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.
In all previous examples links where drawn as curves of uniform thickness. The thickness was set using a parameter and was unrelated to the size of the spans defined in the link file. Thus, although the thickness of the line could be individually set to a certain pixel value, fundamentally the visual representation of links by simple curves does not convey the size of the link's spans.
By using ribbon links, demonstrated in this example, you can create links that convey the size of the linked regions. This is very useful when the size of the regions is sufficiently large, relative to the size of the image, as to have various sizes distinguishable.
A normal link is a bezier curve, whose control points are customizable using bezier_radius and crest parameters. The curve curve connects the two spans of a link, with the ends of the curve placed in the middle of each span.
When a link is turned into a ribbon, the link's thickness is variable, scaling smoothly across its length. You can toggle a link to be a ribbon using
ribbon = yes
On each end, the ribbon's thickness is the same as the size of the corresponding link span.
Once a link becomes a ribbon, you can use stroke_color and stroke_thickness to outline the link.
Adjusting the z-depth for ribbons is extremely effective in layering the data - the resulting interweaving of ribbons is visually appealing.
The next tutorial in this section discusses how to control ribbon twisting.