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

9. Drawing on Top of Data

Highlights defined in <highlight> blocks are always drawn behind links, data, and grids.

In order to draw highlights on top of links, you need to use the <plot>.

type = highlight
file = data/3/chr.highlights.txt
r0   = 0.7r
r1   = 0.75r
z    = 10

The plot type must be set to type=highlight, with the rest of the syntax being the same as for the highlight block.

The z parameter in the <plot> block will define the layer, relative to other plots, on which the highlights will be drawn. Tracks with larger z are drawn on top of those with smaller z.

If you want to place the highlight within the ideogram, set the inner and outer track radii to

r0 = dims(ideogram,radius_inner)
r1 = dims(ideogram,radius_outer)

Plot blocks are discussed in detail in the 2D Data Tutorial. Briefly, these blocks are used to define and format 2D data plots such as scatter plots, histograms, and heatmaps.