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.
Ideogram highlights are particularly suitable for data that draws attention to some parts of the ideograms, leaving most of the ideogram uncovered. Remember that ideogram highlights obscure the cytogenetic bands, if any, that you've drawn. Thus, as you increase highlight coverage, you are actually obscuring one data set (cytogenetic bands) in favour of display another (the highlights themselves).
In this example, I've created highlights from two gene lists. One gene list is the set of genes in the OMIM database, which lists genes associated with any kind of disease. The other list is a set of genes that have been implicated in cancers. The latter list is much smaller than the former.
I've defined two ideogram highlight tracks, the OMIM genes drawn in orange and the cancer genes in blue. Since the cancer genes are a proper subset of the OMIM genes, I've drawn the cancer genes on top by assigning them a higher z-depth.
<highlights> ideogram = yes z = 5 <highlight> file = data/3/genes.omim.txt fill_color = orange </highlight> <highlight> file = data/3/genes.cancer.txt z = 10 fill_color = blue </highlight> </highlights>
Since both higlight data sets are of the ideogram type, I've put the ideogram parameter in the outer <highlights> block. This applies the parameter value to all inner <highlight;> blocks.
I've set the default z-depth to be 5, and gave the cancer gene highlights a higher z-depth, 10. It's good to space your z-depths by steps of 5 or 10, because this allows you to insert highlight data sets at any relative position to existing higlights without changing existing z-depth values. It's also a good idea not to start z-depth at 0, because you can then insert a data set behind all others, without using a negative z-depth, which is acceptable but simply less aesthetically pleasing than all-positive z-depths.
One of the two fill_color parameters could have been global to both <highlight> blocks. It's up to you how to manage parameter values in a way that's reasonable for your application. Depending on your use, one of the two statements below may be more intuitive