Press n or j to go to the next uncovered block, b, p or k for the previous block.
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* The guided tutorial's steps (§30): one first session, on real data, from the
* landing page to a correlation between the reader's own tracks and the ones a
* consortium published.
*
* ## The data, and why these
*
* **4DNESC23ZYOF**, in situ Hi-C on K562 cells from the 4DN portal (Belaghzal
* et al. 2021), on GRCh38, with **187 million contacts** in a 1.9 GB file —
* enough for domains and their loops at 5 kb, and a map a first session opens
* quickly. Its experiment set carries the three tracks 4DN's own pipeline
* computed from the same map: the compartment eigenvector at 250 kb, the
* insulation score and the boundaries called on it. So the last step compares
* like with like: the reader's E1 and insulation, computed in this page,
* against the consortium's.
*
* **chr15**, because it shows both halves of the story on one screen: an
* acrocentric whose short arm is empty — the blank square at its start is what
* a stretch with no unique sequence looks like — and a long arm with broad,
* clean compartments. **38.1–50.0 Mb** of it is where the tutorial looks at
* domains: at 5 kb, a run of squares along the diagonal nested in bigger ones,
* reached from **30–60 Mb** at 250 kb so that each drag is across a square a
* hand can hit. In it, the domain from **45.66 to 48.32 Mb** is closed by a loop
* between its two borders — the dot at its corner, which the reader marks — and
* split by **one weak border at 47.2 Mb** into two subTADs: the one dip the
* insulation's widest window (400 kb) finds inside it, shallow beside the two
* borders of the domain, and 4DN's own call there is *Weak*. The reader draws a
* line on it, which is what makes the four scales' point: a border the narrow
* windows all see and the wide one barely does is a level down the hierarchy.
*
* ## The steps a reader would not think of
*
* The tour starts with the store drawer shut and aimed at the **lab's store**
* (`app/App.ts`): its first press opens the drawer, and its second is a switch
* to 4DN's that is always there to make, whatever the drawer was last left on.
* It shows the two columns the map comes with — **General**, then **Aesthetics**
* once a map is on screen — and the Analysis panel's **three groups** of tasks,
* one by one, before it asks for any of them.
*
* The map is drawn as a **correlation** before Compartments runs, because the
* plaid that draws is what the task decomposes — the reader sees the pattern
* before the number that summarises it — and back as **balanced** before the
* zoom, because domains are a matter of contact frequency. Compartments is run
* **with no gene model**, which the tour sets itself rather than asking for:
* left to itself the form takes the first set of intervals for one, which on
* this session is 4DN's boundaries, and a sign decided by those is a coin toss
* (its saddle says *phasing r 0.01*). Nothing else phases it either, so the
* drawer says the sign is arbitrary, and the last step says an E1 can match
* 4DN's upside down. And the domains are looked at with **O/E** and **3 × 3
* smoothing** on: at 10 kb a pixel holds a handful of contacts, and divided by
* its distance and averaged with its neighbours, the squares stand out from the
* decay. Neither changes what a task reads — the insulation drawer still says
* *balanced* — so they stay on.
*
* ## How a step is written
*
* Against the window, through {@link TutorialHost}: what is open, at what
* resolution, which drawer, which run. A step's `done` is a *state*, never a
* click, so the reader may get there by the lit control, a key or the palette
* (`ui/Tour.ts` says why). Its `target` is found by the classes and labels the
* reader sees, anywhere in the window — a card can be carried to another column
* (`ui/cardLayout.ts`) — and read again on every tick, so a card rebuilt under
* it is found again rather than lit where it used to be.
*/
import { LEAD_MAP } from '../annotations/placement'
import type { ManualMark } from '../annotations/manual'
import type { AnnotationEntry } from '../annotations/types'
import type { AnnotationStore } from '../annotations/store'
import { displayOf } from '../analysis/surfaces'
import type { TaskResult } from '../analysis/types'
import type { ViewState } from '../types'
import { isMac } from './commands'
import { BALANCED_SCORE, CORRELATION_SCORE } from './scores'
import type { TourSpot, TourStep, TourText } from './Tour'
/** What the steps read from the window. */
export interface TutorialHost {
/** The view of the tab in front, or `null` while it holds nothing. */
view(): ViewState | null
/** The bin size of the map in front, or `null`. */
binsize(): number | null
/**
* The score its cells are drawn from, by the picker's id, with the file's
* default applied — a balanced cooler opens balanced and says so nowhere in
* its view state — or `null`.
*/
score(): string | null
/** The address of the file open in the tab in front, or `null` until it has opened. */
file(): string | null
/** Its sequences' names, in its own order, or `null` before they are read. */
sequences(): string[] | null
/** The store the drawer is open on, or `null` while it is closed. */
store(): string | null
/** Whether a column is open. */
panelOpen(panel: 'analysis' | 'annotations' | 'aesthetics'): boolean
/** The task the Analysis drawer is open on, or `null`. */
task(): string | null
/** Every finished run of a task on the map in front, newest first. */
runs(task: string): readonly TaskResult[]
/** Whether a task is running, or waiting to. */
running(task: string): boolean
/** The rows of the tab in front's Tracks card, or `null`. */
tracks(): AnnotationStore | null
/** Where a stretch of a sequence is drawn on the map in front, as its square on the diagonal. */
square(stretch: { contig: string; start: number; end: number }): DOMRect | null
/** Whether the console is open along the bottom of the window. */
consoleOpen(): boolean
/** The marks drawn on the tab in front's Manual annotations card, or `null`. */
marks(): readonly ManualMark[] | null
/** Every file the window has saved, by the name it offered (`ui/export.ts`). */
saved(): readonly string[]
}
/** The experiment set the tutorial opens. */
export const TUTORIAL_SET = '4DNESC23ZYOF'
/** The store it is on. */
export const TUTORIAL_STORE = '4dn'
/** The sequence every task is run on. */
export const TUTORIAL_SEQUENCE = 'chr15'
/** Its contact map, by the accession its file is named after. */
const MAP_FILE = '4DNFIKI77KEM'
/** 4DN's own tracks from the same set: E1 at 250 kb, and insulation. */
const FOURDN_E1 = '4DNFI3OPG4RB'
const FOURDN_INSULATION = '4DNFI4GZZC7Z'
/** The square the first drag crosses, at 250 kb, and the one the second crosses, at 5 kb. */
const OVERVIEW = { start: 30_000_000, end: 60_000_000 }
const DOMAINS = { start: 38_100_000, end: 50_025_000 }
/** How narrow a window has to be for the second zoom to count: a few domains, not a chromosome arm. */
const DOMAINS_SPAN = 15_000_000
/** The resolution domains and insulation are read at. */
const FINE = 5_000
/** How many windows insulation is run at, each twice the one before (§18.8). */
const SCALES = 4
/** The loop at the corner of the domain the marks are drawn on, as the reader types it (1-based). */
const LOOP = { rows: 45_662_501, cols: 48_312_501 }
/** The weak border between that domain's two subTADs, as the reader types it. */
const SUBTAD_BORDER = 47_215_001
/** How near a mark has to land to count: a few 5 kb bins. */
const MARK_SLACK = 25_000
/** The smoothing the domains are looked at with, as the view state names it (`render/smooth.ts`). */
const SMOOTH_3X3 = '1'
/**
* The rows the reader's own runs leave on the Tracks card: a profile by its
* output (`ui/synthetic.ts`'s `syntheticId`), the insulation score's ending in
* its window — `analysis:insulation-w10` — and a called set by its task and its
* output (`analysis/workspace.ts`'s `adoptIntervals`).
