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.
2 — Quick Start
2. Ticks & Labels
In this tutorial, I will add labels to the ideograms as well as ticks and tick labels.
To do this, the <ideogram> block needs to be expanded to include label parameters. Tick labels are defined in a different block, <ticks>.
ideogram labels
Labels for ideograms can be placed at any radial position and formatted flexibly. The minimum label definition is shown below.
<ideogram> <spacing> default = 0.005r </spacing> # Ideogram position, fill and outline radius = 0.90r thickness = 20p fill = yes stroke_color = dgrey stroke_thickness = 2p # Minimum definition for ideogram labels. show_label = yes # see etc/fonts.conf for list of font names label_font = default label_radius = 1r + 75p label_size = 30 label_parallel = yes </ideogram>
The radial position of the labels can be adjusted using label_radius.
# relative to outer ideogram radius label_radius = 1.1r label_radius = 0.8r # absolute position label_radius = 500p # relative position with absolute offset label_radius = 1r + 100p # using image dimensions label_radius = dims(image,radius) - 50p # using ideogram position label_radius = dims(ideogram,radius_outer) + 50p label_radius = dims(ideogram,radius_inner) - 50p
In other parts of Circos configuration, positional parameters (e.g. inner/outer radius of data tracks) support compound expressions that combine absolute and relative values (e.g. 1r+50p).
The quantity used as the reference for relative units depends on which parameter is defined. It is usually defined as the "parent container" of the element. For example, when definition ideogram position, the reference is image radius. When using track position, the reference is ideogram radius. As a result, when the parent element is moved (e.g. ideogram), all other elements move with it (e.g. data tracks).
tick marks and labels
Ticks are defined by group. You can have absolute or relatively spaced ticks, as well as ticks at specific positions. An entire tutorial is dedicated to ticks. Here, I show a minimum definition.
show_ticks = yes show_tick_labels = yes <ticks> radius = 1r color = black thickness = 2p # the tick label is derived by multiplying the tick position # by 'multiplier' and casting it in 'format': # # sprintf(format,position*multiplier) multiplier = 1e-6 # %d - integer # %f - float # %.1f - float with one decimal # %.2f - float with two decimals # # for other formats, see https://perldoc.perl.org/functions/sprintf.html format = %d <tick> spacing = 5u size = 10p </tick> <tick> spacing = 25u size = 15p show_label = yes label_size = 20p label_offset = 10p format = %d </tick> </ticks>
The primary parameter in each <tick> block is spacing. This defines the distance between adjacent ticks in this group. Typically, this value is defined in terms of chromosomes_units parameter — the suffix u is used for this — to keep the number legible.
If a tick belongs to multiple groups, the group with largest spacing is prefered. Thus, the tick at 50 Mb will take its formatting from the spacing=25u group, not the spacing=5u group.