Everything you see is measured data, not decoration.
A Hi-C experiment counts how often two stretches of DNA are found touching each other.
The result is a square matrix: both axes are the same chromosome, and the value at
(i, j) is how often locus i touched locus j. Here that matrix is the terrain.
Walk along the pale diagonal road and you are walking along the chromosome itself
— there, the two axes read the same coordinate. Step off the road and you are asking
"how often do these two different places touch?" The further from the road, the further
apart the two loci are.
Raw contact counts fall off steeply with distance, which would make the map a single boring
ridge along the diagonal. So height and colour show O/E — observed contacts divided
by the average for that separation. O/E = 1 is exactly average; the landscape is what is left
after distance is accounted for. Press N to switch to raw counts and watch the structure
collapse into that ridge — that comparison is the whole reason O/E exists.
Colour and height both come from that same O/E number, but not on the same scale.
Colour is linear, so the legend and the Juicebox palette mean exactly what they say.
Height is deliberately exaggerated at the top end — ordinary background is O/E = 1,
which sits mid-ramp, and mapping that straight to height would leave the whole map at
half altitude with nowhere for loops to rise. So the background is pressed down into low
plains and the height is saved for the few pixels that earned it. Read colour for the
number; read height for where to look.
Square plateaus hugging the diagonal are TADs: neighbourhoods that contact
themselves far more than they contact their surroundings. The dark ridges (B to toggle)
are the insulating boundaries between them, usually CTCF-bound.
Cyan beacons are called chromatin loops: single pixels far hotter than the ring
of pixels around them, meaning two specific spots are pinned together much more often than
their neighbours are. Walk into one to inspect it.
Not every map can support these calls. Loops and boundaries are both judged against a
local background, and if a neighbourhood only holds a few reads that background rounds to
zero and every ratio explodes into a fake loop. A shallow QC map can be walked and looked at, but
this world will refuse to call structure on it and will say so at the top of the screen. Depth is
not a detail in Hi-C — it is the difference between seeing loops and inventing them.
Black chasms are not loops or voids in the biology — they are bins with no
mappable data (repeats, centromeres, assembly gaps). Real analyses drop them, and so does this world.
Controls
WASD
move
Mouse
look (click the world to capture the cursor)
Left click
swing the held sword (a bare fist does 1)
Right click
drink the held healing potion
Q
drop the held item on the ground
1 – 6
choose an inventory slot
Esc
pause — keep playing, or save and leave to your worlds
Space
jump — clears exactly one block, as in Minecraft
Double-tap W
sprint; ends when you release W or stop moving
Shift
descend while flying
F
toggle fly — Testing mode only
M
map view — rise up and look straight down at the contact map
L
teleport to the next loop — Testing mode only
E
read the loop you are standing in, or open the summit chest
N
O/E ⇄ raw counts
P
cycle colour palette
B
show / hide TAD boundary ridges
G
smoothing — off shows the raw pixel-to-pixel spikes, which are
mostly counting noise and nearly impossible to walk across
R
return to the loader and pick another region
H / Esc
help / release cursor
Playing it
You start in the corner furthest from every beacon, so getting anywhere means walking. Swords
and healing potions lie scattered across the landscape — right-click drinks a potion for
four hearts. A beacon turns green once you clear its loop, and green
loops are finished for good; if the ghosts drive you out it turns
red and stays open to try again.
Explorer is on foot: no flight, no teleport, and swords are found by covering ground.
Testing mode adds flight and loop teleporting for checking a region quickly.
Walk into a cyan beacon and press E to read the loop, then take
The Loop Ascent. That drops you at the contact point between the two anchors — the
place those two stretches of DNA are actually held together — and asks you to go left or right.
Left is the crowded climb: many more ghosts, tougher ones, and two chest rewards for it.
Right is the long quiet way with only a handful of weak ones and a single reward. Ghosts only
notice you from about 14 blocks, so you can pick them off a few at a time rather than pulling
the whole route at once. Clear the route you chose and the chest opens — it stands on a plinth
one block above the summit floor, so you have to jump up onto it, and one jump is always enough. Everything in a summit chest
outguns everything lying in the landscape, and the two best blades are named after
cohesin and CTCF, the proteins that hold a real loop shut.