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.

6 — Links and Relationships

6. Link Rules - Part III

Rules can affect the geometry of a link. This example expands on the previous one and modifies the position of intrachromosomal links to face outward.

The new rules sample intrachromosomal links. The first of these rules, hides any whose ends are within 1 Mb of each other. Here the var(pos1) and var(pos2) are used to sample the middle of the start and end of the link.

The second rule applies to intrachromosomal links whose ends are within 50 Mb. These are colored blue and made to face outward by setting their bezier_radius larger than 1. The next performs a similar function but for any links left within 100 Mb.

The last rule suppresses the display of any other intrachromosomal links (i.e. those whose ends are more than 100 Mb apart). 

<rule>
condition  = var(intrachr)
condition  = abs(var(pos1) - var(pos2)) < 1Mb
show       = no
</rule>

<rule>
condition  = var(intrachr)
condition  = abs(var(pos1) - var(pos2)) < 50Mb
color         = dblue_a2
bezier_radius = 1.1r
bezier_radius_purity = 0.25
</rule>

<rule>
condition  = var(intrachr)
condition  = abs(var(pos1) - var(pos2)) < 100Mb
color         = dgreen_a2
crest         = 2
bezier_radius = 0.75r
bezier_radius_purity = 0.25
</rule>

<rule>
condition  = var(intrachr)
show       = no
</rule>