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.
In this section, we will adjust which chromosomes are drawn and change their scale, color and orientation.
Getting the ideogram layout right is important. For example, making all chromosomes appear to be the same size can emphasize the comparison between relative positions in patterns.
The default behaviour is to display all chromosomes defined in the karyotype file, in order of appearance.
To select a subset of chromosomes, set
chromosomes_display_default = no
and then use the
chromosomes parameter to provide either a list
chromosomes = hs1;hs2;hs3;h4
or regular expression in
chromosomes = /hs[1-4]$/
to specify which chromosomes to show. You can combine these methods
chromosomes = /hs[1-4]$/;hs10;hs11
- prefix to specify that you don't want a chromosome to be drawn
chromosomes = /hs[1-4]$/;-hs3
Note that the list uses
; as the delimiter. The reason why
, is not used is because the chromosome entry can include a list of chromosome regions to draw, such as
chromosomes = hs1:(-100,120-);hs2;hs3;h4
The regular expression can match a partial string, so don't forget to include a trailing
$ anchor if you don't mean to match hs10,hs11,...
The size of the ideogram on the figure can be adjusted using an absolute or relative magnification.
Absolute scale applies a fixed magnification to an ideogram
# hs1 0.25x zoom # hs2 2.00x zoom chromosomes_scale = hs1=0.25,hs2=2.0
Relative scale defines the size of the ideogram relative to image circumference
# hs1 25% of figure # hs2 50% of figure chromosomes_scale = hs1=0.25r,hs2=0.50r
Normalized relative scale distributes several ideograms evenly within a fraction of the figure.
# hs1,hs2 distributed evenly within 50% of figure (each is 25%) chromosomes_scale = /hs/=0.5rn
A useful idiom is to select all ideograms and distribute them across entire figure.
# all ideograms distributed evenly within entire figure chromosomes_scale = /./=1rn
By default, the scale progression is clockwise. You can set the global angle progression using
angle_orientation in the
<image> # The * suffix is used to overwrite a parameter. In this case, the # angle_orientation imported from etc/image is assigned a different value. angle_orientation* = counterclockwise <<include etc/image>> </image>
To reverse it for one or several ideograms, use
chromosomes_reverse = /hs/
In this case the regular expression did not require a trailing
$ because it applies only to those chromosomes that are displayed. Thus, even though
/hs/ does match
hs20, it does not matter because this chromosome is not shown.
The color of each ideogram is taken from the karyotype file. To change it, use
chromosomes_color = hs1=red,hs2=orange,hs3=green,hs4=blue
By default, all ideograms are placed at the same radial position, as defined by the
radius parameter in the
<ideogram> block. You can selectively move one or more of the ideograms radially by definining a new radial position using
Probably the most convenient way to do this is to use relative coordinates (
r suffix), which are interpreted relative to the default ideogram radius. For example,
chromosomes_radius = hs4:0.9r
would place chromosome 4 at
0.9x the radius of all other chromosomes.