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
2. Link geometry
Link geometry is defined by four parameters: radius, bezier_radius, bezier_radius_purity and crest. An additional set of parameters in the perturb* name space permits random adjustment to some of these parameters.
radius
This value sets the radial position of the termini of the links and may be defined as a relative or absolute value.
# 50% of inner ideogram radius radius = 0.5r # 50 pixels inside inner ideogram radius radius = 1r - 50p # 25 pixels outside inner ideogram radius # careful - links will overlap with ideogram radius = 1r + 25p # links terminate 750 pixels from image center radius = 750p
I suggest that you set the radius value to be relative, to make it easier to later resize the figure without having to adjust the radius value.
A combination of relative and absolute values permits an overall relative position with a fixed margin.
bezier_radius
The bezier_radius controls the radial position of the control point used to accentuate the curvature in the link. Without any additional parameters, each link will have its control point placed at the same radial position, regardless of the location of the start and end points of the link.
crest
Two additional Bezier control points can be set by using the crest parameter. When defined, points p3 and p4 are added. These points lie at the same angular position as the start and end link termini and have the radial position
p3r,p4r = radius +/- |bezier_radius - radius| * crest
In the crest=0 extreme, p3 and p4 are at the same position as p0,p1. In this case, crest has no effect. When crest=1, p3,p4 are at the radial position of p2, the control point set by bezier_radius. Keep in mind the difference between p2 and p3,p4 control points - p2 is placed along the radius that bisects angle formed by p0,center,p1 whereas p3,p4 are placed along the same radius as p0,p1.
The purpose of the crest parameter is to make the links terminate perpendicularly to the ideogram radius. Cresting works only if bezier_radius is defined.
bezier_radius_purity
The bezier_radius parameter is constant for all links. Therefore, regardless of a link's start/end position, the p2 control point will always be at the same radial position, as determined by the bezier_radius value. This has the effect of making links that have nearby start/end termini highly curved.
To mitigate this, bezier_radius_purity allows you to define an effective bezier radius, which is a function of the distance between the link's start/end termini.
The bezier_radius_purity adjusts the position of p2 for each link. The p2 control point will move along the line formed by the original p2 location and the intersection of p0-p1 and the bisecting radius. When purity = 1, p2' = p2. When purity = 0, p2' = midpoint(p0,p1).
If bezier_radius_purity is defined, crest will use the new bezier radius control point (p2').
perturb
A set of parameters can be used to randomly adjust bezier_radius, bezier_radius_purity, and crest parameters to give the links a more disorganized, organic feel. By perturbing each link you can also show additional texture in the data among links which would have ordinarily overlapped.
Each parameter's perturbation amount is defined as a pair of values - pmin,pmax. These are the minimum and maximum multipliers by which the value can be perturbed.
Given a perturbation (pmin,pmax), the modification is defined by
new_value = value * [ pmin + (pmax-pmin)*urd ]
where urd is a uniform random deviate in the range [0,1). Thus, the new value will be sampled uniformly from the range [value*pmin, value*pmax].
For example, if you define
perturb = yes perturb_crest = 0 perturb_bezier_radius = 0.5,1.2 perturb_bezier_radius_purity = 0.5,1
then crest will remain unperturbed, and bezier radius and radius purity will be randomly scaled between 50-120% and 50-100% of their original values, respectively.
By using pmin<0, you can force some values to become negative at times. For example, if crest = 0.5, then perturb_crest = -1,2 would perturb crest to lie in the range [-0.5,1).
Experiment with the values, starting small unless you want very organic images. The curves.repeated.txt data set bundled with this tutorial provides a data set with 7 identical sets of 24 links. By applying perturbation, each links from a set will be drawn differently, exposing the effect of parameter adjustment on the final curve.