Use the latest version of Circos and read Circos best practices—these list recent important changes and identify sources of common problems.

If you are having trouble, post your issue to the Circos Google Group and include all files and detailed error logs. Please do not email me directly unless it is urgent—you are much more likely to receive a timely reply from the group.

Don't know what question to ask? Read Points of View: Visualizing Biological Data by Bang Wong, myself and invited authors from the Points of View series.

12 — Circos Reference

5. <image> block

You are strongly encouraged to use the default image block from the Circos distribution (etc/image.conf), rather than rolling your own. Override any parameters with the * suffix. 

################################################################
# circos.conf
<image>
<<include etc/image.conf>>
# now override as necessary
radius*           = 750p
auto_alpha_steps* = 10
</image>

block parameters

Flags R required, + multiple instances allowed.

Units Parameters that require units (p pixel, r relative, u value of chromosomes_units) have acceptable units listed in brackets (e.g. [p], [pr]).

Expressions All parameters can be defined by an expression or code to be evaluated with eval().

Defaults Default values will be used for any required parameters that are missing. If no default value is available, Circos will exit with an error.

parameter
description
examples

dir R
Output file directory
VALUE DIR
.
/tmp

file R
Output file name. Appropriate extension will be added.
VALUE FILE
repeats.png

png R
Toggles creation of PNG file. To suppress this on the command line, use -nopng.
VALUE yes|no
DEFAULT yes

svg R
Toggles creation of SVG file. To suppress this on the command line, use -nosvg.
VALUE yes|no
DEFAULT yes

radius R
Size of the image based on radius of inscribed circle. For a radius r, the image will be 2r×2r.
VALUE INT
1500p
3000p

angle_offset R
Angle offset of the start of the first segment in the circle. 0 corresponds to 3 o'clock and -90 to 12 o'clock.
VALUE FLOAT
0
-90

angle_orientation
Scale and ideogram progression in the image.
VALUE clockwise|counterclockwise
DEFAULT clockwise

auto_alpha_colors
Toggles automatic definition and allocation of transparent colors
VALUE yes|no
REQUIRED BY auto_alpha_steps

auto_alpha_steps
Number of transparency steps for each automatically allocated color. When defined to N, colors COLOR_a1 ... COLOR_aN are available for each named COLOR.
VALUE yes|no
REQUIRES auto_alpha_colors
5

background R
Background of the image. This can be either a color or a PNG file.
VALUE COLOR|FILE
DEFAULT white
white
background.png