Circos Introduced in the New York Times
My first Circos infographic to be published in the New York Times introduces the idea of sequence similarity curves linking circularly composed ideograms.
Working with David Constantine, I illustrated the similarity between chromosome 1 of mouse, rhesus, chimp, and chicken to that of human.
One of the smaller panels in the infographic was subsequently used by the Alliance of Lupus Research in their Faces of Lupus II video.
Naming Names - Circos Engages in Political Mudslinging
Jonathan Corum of the New York Times prepared this infographic with Circos to show the extent and timing of the use of names of by presidential candidates in a series of debates. Each arrow represents one candidate refering to another, with the start of the arrow representing the time within the candidate's speech at which the reference was made.
The figure was part of a larger graphic that identified themes during the debate. Jonathan created an interactive version of this figure and discusses how he approached its design.
Getting Started
Don't know where to start? Start here!
Installation
First, download and install Circos. If you are a Windows user, please read the UNIX vs Windows tutorial, especially if you are not familiar with the command line.
Many users experience issues caused by using new versions of Circos with old configuration files. If you are getting started, always use the newest version of Circos and make sure that your configuration files follow current best practices. For examples of how configuration files should look like, see the Quick Guide tutorial. A longer configuration file example is available in the example/ directory in the Circos distribution.
If you run into problems, first make sure you have all necessary Perl modules. If you are certain that all modules are installed and functioning, use the Google Group to search for similar problems or post a question to the community.
Generate Example Image
To verify that Circos has been installed correctly, generate the example image. This is a complex image which will take about 1 minute to generate.
On UNIX (e.g. Linux), from the Circos installation directory
# UNIX > cd example > ./run # batch file runs 'circos -conf ./circos.conf' debuggroup summary 0.86s parsing karyotype and organizing ideograms debuggroup summary 1.08s applying global and local scaling debuggroup summary 1.15s allocating image, colors and brushes debuggroup summary 7.19s drawing highlights and ideograms debuggroup summary 8.94s processing links debuggroup summary 13.31s processing data tracks Processing text track - this might take a while debuggroup summary 68.75s generating output created image at ./circos.png created image at ./circos.svg # look at circos.png
On Windows, from the Circos installation directory
# Windows
> cd example
> perl ..\bin\circos -conf circos.conf
Tutorials and Documentation
Circos documentation is available as a series of online tutorials which describe all of the features in Circos in a logical progression.
To follow along, download the tutorials, which are available as a separate package.
For questions about configuration file syntax and best practices for drawing images, use the Google Group.
Using Circos in Publications
If you are considering using Circos for a figure in a publication or magazine, look through published images for inspiration.
Keep in mind that
- Circos can be used to visualize genomic data
- Circos can be used to visualize any other data, such as debates, bus schedules, relationships, social network, network traffic, and things we haven't though of
- Circos requires Perl to run
- Circos does not have a user interface — it is controlled through a plain-text configuration file
- Circos can be easily automated
- Circos can generate SVG files which you can post-process in Illustrator or Inkscape
If you are close to publication, I am happy to help you design and/or refine your image. I've done it many times before — drop me a line and we'll get started.
Using Circos as Art
If you like things round, and distrust things square, Circos can be a platform for visual expression.
It has been used artistically before, perhaps most prominently in the David Cronenberg Chromosomes exhibit, where I collaborated with Volumina to give the book and exhibit a scientific feel.