*/
const OWN_E1 = 'analysis:compartment-e1'
const OWN_INSULATION = 'analysis:insulation-w'
const OWN_DOMAINS = 'analysis:insulation:insulation-domains'
// ---------------------------------------------------------------------------
// Finding things on screen
// ---------------------------------------------------------------------------
/** Whether a node is laid out at all — not hidden, not in a folded column. */
function laidOut(node: Element | null): node is HTMLElement {
return node instanceof HTMLElement && node.getClientRects().length > 0
}
/** The first laid-out match. */
function first(selector: string, root: ParentNode = document): HTMLElement | null {
for (const node of root.querySelectorAll(selector)) if (laidOut(node)) return node
return null
}
function words(node: Element | null | undefined): string {
return (node?.textContent ?? '').replace(/\s+/g, ' ').trim()
}
/** The Analysis drawer, while it is open. */
function drawer(): HTMLElement | null {
return first('.analysis-drawer:not(.collapsed)')
}
/** A task's row in the Analysis panel's list. */
function taskRow(title: string): HTMLElement | null {
for (const row of document.querySelectorAll('.analysis-row')) {
if (laidOut(row) && words(row.querySelector('.analysis-row-title')) === title) return row
}
return null
}
/** The columns a step can point into, by their class and the name the header gives them. */
type Column = 'general' | 'analysis' | 'annotations' | 'aesthetics'
/** A folded column's spine, or the header's button for it. */
function columnDoor(panel: Column): HTMLElement | null {
const title = panel.charAt(0).toUpperCase() + panel.slice(1)
return first(`.panel-${panel} .panel-tab`) ?? first(`.head-panels button[aria-label="${title} panel"]`)
}
/** An open column's cards, or the door to it while it is folded. */
function columnCards(panel: Column): HTMLElement | null {
return first(`.panel-${panel}:not(.collapsed) .panel-column-body`) ?? columnDoor(panel)
}
/** One of the Analysis panel's groups of tasks, by its heading. */
function taskGroup(heading: string): HTMLElement | null {
for (const group of document.querySelectorAll('.panel-analysis section.analysis-card')) {
if (laidOut(group) && words(group.querySelector('.card-head')).startsWith(heading)) return group
}
return null
}
/** The resolution control: a dropdown on a long ladder, a row of stops on a short one. */
function resolutionControl(): HTMLElement | null {
return first('select.res-pick, [role="radiogroup"][aria-label="resolution"]')
}
/** The Map card, wherever it has been carried, while it is laid out. */
function mapCard(): HTMLElement | null {
for (const card of document.querySelectorAll('.controls-card')) {
if (laidOut(card) && words(card.querySelector('.controls-title')) === 'Map') return card
}
return null
}
/** A control of the Map card, by the word beside it. */
function mapField(word: string): HTMLElement | null {
for (const label of mapCard()?.querySelectorAll('label.field') ?? []) {
if (words(label.querySelector('.field-label')) === word) return label.querySelector<HTMLElement>('select, input')
}
return null
}
/** The Map card's O/E toggle. */
function oeToggle(): HTMLElement | null {
for (const node of mapCard()?.querySelectorAll<HTMLElement>('button') ?? []) {
if (words(node) === 'O/E') return node
}
return null
}
/**
* A number box of the drawer's form, by the words beside it — a row of its own,
* or a block with a slider under its word, whose box is the number.
*/
function formInput(word: string): HTMLInputElement | null {
for (const field of drawer()?.querySelectorAll('.param-field') ?? []) {
if (words(field.querySelector('.field-label')) !== word) continue
const input = field.querySelector('input[type="number"]') ?? field.querySelector('input:not([type="range"])')
return input instanceof HTMLInputElement ? input : null
}
return null
}
/** Type into a box as a reader would: the value, then the events a keystroke and a commit send. */
function typeInto(box: HTMLInputElement | null, value: string): void {
if (box === null) return
box.value = value
box.dispatchEvent(new Event('input', { bubbles: true }))
box.dispatchEvent(new Event('change', { bubbles: true }))
}
/** The Manual annotations card, wherever it has been carried. */
function manualCard(): HTMLElement | null {
for (const card of document.querySelectorAll('section.annotation-card')) {
if (laidOut(card) && words(card.querySelector('.card-head, .card-title, h3')).startsWith('Manual annotations')) {
return card as HTMLElement
}
}
return null
}
/** One of the Manual annotations card's forms — Lines, Arrowheads, Rectangles — by its title. */
function manualForm(title: string): HTMLElement | null {
for (const form of manualCard()?.querySelectorAll<HTMLElement>('.manual-form') ?? []) {
if (words(form.querySelector('.manual-form-title')) === title) return form
}
return null
}
/** A form's `add` button. */
function addButton(form: HTMLElement | null): HTMLButtonElement | null {
for (const node of form?.querySelectorAll<HTMLButtonElement>('button') ?? []) {
if (words(node) === 'add') return node
}
return null
}
/**
* The Export card's row — its format and its download — wherever the card has
* been carried. Found by the card's title: the Manual annotations card has an
* export row of its own, which writes marks rather than the figure.
