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.
7 — 2D Data Tracks
11. Connectors
Connectors are articulated line segments that relate two positions on an ideogram between two radial positions.
The definition of a connector track is done as a plot type
<plot> type = connector file = data/6/connectors.txt r0 = 0.8925r r1 = 0.999r connector_dims = 0,0.3,0.4,0.3,0 thickness = 2 color = black </plot>
The data file defines the positions at r0 and r1 to be linked by lines
# connectors.txt
...
hs22 15116257 16046604
hs22 15136864 16056568
...
The example images in this section show how the connector_dims parameter controls the shape of the connector line. The line has five segments and the five connector_dims parameters define the size of each of the segments relative to (r1-r0).