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.
4 — Highlights
5. Ideogram Highlights
Ideogram highlights are placed on top of the ideograms in the figure. You do not need to specify the radial position of these highlights, because these parameters are fixed by the size and position of the ideograms.
In this section, I have used the same data file to draw to highlight tracks. One is an ideogram track and one is a wedge-style track, with radial positions specified.
<highlights> <highlight> file = data/3/random.highlights.z_by_size.txt ideogram = yes </highlight> <highlight> file = data/3/random.highlights.z_by_size.txt r0 = 0.5r r1 = 0.6r </highlight> </highlights>
In the example above, the highlights cover each ideogram completely, obscuring the cytogenetic bands. In this kind of situation, it's best to use wedge-style highlights.
Ideogram highlights are very effective when they are used to highlight specific positions on the genome.
When the radial position of individual ideograms is set with chromosome_radius, the position of highlights is automatically adjusted. Relative highlight radial position is computed relative to the new ideogram position. Highlights drawn on the ideogram (ideogram=yes) are drawn at the new ideogram position.
adding transparency to ideogram highlights
It is possible to make ideogram highlights transparent. This is done in the same way as for wedge highlights, and any other elements that require transparency.
Note that if you have colored ideograms, cytogenetic bands with transparency and transparent ideogram highlights these three colors will blend.
To make ideogram highlights transparent, add _aN to their fill_color. Below is the part of circos.conf that achieves this.
<highlights> # transparent wedge highlights at radial position 0.85-0.95 <highlight> file = highlight.txt fill_color = blue_a5 r0 = 0.85r r1 = 0.95r </highlight> # transparent ideogram highlights, using the same data file as for wedge highlights <highlight> file = highlight.txt fill_color = blue_a2 ideogram = yes </highlight> </highlights>