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

6. <ideogram> 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
<<include ideogram.conf>>

################################################################
# ideogram.conf
<ideogram>
 ...
</ideogram>

syntax

<ideogram>

 <spacing>

   <pairwise>
   </pairwise>

   <pairwise>
   </pairwise>

   ...

 </spacing>

 <break_style>
 </break_style>

 <break_style>
 </break_style>

 ...

 <rules>

   <rule>
   </rule>

   <rule>
   </rule>

   ...

 </rules>

</ideogram>

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

<spacing> R
Ideogram spacing.
PARENT
<ideogram>
CHILDREN
<pairwise>, <break_style>

spacing
Spacing between ideogram pair defined by the block.
VALUE FLOAT [ur]
0.25u
0.5r

<break_style> R
Axis break styles.
PARENT
<ideogram>

<rules>
Format rules.
PARENT
<ideogram>
CHILDREN
<rule>

parameter
description
examples

show R
Toggle the display of ideograms. If ideograms are not shown, neither are ticks or grids.
VALUE yes|no
DEFAULT yes

radius R
Radial position of ideograms. Relative position is relative to image size.
VALUE INT [pr]
0.9r
750p

thickness R
Radial thickness of ideogram segments. Relative thickness is relative to image size.
VALUE FLOAT [pr]
15p
0.02r

thickness
Radial extent of axis break. Relative extent is relative to ideogram thickness.
VALUE INT [rp]
25p
2r

fill R
Toggles fill of ideogram segments using color defined in karytoype file.
VALUE yes|no
DEFAULT yes
TUTORIALS ideograms/karyotype

stroke_color
Color of outline for ideogram segments.
VALUE COLOR
REQUIRES stroke_thickness
REQUIRED BY stroke_thickness
black

stroke_color
Color of stroke on axis break.
VALUE COLOR
REQUIRES stroke_thickness
REQUIRED BY stroke_thickness
dgrey

stroke_thickness

VALUE INT [p]
REQUIRES stroke_color
REQUIRED BY stroke_color
2p

stroke_thickness
Thickness of stroke on axis break.
VALUE INT [p]
REQUIRES stroke_color
REQUIRED BY stroke_color
2p

cytogenetic bands

parameter
description
examples

show_bands
Toggles the display of cytogenetic bands. Bands are defined in the karytoype file.
VALUE yes|no

fill_bands
Toggles fill of the cytogenetic bands using the color defined in the karyotype file.
VALUE yes|no

band_transparency
Transparency of cytogenetic band fill.
VALUE INT
TUTORIALS ideograms/karyotype

band_stroke_thickness
Thickness of outline for cytogenetic bands.
VALUE INT [p]
REQUIRES band_stroke_color
REQUIRED BY band_stroke_color
2p

band_stroke_color
Color of outline for cytogenetic bands.
VALUE COLOR
REQUIRES band_stroke_thickness
REQUIRED BY band_stroke_thickness
dgrey

ideogram label

parameter
description
examples

show_label
Toggles the display of ideogram labels.
VALUE yes|no
TUTORIALS ideograms/labels

label_radius
Radial position of ideogram label.
VALUE FLOAT [rp]
1.1r
1r+50p
800p
dims(image,radius)-25p

label_size
Size of ideogram label, in pixels.
VALUE INT
24

label_font
Font of ideogram label.
VALUE FONT
DEFAULT default
default
bold
condensed

label_parallel
Toggles the ideogram label to be parallel to the ideogram segment.
VALUE yes|no

label_with_tag
Toggles presence of ideogram tag in the label. Tags uniquely identify ideograms from the same chromosome and are defined in the chromosomes parameter.
VALUE yes|no

label_case
Case of ideogram label.
VALUE upper|lower

label_format
Format of ideogram label.
VALUE EXPR
eval(sprintf("chr%s",var(label)))

axis breaks

Tutorial Spacing & Axis Breaks.

parameter
description
examples

axis_break
Toggles display of axis breaks.
VALUE yes|no
REQUIRES <break_style>
TUTORIALS ideograms/cropping, ideograms/spacing_breaks

axis_break_style
Axis break style to use.
VALUE 1|2
REQUIRES <break_style>
TUTORIALS ideograms/cropping, ideograms/spacing_breaks

axis_break_at_edge
Toggles display of axis break at edge of cropped ideogram.
VALUE yes|no
REQUIRES <break_style>
TUTORIALS ideograms/cropping, ideograms/spacing_breaks

<spacing> block

Tutorial Spacing & Axis Breaks.

parameter
description
examples

<pairwise> R
Ideogram spacing for specific ideogram pairs.
PARENT
<spacing>

default R
Spacing between ideograms. Relative spacing is relative to circumference of ideogram circle.
VALUE FLOAT [ur]
TUTORIALS ideograms/spacing_breaks
0.5u
0.01r

break R
Size of axis break. Relative size is relative to ideogram spacing.
VALUE FLOAT [ur]
TUTORIALS ideograms/spacing_breaks
0.25u
0.5r

<pairwise> block

Tutorial Spacing & Axis Breaks.

The name of the block defines to which ideogram pair the spacing applies. 

# adjust spacing between chr1 and chr2
<pairwise chr1 chr2>
</pairwise>

# adjust spacing around chr1
<pairwise chr1>
</pairwise>
parameter
description
examples

<spacing> R
Ideogram spacing.
PARENT
<ideogram>
CHILDREN
<pairwise>, <break_style>

spacing
Spacing between ideogram pair defined by the block.
VALUE FLOAT [ur]
0.25u
0.5r

<break_style> block

Tutorial Spacing & Axis Breaks.

This block defines one of two types of axis break styles. 

# style 1 definition
<break_style 1>
</break_style>

# style 2 definition
<break_style 2>
</break_style>

The style to be used is defined by axis_break_style.

parameter
description
examples

stroke_thickness
Thickness of stroke on axis break.
VALUE INT [p]
REQUIRES stroke_color
REQUIRED BY stroke_color
2p

stroke_color
Color of stroke on axis break.
VALUE COLOR
REQUIRES stroke_thickness
REQUIRED BY stroke_thickness
dgrey

thickness
Radial extent of axis break. Relative extent is relative to ideogram thickness.
VALUE INT [rp]
25p
2r

fill_color
Fill color of axis break. Used for <break_style 1>.
VALUE COLOR
black