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

5. Link Rules - Part II

Rules are worth learning—they allow you to customize the layering and formating your links.

In the previous tutorial, we saw how links can be identified by changing their color based on chromosome assignment.

In this tutorial, I extend the example and show you how you can layer and format links based not only on which chromosomes they connect, but also based on position and link end size.

multiple conditions

A rule can have multiple condition parameters. They are evaluated using AND, i.e. all conditions must be satisfied for the rule to pass. This rule tests for links that are interchromosomal and whose start size is greater than 40kb. 

<rule>
condition = var(interchr)
condition = var(size1) > 40kb
...
</rule>

While you can always combine the conditions in one parameter, 

condition = var(interchr) && var(size1) > 40kb

it is more modular and transparent to take advantage of multiple conditions. Just remember: the conditions are combined with AND, not OR.

helper functions

There are several helper functions that simplify testing data point position.

  • on(CHR) returns 1 if data point on chromosome CHR, for links tests both ends
  • from(CHR) returns 1 if start of link is on chromosome CHR, used for links only
  • to(CHR) returns 1 if start of link is on chromosome CHR, used for links only
  • between(CHR1,CHR2) returns 1 if link is between CHR1 and CHR2, regardless of orientation, used for links only
  • fromto(CHR1,CHR2) returns 1 if link is from CHR1 to CHR2, used for links only
  • tofrom(CHR1,CHR2) returns 1 if link is from CHR2 to CHR1, used for links only

The on() function has a variant that tests for both chromosome and coordinate.

  • on(CHR,START,END) returns 1 if data point is on chromosome CHR and intersects coordinate START-END, for links tests both ends

To test that the data point coordinate falls entirely within the interval, use within().

  • within(CHR,START,END) returns 1 if data point is on chromosome CHR and falls entirely within START-END, for links tests both ends

5-rule example

The first rule, colors any interchromosomal links whose either end falls on hs2:65-75Mb.

The next four rules change the color and thickness based on the maximum size of the link ends. The links with the largest ends (> 40kb) are made green and thick and successive rules retest with a lower maximum size cutoff. # multiple conditions are combined with AND # i.e. all conditions must be satisfied condition = var(interchr) condition = on(hs2,65Mb,75Mb) z = 60 color = red thickness = 5 condition = max(var(size1),var(size2)) > 40kb z = 50 color = green thickness = 5 condition = max(var(size1),var(size2)) > 10kb z = 45 color = dgrey thickness = 4 condition = max(var(size1),var(size2)) > 5kb z = 40 color = grey thickness = 3 condition = max(var(size1),var(size2)) > 1000 z = 35 color = lgrey thickness = 2

Notice that I did not set flow = continue for these rules, since they were designed to short-circuit. The first rule that matches is the only rule that I want to affect the format parameters.