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.
3 — Drawing Ideograms
10. Progression and Orientation
angle offset
The angle offset determines the angular position of the first ideogram.
-90
|
180 --+-- 0
|
90
The default value is 0, which makes the first ideogram appear at 3 o'clock. I like to use -90 to make the first ideogram appear at the top of the circle.
<image> angle_offset = -90 ... </image>
ideogram progression
The progression of ideograms around the circle is controlled by
the angle_orientation parameter in the <image> block, which can
be either clockwise (this is the default) or counterclockwise.
<image> angle_orientation = counterclockwise ... </image>
Don't forget that if you've included your image parameters from another file, you can override the any of those parameters using the * suffix.
<image> <<include etc/image.conf>> angle_orientation* = counterclockwise ... </image>
The direction of the scale of each ideogram will, by default, be
the same as the orientation. For example, if
angle_orientation=counterclockwise the direction of the scale of each ideogram
will counterclockwise.
ideogram orientation
The orientation of ideograms is globally controlled by
angle_orientation. To adjust the orientation of the scale
for individual ideograms, use
chromosomes_reverse = hs1,hs2,...
This setting reverses the ideogram orientation relative to the default orientation, which is controlled by the ideogram progression set by angle_orientation.
Why would you want to reverse individual ideograms? If you are using ribbon links to show alignments, you can have control whether the ribbon twists or not by adjusting the ideogram orientation. Or, if you are only showing two ideograms (e.g. a sample and a reference), it may be more instructive to show the ideograms with their start, and end, points near each other, respectively. This would be achieved by
chromosomes = hs1;hs2 chromosomes_reverse = hs2