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.
7 — 2D Data Tracks
4. Tiles
Tile tracks are used to show spans such as genomic regions (genes, exons, duplications) or coverage elements (clones, sequence reads). Tiles will stack within their track to avoid overlap. The stacking process is controlled by several parameters, which are the topic of this example.
The image for this example has 5 different tile tracks. From outside in, these are: assembly clones (black/red), gene regions (green), copy-number polymorphism regions (blue), segmental duplications (orange) and conservation regions (purple). Each track is formatted slightly differently to illustrate various formatting options.
how tiles stack
Tiles are stacked in layers, which are annuli within the tile track. The parameters that define the tile track position, layers and direction of stacking are (in the case of the assembly track for this example)
r1 = 0.98r r0 = 0.86r layers = 15 margin = 0.02u orientation = out thickness = 15 padding = 8
This track is placed within the radial extent defined by
[0.86r,0.98r] (these are radial values relative to the inner ideogram
radius). The r0/r1 values define the baseline from which the tiles are
stacked.
When orientation=out, tiles stack from r0 out towards r1. When
orientation=in, tiles stack from r1 in towards r0. When
orientation=center, tiles stack from the midpoint between r0/r1 in an
alternating fashion towards r0 and r1.
Each tile element has a radial width of 15 pixels with 8 pixels of padding between elements.
Tiles will stack in layers to avoid overlap and each tile is given a margin to control the distance of neighbouring tiles within the same layer.
The full extent of tile elements is defined by the layers
parameter. In this case, there are 15 layers that are allowed. The
value of layers_overflow controls what happens when additional layers
are needed to accomodate tiles. It's important to realize that it is
the layers parameter that controls the radial extent of the track, and
not the r0/r1 values. The radius r0/r1 values are used to define the baselines of
the track whereas the combination of layers/thickness/padding controls
how far in the image the tiles stack.
The illustrations associated with this example explain the tile stacking process.
handling overflow
When tiles cannot fit into the number of layers you have specified
using layers, Circos looks to layers_overflow to determine how to
handle the overflow tiles.
When layers_overflow=hide, overflow tiles are not drawn. Use this
setting for the overflow option with caution, since Circos will not
alert you to the fact that not all of your tiles are drawn.
When layers_overflow=collapse, overflow tiles are drawn on the first
layer. The position of the first layer depends on the track
orientation.
When layers_overflow=grow, new layers are added as required. There
is no limit to how many layers may be added.
To help inform you that overflow actions have been taken, you may
set the fill color of overflow tiles to a specific color using
layers_overflow_color. If you set this value to be different than the
tiles' default color, overflow tiles will be obvious.
Several images in this example show how overflow can be handled.
applying rules
Rules apply to tiles just like for other data points. For example, you may format tile color by its size.
<rules> <rule> condition = var(size) > 100kb color = red </rule> <rule> condition = var(size) > 50kb color = orange </rule> <rule> condition = var(size) > 20kb color = yellow </rule>