*/
function exportRow(): HTMLElement | null {
for (const card of document.querySelectorAll('.controls-card')) {
if (laidOut(card) && words(card.querySelector('.controls-title')) === 'Export') {
return card.querySelector<HTMLElement>('.export-row')
}
}
return null
}
/** A select of the drawer's form, by the words beside it. */
function formSelect(word: string): HTMLSelectElement | null {
for (const label of drawer()?.querySelectorAll('label.param-field') ?? []) {
if (words(label.querySelector('.field-label')) !== word) continue
const select = label.querySelector('select')
return select instanceof HTMLSelectElement ? select : null
}
return null
}
/**
* Compartments' gene model, set to none — the one parameter the tour sets for
* the reader (§30.2). Through the select and its `change`, as a press would, so
* the form records it as its own.
*/
function noGeneModel(): void {
const select = formSelect('phase by gene density')
if (select === null || select.value === '') return
select.value = ''
select.dispatchEvent(new Event('change', { bubbles: true }))
}
/** A figure of the drawer's result, by the start of its heading. */
function figure(heading: string): HTMLElement | null {
for (const node of drawer()?.querySelectorAll<HTMLElement>('.analysis-figure') ?? []) {
if (words(node.querySelector('.analysis-figure-head')).startsWith(heading)) return node
}
return null
}
/** The experiment set's heading in the store's list. */
function setGroup(): HTMLElement | null {
for (const group of document.querySelectorAll('.store-drawer .portal-group')) {
if (laidOut(group) && words(group.querySelector('.portal-group-key')) === TUTORIAL_SET) return group
}
return null
}
function searchBox(): HTMLInputElement | null {
const box = first('.store-drawer .portal-search')
return box instanceof HTMLInputElement ? box : null
}
/** The sequences ticked in the drawer's form, or `null` where it has no such list. */
function tickedSequences(): string[] | null {
const list = drawer()?.querySelector('.param-sequences')
if (list === null || list === undefined) return null
return [...list.querySelectorAll('label.param-check')]
.filter((label) => label.querySelector('input')?.checked === true)
.map((label) => words(label.querySelector('span')))
}
/** One sequence's tick box in the drawer's form. */
function sequenceBox(name: string): HTMLElement | null {
for (const label of drawer()?.querySelectorAll<HTMLElement>('.param-sequences label.param-check') ?? []) {
if (words(label.querySelector('span')) === name) return label
}
return null
}
/** One track's tick box in the drawer's form, found by the name its row has now. */
function trackBox(entry: AnnotationEntry | undefined): HTMLElement | null {
if (entry === undefined) return null
for (const label of drawer()?.querySelectorAll<HTMLElement>('label.param-check') ?? []) {
if (words(label.querySelector('span')) === entry.label) return label
}
return null
}
/** The run button of the drawer's form. */
function runButton(): HTMLElement | null {
return drawer()?.querySelector<HTMLElement>('.analysis-run > button') ?? null
}
function sameNames(a: readonly string[] | null, b: readonly string[]): boolean {
return a !== null && a.length === b.length && a.every((name, at) => name === b[at])
}
/** A parameter's value as a list of names, or `null` where it is not one. */
function namesIn(value: unknown): string[] | null {
return Array.isArray(value) ? value.filter((item): item is string => typeof item === 'string') : null
}
/** The sequence a view is on, or `null`. */
function sequenceOf(view: ViewState | null): string | null {
if (view === null || view.view !== 'region' || view.region === undefined) return null
return view.region.split(':')[0]
}
/** The stretch a view is on, in base pairs, or `null` on a whole sequence or none. */
function stretchOf(view: ViewState | null): { contig: string; start: number; end: number } | null {
if (view === null || view.view !== 'region' || view.region === undefined) return null
const match = /^([^:]+):([\d,]+)-([\d,]+)$/.exec(view.region)
if (match === null) return null
return { contig: match[1], start: Number(match[2].replace(/,/g, '')), end: Number(match[3].replace(/,/g, '')) }
}
/** The Chromosomes table's name cell for one sequence, which is what a press opens it by. */
function sequenceRow(name: string): HTMLElement | null {
return first(`.content .tviewport .tr .td[title="${name}"]`)
}
/** The map's locus box, typed into and committed, as a reader who would rather not drag does it. */
function goTo(region: string): void {
const box = first('.content input.input-region')
if (!(box instanceof HTMLInputElement)) return
box.value = region
box.dispatchEvent(new Event('input', { bubbles: true }))
box.dispatchEvent(new KeyboardEvent('keydown', { key: 'Enter', bubbles: true }))
}
/** Base pairs as the locus box takes them, `41,000,000`. */
function bp(at: number): string {
return at.toLocaleString('en-US')
}
// ---------------------------------------------------------------------------
// The steps
// ---------------------------------------------------------------------------
/** Every step of the tutorial, in order. */
export function tutorialSteps(host: TutorialHost): TourStep[] {
/**
* The tab in front is on the tutorial's map — opened, or still opening.
*
* Read from the view rather than the file because a workspace names its map
* the moment it is read and opens it a few seconds later; a step that waited
* for the file would send the reader back to the store while the map they had
* just asked for was arriving.
