noteworthy new(ish) features
axis breaks
I've finally added the ability to exclude regions from an ideogram and add axis breaks. Creating breaks is as easy as adding a chromosomes_break parameter
chromosomes = hs1;hs2;hs3 chromosomes_breaks = -hs1:20-50;-hs2:100-120;-hs2:150-180
The images below show two style of breaks. The size of the break itself is customizable.
global scale adjustment
Individual ideograms can be resized to occupy less/more distance along the circle. Specific chromosomes can be, for example, enlarged to show fine details of feature layout.
local scale adjustment
One of the facts that complicates figures of genomic features is that the genome is (a) mostly uninteresting (i.e. to you, your application, or your audience) with (b) interspersed regions worthy of focus. Think of grains of sand scattered on a table, you can't draw an image that shows the entire table and the grains in detail - you either zoom in (and lose large parts of the table) or (b) zoom out and, while showing the entire table, lose detail in the grains. Keeping the table in the field of view helps put the features of interest (sand) in spatial context.
To address this challenge, Circos now supports both global and local variable length scale. This means that the genomic distance, ds, spanned by an angular element, da, is not necessarily constant for all angles. You can plot with Circos, 50 Mb of chr1 and 5 Mb of chr2, but in such a way that they both occupy the same angular distance. This would be useful if you wanted to relate the features in the 50 Mb range were related to features in the 5 Mb range, and maximize the part of the circumference of the plot that is used to show features.
In addition to local scale adjustment, this adjustment can be made smoothly. That is, scale can vary from the default scale of the ideogram (e.g. 1x) to a zoom factor (e.g. 10x) over some distance. In effect, the data domain acts as a rubber band which can be stretched and compressed to your liking creating a gradual zoom into your region of interest. The two figures below illustrate scale smoothing.
Global and local scale adjustments can be combined, as shown below. In this example chr2 is enlarged 15X and a region on the chromosome is further zoomed 30X.
text label track
Finally, text labels are implemented, as of v0.33. This is the first version of the text track. I've put some effort into optimizing label layout when drawing labels from neighbouring coordinates.
glyph track
By subverting the text track, you can create fancy tracks with glyphs (see tutorial 6.9).
variable ideogram radius
Radial position of ideograms (and region) can be adjusted. This is useful if you need to squeeze in a plot track without making the image bulge.
connector track relates two radial positions
A connector is a multi-line segment that relates one radial position to another. An example of a connector (black line segment) shown below.
Connectors are excellent at relating positions with annotations, or structures drawn at a different magnification.
transparency support
Is your data hiding? Bring it out with transparent colors.
