HiC contact matrix visualization

View the Project on GitHub

Back to juicebox.js // Back to Developer Doc  

juicebox.js URL structure.

Note: all parameter values must be URL encoded

Parameter Description
hicUrl URL to the current .hic file
state string encoding current state of the map (optional, see below)
colorScale max value and RGB components of the map color scale (optional, see below)
track string encoding URL to tracks and associated state (optional, see below)


state is comma separated string with following tokens:

token description
1 index of x axis chromosome. Whole genome is represented by 0, chr1 by index 1, chr2 index 3, etc
2 index of y axis chromosome.
3 index of resolution level, lowest resolution is index 0
4 x position of map origin in bins
5 y position of map origin in bins
6 pixel size (size of each bin in screen pixels)
7 normalization


colorScale is a comma separated string with 4 fields. The color ranges from 0 (white) - max (color).

field description
1 max value (contact map value at maximum color intensity)
2 red component of max color (0-255)
3 green component of max color (0-255)
4 blue component of max color (0-255)


track is a string encoding all tracks, with each track section delimited by triple bars (“|||”). Track fields are delimited by a single bar (“|”) with the following tokens:

token description
1 URL to the track file
2 data range as a dash delimited string (e.g. 0-50)
3 color string, any JavaScript-recognized color declaration (e.g. “rgb(100, 0, 0)”