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.
In many of the examples in this series of tutorials, the highlights were used to draw data sets, such as gene position. Highlights are very useful for drawing data because you have a high degree of control in formatting each highlight wedge.
In other cases, highlights are useful to help the eye focus on a part, or parts, of your diagram.
All other data types, as well as tick mark grids, are placed on top of the highlights.
For the first image in this section, I've prepared two highlight files. The first file, recapitulates the chromosome size and uses the chromosome color scheme.
hs1 0 247249719 fill_color=chr1 hs2 0 242951149 fill_color=chr2 hs3 0 199501827 fill_color=chr3 hs4 0 191273063 fill_color=chr4 hs5 0 180857866 fill_color=chr5 hs6 0 170899992 fill_color=chr6 hs7 0 158821424 fill_color=chr7 hs8 0 146274826 fill_color=chr8 hs9 0 140273252 fill_color=chr9 hs10 0 135374737 fill_color=chr10 hs11 0 134452384 fill_color=chr11 hs12 0 132349534 fill_color=chr12 hs13 0 114142980 fill_color=chr13 hs14 0 106368585 fill_color=chr14 hs15 0 100338915 fill_color=chr15 hs16 0 88827254 fill_color=chr16 hs17 0 78774742 fill_color=chr17 hs18 0 76117153 fill_color=chr18 hs19 0 63811651 fill_color=chr19 hs20 0 62435964 fill_color=chr20 hs21 0 46944323 fill_color=chr21 hs22 0 49691432 fill_color=chr22 hsX 0 154913754 fill_color=chrX hsY 0 57772954 fill_color=chrY
Using this file, I can recreate the ideogram size in chromosome-specific color anywhere in the image. I've drawn two highlight tracks using this file.
The first track is drawn in side the circle from 0.5 to 1.0 times the inner ideogram radius.
<highlight> file = data/3/chr.highlights.txt r0 = 0.5r r1 = 1r </highlight>
The second track is drawn outside the circle, and includes a black stroke.
<highlight> file = data/3/chr.highlights.txt stroke_thickness = 2 stroke_color = black r0 = 1.1r r1 = 1.15r </highlight>
The second file stores the position of cytogenetic bands classified as centromeres and stalks in the karyotype. This is a union of all coordinates whose bands were labeled as acen or stalk.
hs1 121100000 128000000 hs10 38800000 42100000 hs11 51400000 56400000 hs12 33200000 36500000 hs13 3800000 8300000 hs13 13500000 18400000 hs14 3100000 6700000 hs14 13600000 19100000 hs15 3500000 7900000 hs15 14100000 18400000 hs16 34400000 40700000 hs17 22100000 23200000 hs18 15400000 17300000 hs19 26700000 30200000 hs2 91000000 95700000 hs20 25700000 28400000 hs21 2900000 6300000 hs21 10000000 13200000 hs22 3000000 6600000 hs22 9600000 16300000 hs3 89400000 93200000 hs4 48700000 52400000 hs5 45800000 50500000 hs6 58400000 63400000 hs7 57400000 61100000 hs8 43200000 48100000 hs9 46700000 60300000 hsX 56600000 65000000 hsY 11200000 12500000
This set of highlights is drawn on top of the previous, outer track and filled white, effectively splitting the highlights along centromeres and stalks.
<highlight> file = data/3/chr.hetero.highlights.txt stroke_thickness = 2 stroke_color = black fill_color = white r0 = 1.1r r1 = 1.15r z = 10 </highlight>
If you have a figure in which certain genomic areas are of interest, highlights are the best way to guide your audience's eyes.
For this example, I've created a data file with just a few highlights.
hs1 15000000 50000000 hs2 100000000 150000000 hs3 50000000 60000000 hs3 80000000 90000000 hs3 100000000 105000000 hs14 0 106368585
Using this data set, I've drawn three sets of highlights that isolate these regions. These are shown in the second image in this section. The first set of highlights is light grey and spans 0.5r-1.0r radial region. These second falls outside of the ideogram circle and is light yellow from 1.0r to 1.1r. The last is light grey again from 1.1r to 1.15r.
Note that unless you are using ideogram highlights, Circos does not support highlights that cross the circle of ideograms. I strongly advise against setting r0<1 and r1>1 for a set of highlights :)