Links and Rules

We have come to the essence of Circos. Links.

When you are creating your instances different data tracks, rules, etc. I encourage you to make your variable names descriptive so you can make sense of the code you are writing, allowing people to easily understand what you are doing and lastly, reusable instances (especially rules!).

This is the 4th example which we are making links. So we should create a variable named $segdup_link_black to describe the segdup data and the links are black.

Creating link

my $segdup_link_black = Link->new(file => 'data/5/segdup.txt', radius => '0.8r', bezier_radius => '0r', color => 'black_a4', thickness => 2);

I understand it could become very verbose, but many text editors can help autocomplete your variable names. So you shouldn’t worry. Check out Sublime Text 2 if you do not have a great text editor.

Adding rules to link blocks

Adding rules are simple. You can make either add the rule instance into the link instance directly.

$segdup_link_black->addRule(Rule->new(condition => 'var(intrachr)', params => { show => 'no' } ));
$segdup_link_black->addRule(Rule->new(condition => '1', params => { color => 'eval(var(chr2))', flow => 'continue' }));

Or, you can create a variable that contains the rule.

my $rule_fromhs1 = Rule->new(condition => 'from(hs1)', params => { radius1 => '0.99r' });
my $rule_tohs1 = Rule->new(condition => 'to(hs1)', params => { radius2 => '0.99r' });

$segdup_link_black->addRule($rule_fromhs1, $rule_tohs1);

A important note for rules. As you might have noticed, the rule instance has params, which does not exist in the original Circos configuration. This params is a hash that you can specify any parameters that can be implemented in Circos’ rule block. This is to allow flexibility.

Lastly, add the link to the CircosAPI instance.

$c->addLink($segdup_link_black);