Keyboard and command palette

Every action in chromosomix is a command with a name, and the ones you reach for often have a key. The command palette lists every command; the shortcuts dialog lists every key.

The command palette

Press Ctrl+P (⌘P on a Mac), even from a box you are typing in, or click Search commands… in the header.

It lists every command, with what it does and its key, grouped as App, File, Go, View and Help, and Structure for a 3D model. A command that cannot act right now is greyed, not hidden. A switch is listed once, with on or off beside it, such as Crosshair on.

• Type to narrow the list, best matches first; letters in order are enough, so wg finds Whole genome.
• Start with a group’s name to search within it: file copy finds Copy this plot to the clipboard.
• ↑ and ↓ choose, Enter or a click runs, and Esc closes.

Some commands have no key:

Group	Commands with no key
File	Add a file to this tab, Connect a local or remote folder (Connect a folder in the single-file version), Open a different file, Close this tab, Share this tab as a link, Add a map beside this one, and in the 1D browser Open a contact map on this genome
View	Shrink the tracks to the shortest of them, Legend, Refine on zoom, Put every card back in its own panel
Help	What this browser is remembering, Guided tutorial (not in the single-file version), About this viewer, Documentation, Source on GitHub
Structure	Mark a bead, Mark a loop, Measure

The shortcuts dialog

Press ?, or the keyboard button at the right of the header, for Keyboard shortcuts: every key, in the palette’s groups, as your computer writes it, then what the mouse and keys do On a contact map and On the genome browser. It follows the tab in front, so a map and the 1D browser list a few keys differently.

How keys are read

• Ctrl and ⌘. The palette, saving and copying use Ctrl on Windows and Linux and ⌘ on a Mac. Moving between tabs and opening the console use Control everywhere, a Mac included.
• Letters work whatever their case, and with Caps Lock on.
• − + < > are read by the character they type, from either half of their key: on an English keyboard , and . step between sequences without Shift, and = and _ change the resolution.
• The digits and the key left of 1 are read by where they are. On a French keyboard the bare & é " ' keys are 1 to 4, and the keypad’s digits work too.
• A bare key never acts with Ctrl, ⌘ or Alt held, AltGr included.
• While you type in a box, keys type. Only the chords with Ctrl or ⌘ still act: the palette, saving, moving between tabs and the console.
• Ctrl+C and Space give way. With text selected or the caret in a box, Ctrl+C copies the text. Space presses a focused button or tickbox rather than locking the diagonal.

A button’s tooltip also prints the key that does the same.

Every key

In the dialog’s order and wording. ⌘ is for a Mac, Ctrl for everything else.

App

Key	Command	What it does
Ctrl+P / ⌘P	Search commands	Opens the command palette
?	Keyboard shortcuts	Opens the shortcuts dialog

File

Key	Command	What it does
\	Stores	The data stores, as a drawer down the left. Not in the single-file version
O	New tab	Another tab, with its own file and settings
Ctrl+S / ⌘S	Save every tab as a file	One file to drop back on the page
F2	Rename this tab	The name travels with the link
S	Save this plot as a figure	The Export card’s button, in its format and resolution
Ctrl+C / ⌘C	Copy this plot to the clipboard	A PNG at the Export card’s resolution. With maps side by side, Copy the deck to the clipboard: every panel as one PNG

Go

Key	Command	What it does
Ctrl+>	Next tab	The tab after this one
Ctrl+<	Previous tab	The tab before this one
/	Find	The caret in the region box on a map, the filter above a table, or the 1D browser’s locus box, which takes a gene name too
G	Cells table	An .scool’s table of cells
C	Chromosomes table	The file’s table of sequences. On a map
W	Whole genome	On a map, every sequence against every other, asking first when the block is large. In the 1D browser, every sequence end to end
<	Previous sequence	The sequence before this one, in the file’s order. The palette names it
>	Next sequence	The sequence after this one
B	Bookmark this view	The place and resolution, on the Bookmarks card. On a map

View

Key	Command	What it does
V	Read this genome as tracks	The chromosomes end to end, the map kept open. The same key, then named The map and its tracks (or, in a 1D browser with a map behind it, The contact map on its own), goes back
H	Stretch the tracks to fill the height	One height for every track, filling the space
Y	Autoscale every track	Every value axis back to what is in view; a group as a group
Space	Diagonal lock	Every drag, scroll and box runs along the diagonal until pressed again. On a map
0	Fit the view	On a map, every pan and zoom undone, as a double click does. In the 1D browser, the whole genome
E	Observed over expected	Each cell over what its distance from the diagonal predicts: the Map card’s O/E toggle. On a map
−	Coarser resolution	One rung on the resolution bar. On a map
+	Finer resolution	One rung on the resolution bar. On a map
A	Manual annotations	Your hand-drawn marks, on every map, track and model; on brings back the ones it hid
N	Track text	Track names, value ranges and feature names
R	Track floor	A rule along the bottom of every track lane
F	Track fill	The area under a track’s line, filled
I	Track outline	A dark rule along the top of every track and round every feature’s box
U	Name column	Track names beside the tracks, in a column or the map’s corners, rather than over them
X	Crosshair	Guide lines through the cell under the pointer
P	Tooltip	The card that follows the pointer; the status line reads out either way
D	Dividers	Sequence boundaries, as lines across the map
M	Breaks	The same boundaries as ticks outside the plot
L	Labels	Block names in the gutters
K	Ticks	Base-pair coordinates along the axes, inside a block with a single contig
1	General panel	What the open file is, its genome, its metadata
the key left of 1	Files panel	The folders you connected
2	Annotations panel	The tracks, structures, marks and bookmarks on this file
3	Aesthetics panel	How the picture is drawn: colours, scales, overlays, export
4	Analysis panel	What can be computed from this file
Ctrl+backtick	Console	Every run, open and export of this window, as commands that repeat them
T	Cycle the theme	System follows the machine; every press changes what is on screen

In an enlarged 3D model

Only while a 3D model is enlarged; elsewhere these letters keep the meanings above.

