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.
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> ... 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 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.
When decreasing the radius of an ideogram you may find that the ticks and their labels crowd together. In these cases, it is useful to use the
label_separation parameters in the <ticks> block to define the minimum distance between ticks and their labels.