroll' },
output.rows.length === 0
? el('div', { class: 'tempty', text: 'This run produced no rows.' })
: table,
)
return {
el: host,
// Nothing to release: the table is DOM and goes when its parent does. It is
// still here so the drawer can hold every figure in one list and tear them
// all down the same way, rather than branching on which kind it has.
destroy(): void {},
}
}
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