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.
Don't know where to start? Start here!
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.
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.
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 etc/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 etc\circos.conf
You can always leave out the
-conf etc\circos because Circos will find it automatically.
> perl ..\bin\circos
If you get a "configuration file not found" error, then you are very likely not in the example directory. To check, use
cd which will report the current directory. It should be where you installed circos.
> cd C:\circos\example
Circos documentation is available as a series of online tutorials which describe all of the features in Circos in a logical progression.
If you are impatient and want the shortest route to creating an image, read the Quick Guide tutorials. This is a series of 8 tutorials that show you how to build up an image from scratch, using data displayed on the human genome chromosomes.
It's not always clear how to proceed when you're starting out. Refer to the Circos Best Practices guide for tips to make your configuration modular and streamlined.
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.
The data and configuration files for all online tutorials can be downloaded as a separate package. If one of the tutorials can act as a template for your image, use it as a starting point.
Direct your Circos questions (installation, configuration, best practices) to the Google Group.
If you are considering using Circos for a figure in a publication or magazine, look through published images for inspiration.
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.
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.