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.
9 — Recipes
21. Cell Cycle — Part 2
This tutorial will show you how to use Circos to create a diagram of a typical cell cycle (G1, S, G2, M) and annotate it with links and text.
This is the second part of the tutorial, continuing from Cell Cycle — Part 1.
This tutorial shows a more advanced way to define the phase axes. Depending on how you wish to define your coordinate system (e.g. relative to cycle, not phase), the approach taken by this tutorial may be more helpful.
In general, this tutorial should be of interest to anyone who wishes to use Circos for display of data that is not based on sequence coordinates.
cycle segment
There are four phases in the cell cycle: gap 1 (G1), synthesis (S), gap 2 (G2) and mitosis (M). There's also a senescence phase (gap 0, G0), into which the cell can pass to/from G1. I'll ignore G0 in this example.
Instead of defining one axis per phase, like in Cell Cycle — Part 1, I will create an axis segment for the whole cycle.
# cycle.txt
chr - cycle cycle 0 100 greys-6-seq-5
phases as cycle segment ideograms — using cropping
Each phase will be defined as a cropped region of the cycle axis.
karyotype = cycle.txt chromosomes = cycle[g1]:0-45;cycle[s]:45-80;cycle[g2]:80-95;cycle[m]:95-100
The spacing between the cropped regions is defined by the break parameter in <spacing> block
<ideogram> <spacing> default = 0.005r break = 1r </spacing> </ideogram>
segment colors
Colors are defined in the same way as Cell Cycle — Part 1, except now the arguments to chromosomes_color are the ideogram tags, not axis names.
palette = greys-6-seq <phases> g1 = 3 s = 4 g2 = 5 m = 6 </phases> # g1, s, g2, m are tags defined in 'chromosomes' above chromosomes_color = g1=conf(palette)-conf(phases,g1), s=conf(palette)-conf(phases,s), g2=conf(palette)-conf(phases,g2), m=conf(palette)-conf(phases,m)
tick marks
There are two options in this tutorial for tick marks.
The ticks.absolute.conf file defines them across the full cycle (e.g. first tick on G2 is 80%). Nothing special needs to be done in this case, because ticks are automatically generated relative to the original axis segment, and not to any cropped regions. The tick labels will run from the start of the segment (position 0 on cycle axis) to the end (position 100 on cycle axis).
The ticks.relative.conf defines them relative to each ideogram (e.g. first tick on G2 is 0%). The definition is almost identical to that of Cell Cycle — Part 1 except for the rdivisor = ideogram parameter, which tells Circos to label the ticks relative to their position on the cropped ideogram and not on the underlying axis segment.