*/
const onMap = (): boolean =>
host.view()?.uri.includes(MAP_FILE) === true || host.file()?.includes(MAP_FILE) === true
const onSequence = (): boolean => sequenceOf(host.view()) === TUTORIAL_SEQUENCE
const ranOn = (task: string): boolean =>
host.runs(task).some((run) => sameNames(namesIn(run.provenance.params.sequences), [TUTORIAL_SEQUENCE]))
/** A track loaded from 4DN's set, by the accession in its address. */
const fourdn = (accession: string): AnnotationEntry | undefined =>
host.tracks()?.entries.find((entry) => entry.source.kind === 'remote' && entry.source.url.includes(accession))
const ownE1 = (): AnnotationEntry | undefined => host.tracks()?.byId(OWN_E1)
/** The reader's insulation, one row per window, narrowest first. */
const ownInsulations = (): AnnotationEntry[] =>
host.tracks()?.entries.filter((entry) => entry.id.startsWith(OWN_INSULATION)) ?? []
const insulationRow = (): HTMLElement | null => {
const entry = ownInsulations()[0]
return entry === undefined ? null : first(`.ann-row[data-id="${entry.id}"]`)
}
const insulationOpen = (): boolean =>
insulationRow()?.querySelector('.ann-more')?.getAttribute('aria-expanded') === 'true'
/** A file of this kind saved since the tutorial began. */
const savedAny = (suffix: string): boolean => host.saved().some((name) => name.toLowerCase().endsWith(suffix))
/** A mark the reader drew near a place on the tutorial's sequence. */
const near = (point: { contig: string; bp: number }, at: number): boolean =>
point.contig === TUTORIAL_SEQUENCE && Math.abs(point.bp - at) <= MARK_SLACK
const loopMarked = (): boolean =>
(host.marks() ?? []).some(
(mark) =>
mark.kind === 'arrowhead' &&
((near(mark.a, LOOP.rows) && near(mark.b, LOOP.cols)) ||
(near(mark.a, LOOP.cols) && near(mark.b, LOOP.rows))),
)
const borderMarked = (): boolean =>
(host.marks() ?? []).some(
(mark) => mark.kind === 'line' && mark.axis !== 'horizontal' && near(mark.at, SUBTAD_BORDER),
)
const domainsRow = (): HTMLElement | null => first(`.ann-row[data-id="${OWN_DOMAINS}"]`)
const domainsOpen = (): boolean =>
domainsRow()?.querySelector('.ann-more')?.getAttribute('aria-expanded') === 'true'
const domainsLane = (): boolean => {
const entry = host.tracks()?.byId(OWN_DOMAINS)
return entry !== undefined && displayOf(entry) === 'lane'
}
const domainsPlaced = (): { bottom: boolean; left: boolean } | null => {
const placement = host.tracks()?.laneFor(OWN_DOMAINS, LEAD_MAP)?.placement
return placement === undefined ? null : { bottom: placement.bottom, left: placement.left }
}
const placeToggle = (edge: 'bottom' | 'left'): HTMLElement | null => {
for (const toggle of domainsRow()?.querySelectorAll<HTMLElement>('.ann-place') ?? []) {
if (laidOut(toggle) && new RegExp(`\\b${edge} edge\\b`).test(toggle.title)) return toggle
}
return null
}
const mapPicture = (): HTMLElement | null => first('.content .panel-grid')
/** A Map card control, or the door to the column it is in while that is folded. */
const inMapCard = (find: () => HTMLElement | null) => (): HTMLElement | null =>
find() ?? columnDoor('aesthetics')
/** The square a stretch of chr13 makes on the map, lit within the map's canvas. */
const square =
(stretch: { start: number; end: number }) =>
(): Element | TourSpot | null => {
const canvas = first('.content .heatmap-canvas')
if (canvas === null) return null
const box = host.square({ contig: TUTORIAL_SEQUENCE, ...stretch })
return box === null
? canvas
: { within: canvas, box: { left: box.left, top: box.top, right: box.right, bottom: box.bottom } }
}
const keys = isMac() ? '⇧ Shift and ⌥ Option' : 'Shift and Alt'
// The Chromosomes table draws only the rows in view, so a short window may
// not have drawn chr13's at all. Scrolled to it once per entry into the step.
let revealed = false
const revealRow = (): void => {
if (revealed || sequenceRow(TUTORIAL_SEQUENCE) !== null) return
const viewport = first('.content .tviewport')
const at = host.sequences()?.indexOf(TUTORIAL_SEQUENCE) ?? -1
if (viewport === null || at < 0) return
revealed = true
const height = viewport.querySelector<HTMLElement>('.tr')?.offsetHeight ?? 28
viewport.scrollTop = Math.max(0, at * height - viewport.clientHeight / 2)
viewport.dispatchEvent(new Event('scroll'))
}
const analysisPanel = (id: string, chapter: string): TourStep => ({
id,
chapter,
title: 'Open the Analysis panel',
text: 'Analyses run here, in this page, on the map on screen.',
target: () => columnDoor('analysis'),
done: () => host.panelOpen('analysis'),
needs: { holds: onMap, back: 'open-set' },
})
/** The map's score, set in the Map card. */
const scoreStep = (id: string, chapter: string, score: string, title: string, text: TourText): TourStep => ({
id,
chapter,
title,
text,
action: 'choose',
target: inMapCard(() => mapField('score')),
done: () => host.score() === score,
needs: { holds: onMap, back: 'open-set' },
})
/**
* A task run on chr13 alone, then its drawer closed: open the panel, look at
* what `tour` shows of it, choose the task, untick every sequence, tick chr13,
* run — with `setup` done to the form on the way — and look at what `after`
* lights before closing.
*/
const sequenceTask = (
chapter: string,
task: string,
row: string,
say: { choose: string; none: string; tick: string; run: string },
extra: {
tour?: (panel: string) => TourStep[]
setup?: () => void
/** Steps on the form, between the sequence and the run. */
form?: (open: () => boolean) => TourStep[]
/** What else a run has to have been asked for to count. */
ran?: (params: Record<string, unknown>) => boolean
after?: (open: () => boolean) => TourStep[]
} = {},
): TourStep[] => {
const panel = `analysis-${task}`
const open = (): boolean => host.task() === task
return [
analysisPanel(panel, chapter),
...(extra.tour?.(panel) ?? []),
{
id: task,
chapter,
title: `Choose ${row}`,
text: say.choose,
target: () => taskRow(row),
done: open,
needs: { holds: () => host.panelOpen('analysis'), back: panel },
missing: 'Not in the list — empty the box over it if a word is typed there.',
},
{
id: `${task}-none`,
chapter,
title: 'Untick every sequence',
text: say.none,
prepare: extra.setup,
target: () => drawer()?.querySelector<HTMLElement>('button[title="Untick every sequence"]') ?? null,
done: () => {
const now = tickedSequences()
return now !== null && (now.length === 0 || sameNames(now, [TUTORIAL_SEQUENCE]))
},
needs: { holds: open, back: task },
},
{
id: `${task}-sequence`,
chapter,
title: `Tick ${TUTORIAL_SEQUENCE}`,
text: say.tick,
target: () => sequenceBox(TUTORIAL_SEQUENCE),
done: () => sameNames(tickedSequences(), [TUTORIAL_SEQUENCE]),
needs: { holds: open, back: task },
},
...(extra.form?.(open) ?? []),
{
id: `${task}-run`,
chapter,
title: 'Run it',
text: say.run,
// Again on the step the run is pressed from: the one before it is
// passed over when it is already done, and its setup with it.
