Use the latest version of Circos and read Circos best practices—these list recent important changes and identify sources of common problems.
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By default, every ideogram is placed at the same radial position. This is controlled by the radius parameter within the <ideogram> block (conventionally found in ideogram.conf).
<ideogram> ... radius = 0.85r ... </ideogram>
The value is relative to the image radius.
You can place individual ideograms at different radial positions by using the chromosomes_radius parameter in the root of the configuration tree.
chromosomes_radius = hs1:0.5r;hs2:0.55r;hs3:0.6r;hs4:0.65r;hs5:0.7r;hs6:0.75r;hs7:0.8r;hs8:0.85r;hs9:0.9r;hs10:0.95r
The radial position values in this parameter are relative to the default ideogram radius, defined by radius in the <ideogram> block.
For example, if the image radius is 1500p and the default ideogram radius is 0.9r, then all ideograms are at 1350 pixels (1500 * 0.9) from the center. Now, if chromosomes_radius further specifies hs1:0.5r, then hs1 will appear at 675 pixels from the center (1500 * 0.9 * 0.5).
Once the radial position of an ideogram has been redefined using chromosomes_radius, all features associated with that ideogram (plots, links, text, etc) will be automatically relocated to match the new ideogram position. In other words, you do not need to remember that specific ideograms may be at different positions.
If you've tagged your ideograms when creating regions,
chromosomes = hs1[a]:0-50;hs1[b]:150-);hs2[c]:0-50;hs2[d]:150-);hs3[e]
then adjusting the radius of any region can be done by using the tag
chromosomes_radius = hs1:0.8r;a:0.9r;d:0.8r
The radius values will be processed in order, with subsequent radius values overriding previous ones. For example, each region of hs1 will be set to 0.8r, but the region tagged by "a" will be 0.9r.