Key	Command
F	Frame what the maps are looking at
A	Show the whole model
1	Beads
2	Sticks
3	Tube
L	Sequence names
R	Turntable: the model turns slowly by itself

On a contact map

Gesture	What it does
drag	Pan
Alt + drag (⌥ on a Mac)	Select a square and open it as a region, on the diagonal while it is locked
Shift + Alt + drag	The same, pinned to the diagonal from the nearest bin on it
Shift + drag	Zoom to the stretch it spans, on the diagonal, and copy its locus
double click	Fit the block back to the canvas
wheel	Zoom about the pointer
two fingers sideways	Slide sideways, down the diagonal while it is locked (Space)
Win + wheel (⌘ on a Mac)	Slide the map up and down, and sideways with it
click	Open what the cell refers to
← ↑ → ↓	Pan by a tenth of the view (half a view with Shift)
Page Up / Page Down	Zoom in and out about the centre
Home	Fit the block to the canvas
drag a lane’s far edge	Resize that track
drag across a lane	Raise or lower that track’s ceiling
drag a lane’s grip	Reorder it, or drop it round this map or another, on a + or an empty cell for a cell of its own, or on a tracks cell
drag a track’s row from the panel	Reorder it, or drop it round any map, on a + or an empty cell
click a lane	Open that track’s settings
click a feature in a lane	Open its card: names, attributes, exons
drop a file on an edge of the map	Load it as a track on that edge

On the genome browser

Gesture	What it does
drag	Pan along the genome
drag on the chromosome bar	Select a span, both ends written out to the base
Alt + drag (⌥ on a Mac)	The same selection, over the tracks
drag a track’s lower edge	Make that track taller or shorter
drag the bar under the tracks	Make every track taller or shorter, in proportion
drag a track’s grip	Move it up or down the stack
double click	The whole genome
wheel	Zoom about the pointer
Alt + wheel over a track (⌘ on a Mac)	Raise or lower that track’s ceiling
click a chromosome’s name	Go to that chromosome
click a feature	Open its card: names, attributes, exons, and a zoom
click a track’s range	Type a limit
drop a file on the tracks	Load it; a .cool opens the map on this genome
← →	Pan by a fifth of the window
+ / −	Zoom about the centre

Folding the panels

The digit row folds and opens the side columns, in the order they stand: the key left of 1 for Files, outermost on the left, then 1 General, 2 Annotations, 3 Aesthetics and 4 Analysis, outermost on the right. The key left of 1 is a backtick on an English keyboard, ² on a French PC and @ on a French Mac. The Files column exists only once you have connected a folder; the Annotations and Analysis columns start folded.

Drag a card by its heading into any open column; Escape during the drag puts it back. With the focus on a card’s heading, Alt+↑ and Alt+↓ (⌥↑ and ⌥↓) move it one place. Put every card back in its own panel, in the palette, undoes every move.

Tab walks the fields of one kind

In a name or number edited where it is drawn, Tab keeps what you typed, as Enter does, and moves to the next field of the same kind; Shift+Tab moves to the one before. Past either end of the run, the caret is let go. It walks:

• a track’s name, and the two ends of its range, beside a map and in the 1D browser;
• the two ends of a map’s colour key, and of a 3D model’s key;
• a tab’s name;
• the heading of a cell of the deck, and a name on the Tracks, Metadata annotations, Structures or Contact maps card;
• the place of a mark on the Manual annotations card.

Beside a map, a run goes through the tracks under it, then clockwise round it; in the 1D browser, down the tracks; on a deck, cell by cell as they stand. A range goes from its bottom to its top, then to the next track’s bottom.

A refused value keeps the caret. A bound you only tab through stays automatic. Only a bare Tab walks: Ctrl+Tab is still your browser’s.

Other keys

• A tab’s name: F2 or a double-click to rename, Enter to keep the name, Esc to abandon it.
• Dialogs close with Esc, and so do the Analysis drawer, the stores drawer and the console.
• Placing marks: Esc stops placing them, as done does, and Shift while drawing a rectangle locks it to the diagonal (Annotations and bookmarks).
• A 3D model: drag to turn, scroll to zoom, Shift and drag to move it, ⌘ or Ctrl and a click on a bead to turn about it (a tap alone shows or hides the centre), Space and scroll for the fog, the arrow keys to turn it once its canvas has the focus, and Esc to let go of a half-made loop or measurement (3D models beside the map).
• A task’s figure: the wheel, a drag, Shift and the wheel, and ⌘ or Ctrl with a drag zoom and pan it (Figures and export).