prepare: extra.setup,
target: runButton,
done: () =>
extra.ran === undefined
? ranOn(task)
: host
.runs(task)
.some(
(run) =>
sameNames(namesIn(run.provenance.params.sequences), [TUTORIAL_SEQUENCE]) &&
extra.ran!(run.provenance.params),
),
// A run carries on with its drawer closed, and is still a run.
needs: { holds: () => open() || host.running(task), back: task },
},
...(extra.after?.(open) ?? []),
{
id: `${task}-close`,
chapter,
title: 'Back to the map',
text: 'The result is a track as well as a figure. Close the drawer to see it beside the map.',
target: () => drawer()?.querySelector<HTMLElement>('.analysis-drawer-head .btn-close') ?? null,
done: () => host.task() === null,
},
]
}
/**
* Every track the correlation is run over: 4DN's insulation and E1, the
* reader's E1, and the reader's insulation at each of its four windows.
*/
const everyTrack = (): Array<AnnotationEntry | undefined> => {
const own = ownInsulations()
return [
fourdn(FOURDN_INSULATION),
fourdn(FOURDN_E1),
ownE1(),
...(own.length === 0 ? [undefined] : own),
]
}
/** The tick boxes the correlation's form shows for them. */
const everyBox = (): Array<HTMLElement | null> => everyTrack().map((entry) => trackBox(entry))
/** A group of the Analysis panel's tasks, shown while the panel is open. */
const groupStep = (id: string, heading: string, text: string, panel: string): TourStep => ({
id,
chapter: 'Compartments',
title: heading,
text,
target: () => taskGroup(heading),
needs: { holds: () => host.panelOpen('analysis'), back: panel },
})
return [
// -- Welcome --------------------------------------------------------------
{
id: 'welcome',
chapter: 'Welcome',
title: 'A first session, on real data',
text:
`Open a Hi-C map from the 4D Nucleome project, find its compartments, domains and a loop on ` +
`${TUTORIAL_SEQUENCE}, save what you made, and set it against 4DN’s own — in the real app, one step at ` +
'a time.',
hero: true,
agenda: true,
next: 'let’s go',
},
// -- The store -----------------------------------------------------------
{
id: 'stores',
chapter: 'The 4DN store',
title: 'Open the data stores',
text:
'Stores are catalogues of published data, read from where they are kept. Press this button to open ' +
'the drawer that holds them.',
target: () => first('.head-files button[aria-label="stores"]'),
done: () => host.store() !== null,
},
{
id: 'store',
chapter: 'The 4DN store',
title: 'Switch to 4DN',
text: 'It opens on the lab’s own store, RSG. Press 4DN to switch to the 4D Nucleome project’s.',
target: () => first(`.store-drawer .store-tile[data-store="${TUTORIAL_STORE}"]`),
done: () => host.store() === TUTORIAL_STORE,
needs: { holds: () => host.store() !== null, back: 'stores' },
},
{
id: 'search',
chapter: 'The 4DN store',
title: 'Find an experiment',
text: [
'Type ',
{ name: TUTORIAL_SET, copy: true },
' in the search box: Hi-C on K562 cells, about 190 million contacts.',
],
action: 'type',
target: searchBox,
focus: true,
done: () => searchBox()?.value.toUpperCase().includes(TUTORIAL_SET) === true && setGroup() !== null,
// Wrong is what cannot become the accession by typing on: a beginning of
// it is a reader on their way, and anything holding it is done.
mistake: () => {
const typed = (searchBox()?.value ?? '').trim().toUpperCase()
return typed === '' || TUTORIAL_SET.startsWith(typed) || typed.includes(TUTORIAL_SET) ? null : typed
},
needs: { holds: () => host.store() === TUTORIAL_STORE, back: 'store' },
assist: {
label: 'type it for me',
title: `Put ${TUTORIAL_SET} in the search box`,
run: () => {
const box = searchBox()
if (box === null) return
box.value = TUTORIAL_SET
box.dispatchEvent(new Event('input', { bubbles: true }))
},
},
},
{
id: 'open-set',
chapter: 'The 4DN store',
title: 'Open it with its tracks',
text:
'One press opens the contact map with the tracks 4DN computed from it — compartments, insulation and ' +
'boundaries — without downloading its 1.9 GB.',
target: () => setGroup()?.querySelector<HTMLElement>('.portal-session') ?? null,
done: onMap,
needs: { holds: () => host.store() === TUTORIAL_STORE || onMap(), back: 'store' },
missing: `Not on screen — type ${TUTORIAL_SET} in the store’s search box again.`,
},
// -- The map -------------------------------------------------------------
{
id: 'look-general',
chapter: 'The map',
title: 'The General panel',
text:
'What the file is: its bin size and contacts under File, its sequences under Sequences, and anything ' +
'else it carries under Metadata.',
target: () => columnCards('general'),
},
{
id: 'resolution-250',
chapter: 'The map',
title: 'Pick 250 kb',
text:
'A map is stored at several resolutions, the size of one bin. 250 kb is coarse enough to show a whole ' +
'chromosome’s compartments.',
action: 'choose',
target: resolutionControl,
done: () => host.binsize() === 250_000,
needs: { holds: onMap, back: 'open-set' },
missing: 'Waiting for the map to open.',
},
{
id: 'chromosome',
chapter: 'The map',
title: `Open ${TUTORIAL_SEQUENCE}`,
text: `Press ${TUTORIAL_SEQUENCE} in the table to open its map.`,
prepare: () => {
revealed = false
},
target: () => {
revealRow()
return sequenceRow(TUTORIAL_SEQUENCE)
},
done: onSequence,
needs: { holds: onMap, back: 'open-set' },
missing: `Not on screen — scroll the table to ${TUTORIAL_SEQUENCE}.`,
},
{
id: 'look-map',
chapter: 'The map',
title: 'The contact map',
text:
`Each pixel is how often two stretches of ${TUTORIAL_SEQUENCE} touch; 4DN’s tracks are drawn under it. ` +
