Use the latest version of Circos and read Circos best practices—these list recent important changes and identify sources of common problems.
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In the previous section I demonstrated how you can adjust the radial extent, by setting r0,r1 in the data file, to encode information about the highlight. In that example, I used the highlight region size to control the radial extent.
There are three data files for this section. All highlights regions are randomly generated. Highlight color is encoded by the chromosome color scheme.
From the images you can see that a little planning when it comes to radial position can produce a much cleaner figure. The first figure is a mess, of course. The last image, in which the small highlights are near the ideograms presents the data clearly. Smaller features are best shown at larger radial positions because they will subtend a larger angular distance along the circle than if drawn closer to the center, and therefore are more clearly visible. Larger structures can be drawn at smaller radial values.
Here is an excerpt of one of the data files used in this section (random.highlights.rrr.txt).
... hs1 135818329 137808916 fill_color=chr7,z=67,r0=0.709600r,r1=0.759600r hs1 107513875 108981462 fill_color=chr5,z=76,r0=0.772761r,r1=0.822761r hs1 227449772 228946659 fill_color=chr5,z=75,r0=0.769223r,r1=0.819223r hs1 24598766 26578839 fill_color=chr7,z=68,r0=0.710869r,r1=0.760869r hs1 145258423 147866442 fill_color=chr10,z=58,r0=0.635033r,r1=0.685033r hs1 110729772 111813392 fill_color=chr4,z=82,r0=0.819133r,r1=0.869133r hs1 136155686 138376393 fill_color=chr8,z=64,r0=0.681808r,r1=0.731808r ...
All the radial positions are specified as relative values, indicated by the "r" suffix. The relative value is expressed in terms of the inner ideogram radius, if the value is <1, and in terms of the outer radius, if the value is >1. This way, highlights don't ever cross ideograms. By the way, if you would like highlights inside the ideograms, use ideogram highlights, covered in the next section.
In addition to relative radial positions, you can specify absolute positions (suffix is "p", for pixel), or a combination of the two. Here are some examples
# absolute positioning r0 = 500p # start at 500 pixels from center r1 = 600p # end at 600 pixels from center # relative positioning - helpful when resizing figure r0 = 0.5r # start at 0.5*inner_ideogram_radius r0 = 0.6r # end at 0.6*inner_ideogram_radius # relative radial position start, but absolute size r0 = 0.5r # start at 0.5*inner_ideogram_radius r1 = 0.5r+100p # start at 0.5*inner_ideogram_radius + 100 pixels # like above, but centered at a radial position r0 = 0.5r-50p # start at 0.5*inner_ideogram_radius r1 = 0.5r+50p # start at 0.5*inner_ideogram_radius + 100 pixels