Circos > Documentation > Tutorials > 2d Tracks > Tiles
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6 — 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.

condition  = var(size) > 100kb
color      = red

condition  = var(size) > 50kb
color      = orange

condition  = var(size) > 20kb
color      = yellow