'Scroll to zoom into the picture at this resolution, drag to move around, and double-click to fit it ' +
'back.',
target: mapPicture,
},
{
id: 'look-aesthetics',
chapter: 'The map',
title: 'The Aesthetics panel',
text:
'How the picture is drawn: the Map card sets its score, smoothing and colours, the Tracks card its ' +
'tracks, and Export saves it as a figure.',
target: () => columnCards('aesthetics'),
},
// -- Compartments ---------------------------------------------------------
scoreStep(
'score-correlation',
'Compartments',
CORRELATION_SCORE,
'Draw it as a correlation',
'In the Map card, set score to correlation.',
),
{
id: 'look-correlation',
chapter: 'Compartments',
title: 'The plaid',
text:
'Red where two stretches share a compartment, blue where they do not. Compartments sums this pattern ' +
'up as one track, E1, positive in one compartment and negative in the other.',
target: mapPicture,
},
...sequenceTask(
'Compartments',
'compartments',
'Compartments',
{
choose: 'It splits a chromosome into A and B compartments from the map’s plaid.',
none: 'It runs on every sequence of the file to begin with. Press none…',
tick: `…then tick ${TUTORIAL_SEQUENCE}, the chromosome on screen.`,
run: 'Press run. It takes a few seconds.',
},
{
tour: (panel) => [
groupStep(
'tasks-2d',
'2D tasks',
'These read the contact map: its decay with distance, insulation, compartments, loops and more.',
panel,
),
groupStep(
'tasks-3d',
'3D tasks',
'These build a model of the chromosome’s shape from the map, or set one against it.',
panel,
),
groupStep(
'tasks-1d',
'1D tasks',
'These read tracks rather than the map: peaks, profiles over features, correlations between tracks.',
panel,
),
],
setup: noGeneModel,
after: (open) => [
{
id: 'look-saddle',
chapter: 'Compartments',
title: 'The saddle',
text:
'Bins sorted by E1, low to high: bright corners on the diagonal mean like touches like, A with A ' +
'and B with B. The numbers under it say how much.',
target: () => figure('Saddle'),
needs: { holds: open, back: 'compartments' },
},
],
},
),
{
id: 'look-compartments',
chapter: 'Compartments',
title: 'Your compartments',
text:
'E1 and its A and B calls are drawn left of the map. Compare them with 4DN’s compartment track under ' +
'it.',
target: mapPicture,
},
// -- Zooming in -----------------------------------------------------------
scoreStep(
'score-balanced',
'Zooming in',
BALANCED_SCORE,
'Back to contacts',
'Domains are about how often stretches touch, not how alike they are: set score back to balanced.',
),
{
id: 'zoom',
chapter: 'Zooming in',
title: 'Zoom along the diagonal',
text: `Hold ${keys}, then drag across the lit square, from one corner to the other: that stretch opens.`,
action: 'drag',
target: square(OVERVIEW),
done: () => {
const view = host.view()
return onSequence() && view?.region?.includes(':') === true && view.region2 === undefined
},
needs: { holds: onSequence, back: 'chromosome' },
assist: {
label: 'zoom for me',
title: `Open ${TUTORIAL_SEQUENCE}:${bp(OVERVIEW.start)}-${bp(OVERVIEW.end)}`,
run: () => goTo(`${TUTORIAL_SEQUENCE}:${bp(OVERVIEW.start)}-${bp(OVERVIEW.end)}`),
},
},
{
id: 'resolution-5',
chapter: 'Zooming in',
title: 'Switch to 5 kb',
text: 'At 5 kb the domains along the diagonal come into view, and the loops at their corners.',
action: 'choose',
target: resolutionControl,
done: () => host.binsize() === FINE,
needs: { holds: onMap, back: 'open-set' },
},
{
id: 'zoom-domains',
chapter: 'Zooming in',
title: 'Closer, on a few domains',
text: `Once more: hold ${keys} and drag across the lit square.`,
action: 'drag',
target: square(DOMAINS),
done: () => {
const stretch = stretchOf(host.view())
return (
stretch !== null &&
stretch.contig === TUTORIAL_SEQUENCE &&
stretch.end - stretch.start <= DOMAINS_SPAN &&
host.binsize() === FINE
)
},
needs: { holds: () => onSequence() && host.binsize() === FINE, back: 'resolution-5' },
missing: 'Not in view — press zoom for me, or go back a step.',
assist: {
label: 'zoom for me',
title: `Open ${TUTORIAL_SEQUENCE}:${bp(DOMAINS.start)}-${bp(DOMAINS.end)}`,
run: () => goTo(`${TUTORIAL_SEQUENCE}:${bp(DOMAINS.start)}-${bp(DOMAINS.end)}`),
},
},
{
id: 'look-domains',
chapter: 'Zooming in',
title: 'Domains',
text:
'Each dark square along the diagonal is a domain, or TAD: a stretch that touches itself more than its ' +
'neighbours. Most sit inside bigger ones — the big square from 45.7 to 48.3 Mb holds two.',
target: mapPicture,
},
{
id: 'oe-on',
chapter: 'Zooming in',
title: 'Turn on O/E',
text: 'O/E divides each pixel by what its distance predicts, so what is left is structure rather than distance.',
target: inMapCard(oeToggle),
done: () => host.view()?.oe === true,
needs: { holds: onMap, back: 'open-set' },
},
{
id: 'smooth',
chapter: 'Zooming in',
title: 'Smooth it',
text:
'At 5 kb most pixels hold a handful of contacts. Set smooth to 3 × 3, which averages each pixel with ' +
'the eight around it.',
action: 'choose',
target: inMapCard(() => mapField('smooth')),
done: () => host.view()?.smooth === SMOOTH_3X3,
needs: { holds: onMap, back: 'open-set' },
},
{
id: 'look-oe',
chapter: 'Zooming in',
title: 'Domains and compartments',
text:
'Red is more contact than the distance predicts, blue less: the domains are red squares, and the ' +
'checkerboard behind them is A and B again.',
target: mapPicture,
},
// -- Insulation -----------------------------------------------------------
...sequenceTask(
'Insulation',
'insulation',
'Diamond insulation',
{
choose: 'It scores how much contact crosses each bin; its dips are the boundaries between domains.',
