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

8. Recipe 3 - Plot Axis Range Highlights

In this section, I'll look ahead and show how you can use highlights to annotate 2D data plots (e.g. scatter plots).

By defining highlights to span the entire data domain (e.g. entire genome), you can draw multiple instances of the highlight using different colors and radial positions, in effect setting up a set of concentric circles that provide radial axis highlights.

By drawing a scatter plot, for example, and synchronizing the radial extent of the scatter plot with the position of the highlights, you can draw attention to outlying data in your scatter plot. 

<highlight>
file       = data/3/chr.highlights.colourless.txt
r0 = 0.715r
r1 = 0.725r
fill_color = lred
</highlight>

<highlight>
file       = data/3/chr.highlights.colourless.txt
r0 = 0.725r
r1 = 0.75r
fill_color = lorange
</highlight>

<highlight>
file       = data/3/chr.highlights.colourless.txt
r0 = 0.75r
r1 = 0.80r
fill_color = lyellow
</highlight>

<highlight>
file       = data/3/chr.highlights.colourless.txt
r0 = 0.8r
r1 = 0.9r
fill_color = lgrey
</highlight>

<highlight>
file       = data/3/chr.highlights.colourless.txt
r0 = 0.9r
r1 = 0.95r
fill_color = lyellow
</highlight>

<highlight>
file       = data/3/chr.highlights.colourless.txt
r0 = 0.95r
r1 = 0.975r
fill_color = lorange
</highlight>

<highlight>
file       = data/3/chr.highlights.colourless.txt
r0 = 0.975r
r1 = 0.985r
fill_color = lred
</highlight>