Circos > Documentation > Tutorials > Highlights > Parameters
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3 — Highlights

2. Highlight Parameters - Part I - Embedded in Data File

In this tutorial, I'll cover how to embed highlight parameters in your highlight data file. This is a convenient way of formatting highlights because generation of the parameters can be incorporated into your data analysis and reporting pipeline.

formatting a gene list

Using the genes.txt file used in the previous section, I added a random fill color (red, green, blue, purple, yellow, orange, grey) to each entry. For entries that received a red color, I adjusted the radial start/end positions to be closer to the center of the circle than other colors. For entries that received a green color, I similiarly adjusted r0,r1 to format these entries to fall outside of the circle.

Here is an excerpt of the data file, with the additional formatting option fields.

hs1 1298972 1300443 fill_color=blue
hs1 1311738 1324571 fill_color=red,r0=0.6r,r1=0.6r+50p
hs1 1397026 1421444 fill_color=green,r0=1.1r,r1=1.15r
hs1 1437417 1459927 fill_color=green,r0=1.1r,r1=1.15r
hs1 1540746 1555847 fill_color=yellow
hs1 1560962 1645635 fill_color=purple
hs1 1624179 1645623 fill_color=grey

The configuration block for this highlight set defines a default r0,r1 value, which applies to any entries in the data file that don't have overriding r0,r1 values. Thus, most of the highlights fall between r0,r1 = 0.7r,0.7r+200p, with the red and green entries shifted inward and outward in the circle, respectively.

All of the other highlight parameters may be specified in a similar manner in the data file.