none: 'Again, press none…',
tick: `…then tick ${TUTORIAL_SEQUENCE}.`,
run: 'Press run. Four windows over a whole chromosome at 5 kb take a little while.',
},
{
form: (open) => [
{
id: 'insulation-scales',
chapter: 'Insulation',
title: `Four scales`,
text:
`Set scales to ${SCALES}. The window is 10 bins, 50 kb here, and each scale doubles it: 50, 100, ` +
'200 and 400 kb, one insulation track each.',
action: 'type',
target: () => formInput('scales'),
focus: true,
done: () => Number(formInput('scales')?.value) === SCALES,
needs: { holds: open, back: 'insulation' },
assist: {
label: 'set it for me',
title: `Set scales to ${SCALES}`,
run: () => typeInto(formInput('scales'), String(SCALES)),
},
},
],
ran: (params) => params.scales === SCALES && host.binsize() === FINE,
},
),
{
id: 'look-insulation',
chapter: 'Insulation',
title: 'Your insulation, at four scales',
text:
'Four scores are drawn left of the map, one per window, with the boundaries and the domains between ' +
'them. The scales are the TAD hierarchy: the 50 kb window dips at the edge of every small domain, the ' +
'400 kb one only at the borders of the big ones. A border every window finds is high in the hierarchy; ' +
'one only the narrow windows see is a subTAD’s, nested inside a bigger domain.',
target: mapPicture,
},
// -- Marks ----------------------------------------------------------------
{
id: 'annotations',
chapter: 'Marks',
title: 'Open the Annotations panel',
text: 'Every track has a row here, the ones you computed among them, and so do the marks you draw.',
target: () => columnDoor('annotations'),
done: () => host.panelOpen('annotations'),
needs: { holds: onMap, back: 'open-set' },
},
{
id: 'mark-loop',
chapter: 'Marks',
title: 'Mark the loop',
text: [
'The big domain has a dot at its corner: a loop, its two borders held together. In Manual annotations, ' +
'under Arrowheads, type ',
{ name: `${TUTORIAL_SEQUENCE}:${bp(LOOP.rows)}`, copy: true },
' in rows and ',
{ name: `${TUTORIAL_SEQUENCE}:${bp(LOOP.cols)}`, copy: true },
' in columns, then press add.',
],
target: () => manualForm('Arrowheads') ?? manualCard(),
done: loopMarked,
needs: { holds: () => host.panelOpen('annotations'), back: 'annotations' },
missing: 'Not on screen — scroll the Annotations panel to Manual annotations.',
assist: {
label: 'mark it for me',
title: `An arrowhead at ${TUTORIAL_SEQUENCE}:${bp(LOOP.rows)} × ${TUTORIAL_SEQUENCE}:${bp(LOOP.cols)}`,
run: () => {
const form = manualForm('Arrowheads')
const [rows, cols] = [...(form?.querySelectorAll<HTMLInputElement>('input') ?? [])]
if (rows === undefined || cols === undefined) return
rows.value = `${TUTORIAL_SEQUENCE}:${bp(LOOP.rows)}`
cols.value = `${TUTORIAL_SEQUENCE}:${bp(LOOP.cols)}`
addButton(form)?.click()
},
},
},
{
id: 'mark-border',
chapter: 'Marks',
title: 'Mark the weak border',
text: [
'Inside that domain one border is weak: the 400 kb window barely dips there, 4DN calls it Weak, and it ' +
'splits the domain into two subTADs. Under Lines, keep vertical, type ',
{ name: `${TUTORIAL_SEQUENCE}:${bp(SUBTAD_BORDER)}`, copy: true },
' and press add.',
],
target: () => manualForm('Lines') ?? manualCard(),
done: borderMarked,
needs: { holds: () => host.panelOpen('annotations'), back: 'annotations' },
missing: 'Not on screen — scroll the Annotations panel to Manual annotations.',
assist: {
label: 'mark it for me',
title: `A vertical line at ${TUTORIAL_SEQUENCE}:${bp(SUBTAD_BORDER)}`,
run: () => {
const form = manualForm('Lines')
const axis = form?.querySelector('select')
const at = form?.querySelector<HTMLInputElement>('input')
if (axis === null || axis === undefined || at === null || at === undefined) return
axis.value = 'vertical'
at.value = `${TUTORIAL_SEQUENCE}:${bp(SUBTAD_BORDER)}`
addButton(form)?.click()
},
},
},
{
id: 'look-marks',
chapter: 'Marks',
title: 'A loop and a subTAD border',
text:
'The arrowhead points at the loop closing the big domain, and the line marks the border inside it. ' +
'Find the same place on your four insulation tracks, left of the map: a deep dip at 50 kb, barely one ' +
'at 400 kb — that is the hierarchy, read off one bin.',
target: mapPicture,
},
// -- Tracks ---------------------------------------------------------------
{
id: 'insulation-row',
chapter: 'Tracks',
title: 'Unfold your insulation’s settings',
text: 'A computed track is a track like any other: press the arrow on your first insulation row.',
target: () => insulationRow()?.querySelector<HTMLElement>('.ann-more') ?? null,
done: insulationOpen,
needs: { holds: () => host.panelOpen('annotations'), back: 'annotations' },
missing: 'No insulation row — run Diamond insulation again.',
},
{
id: 'insulation-bigwig',
chapter: 'Tracks',
title: 'Save it as a bigWig',
text:
'Press bigWig to save the score as a file IGV, deepTools and pyBigWig open — written here, in this ' +
'page, with nothing uploaded.',
target: () => {
for (const node of insulationRow()?.querySelectorAll<HTMLElement>('.ann-exports button') ?? []) {
if (words(node) === 'bigWig') return node
}
return null
},
done: () => savedAny('.bw'),
needs: { holds: () => host.panelOpen('annotations') && insulationOpen(), back: 'insulation-row' },
},
{
id: 'domains',
chapter: 'Tracks',
title: 'Unfold the domains’ settings',
text: 'Press the arrow on the Insulation domains row.',
target: () => domainsRow()?.querySelector<HTMLElement>('.ann-more') ?? null,
done: domainsOpen,
needs: { holds: () => host.panelOpen('annotations'), back: 'annotations' },
