Circos > Documentation > Tutorials > Ideograms > Progression And Orientation

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3 — Drawing Ideograms

10. Progression and Orientation

angle offset

The angle offset determines the angular position of the first ideogram.

 180 --+-- 0

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.

angle_offset = -90

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.

angle_orientation = counterclockwise

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.

<<include etc/image.conf>>
angle_orientation* = counterclockwise

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