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.
6 — Links and Relationships
3. Link Formatting
In this example, the image will be created using multiple data sources for links. I'm also going to subvert the record_limit setting, and in combination with z depth, to sample different links from the same data file.
In general, if you have multiple data files, each is associated with its own <link> block.
<links> # global parameters here ... <link> file = /path/to/file # local parameters for this data set ... </link> <link> file = /path/to/file # local parameters for this data set ... </link> ... </links>
When combining multiple link data sets in one image, there are a few things to keep in mind.
First, set the z depth for each data set accordingly. Data sets with a higher the z depth value are drawn on top of data sets with a lower value. In this example, I draw the first 10,000 records from segdup.txt in very light grey (z=5), then the first 2,500 records in light grey (z=10, thus on top of any z<10 data), then the first 1,000 records in grey (z=15, thus on top of any z<15 data), and so on.
Second, you can adjust link geometry for each data set. In this
example, I've modified the crest and bezier radius purity for links
drawn from the three segdup.bundle*.txt files.
Finally, thickness and color can be effectively used to help layer the data. I typically draw links with a lower z value in a light shade of a color and with thin lines.