missing: 'No Insulation domains row — run Diamond insulation with its domains on.',
},
{
id: 'domains-display',
chapter: 'Tracks',
title: 'Draw the domains as a 1D track',
text: 'Domains are outlined on the map. Choose 1D track to draw them as a lane beside it instead.',
action: 'choose',
target: () => domainsRow()?.querySelector<HTMLElement>(`select[data-display="${OWN_DOMAINS}"]`) ?? null,
done: domainsLane,
needs: { holds: domainsOpen, back: 'domains' },
},
{
id: 'domains-bottom',
chapter: 'Tracks',
title: 'Put it under the map',
text: 'Press the bottom edge to draw the lane under the map…',
target: () => placeToggle('bottom'),
done: () => domainsPlaced()?.bottom === true,
needs: { holds: () => domainsOpen() && domainsLane(), back: 'domains-display' },
},
{
id: 'domains-left',
chapter: 'Tracks',
title: 'Take it off the side',
text: '…and the left edge to take it off the left.',
target: () => placeToggle('left'),
done: () => {
const placed = domainsPlaced()
return placed !== null && placed.bottom && !placed.left
},
needs: { holds: () => domainsOpen() && domainsLane(), back: 'domains-display' },
},
// -- The figure -----------------------------------------------------------
{
id: 'export-format',
chapter: 'The figure',
title: 'Choose PDF',
text:
'The Export card at the top of the Aesthetics panel saves what is on screen — the map, your marks and ' +
'every track — as a figure. Choose PDF (vector): lines and text stay sharp at any size.',
action: 'choose',
target: () => exportRow()?.querySelector<HTMLElement>('select.select-format') ?? columnDoor('aesthetics'),
done: () => (exportRow()?.querySelector('select.select-format') as HTMLSelectElement | null)?.value === 'pdf',
needs: { holds: onMap, back: 'open-set' },
},
{
id: 'export-save',
chapter: 'The figure',
title: 'Save the figure',
text: 'Press the download button beside it.',
target: () => exportRow()?.querySelector<HTMLElement>('.export-acts button') ?? columnDoor('aesthetics'),
done: () => savedAny('.pdf'),
needs: {
holds: () => (exportRow()?.querySelector('select.select-format') as HTMLSelectElement | null)?.value === 'pdf',
back: 'export-format',
},
},
// -- Track correlation ----------------------------------------------------
analysisPanel('analysis-trackcorr', 'Track correlation'),
{
id: 'trackcorr',
chapter: 'Track correlation',
title: 'Choose Track correlation',
text: 'It measures how closely every pair of loaded tracks agrees.',
target: () => taskRow('Track correlation'),
done: () => host.task() === 'trackcorr',
needs: { holds: () => host.panelOpen('analysis'), back: 'analysis-trackcorr' },
missing: 'Not in the list — empty the box over it if a word is typed there.',
},
{
id: 'tick-tracks',
chapter: 'Track correlation',
title: 'Tick every track',
text: [
{ name: FOURDN_INSULATION },
' and ',
{ name: FOURDN_E1 },
', 4DN’s insulation and E1, your E1, and your insulation at all four scales.',
],
// The list rather than one box in it: the ticks are one step, and the
// reader is shown the whole of what they are choosing from.
target: () =>
everyBox()
.map((box) => box?.closest<HTMLElement>('.param-field') ?? null)
.find((field) => field !== null) ?? null,
done: () => everyBox().every((box) => box?.querySelector('input')?.checked === true),
needs: { holds: () => host.task() === 'trackcorr', back: 'trackcorr' },
missing: 'Not in the list — a track did not load, or was closed.',
assist: {
label: 'tick them for me',
title: 'Tick every track in the list',
run: () => {
for (const box of everyBox()) {
const input = box?.querySelector('input')
if (input !== null && input !== undefined && !input.checked) input.click()
}
},
},
},
{
id: 'trackcorr-run',
chapter: 'Track correlation',
title: 'Run it',
text: `Every pair is compared over the windows all of them have values in, which is ${TUTORIAL_SEQUENCE}.`,
target: runButton,
done: () => {
const wanted = everyTrack()
if (wanted.some((entry) => entry === undefined)) return false
return host.runs('trackcorr').some((run) => {
const chosen = new Set(namesIn(run.provenance.params.tracks) ?? [])
return wanted.every((entry) => entry !== undefined && chosen.has(entry.id))
})
},
needs: { holds: () => host.task() === 'trackcorr' || host.running('trackcorr'), back: 'trackcorr' },
},
{
id: 'look-trackcorr',
chapter: 'Track correlation',
title: 'Yours against 4DN’s',
text:
'Each square compares two tracks: red where they rise and fall together, blue where one rises as the ' +
'other falls. Find yours against 4DN’s — an unphased E1 can match upside down, at −1 — and your four ' +
'scales against each other: neighbouring windows agree most, the hierarchy again.',
target: () => figure('Track correlation'),
},
// -- The console ----------------------------------------------------------
{
id: 'console',
chapter: 'The console',
title: 'Every step is a command',
text:
'Open the console: each file you opened and each run you made is a line you can paste into a terminal ' +
'to do it again.',
target: () => first('.head-actions button[aria-label="console"]') ?? first('button[aria-label="console"]'),
done: () => host.consoleOpen(),
},
{
id: 'finish',
chapter: 'Done',
title: 'That’s the tour',
text:
`You opened a map from 4DN, called compartments and domains at four scales on ${TUTORIAL_SEQUENCE}, ` +
'marked a loop and a subTAD border, saved a track and a figure, and set it all against 4DN’s own. The ' +
'tutorial is on the landing page and in About whenever you want it again.',
hero: true,
},
]
}
|