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Circos at the EMBO NGS workshop in Tunis, Sept 15–25.

Circos Maps America’s Restless Interstate Migration Without a Map

Wired has a writeup about migration patterns within the US that shows the data using d3.js chord diagrams, modeled after how Circos shows tabular data.

Circos reaches 500 literature citations

In October 2013 Circos reached a milestone - 500 citations in peer-reviewed literature.

To celebrate, I've made a commemorative poster that features over 400 Circos images from the literature.

citation list | image gallery | press highlights

Circos for R

Zhang et al. implement Circos in R.

Same round shape you expect. And now, in everyone's favourite open source statistics and data analysis environment.

CRAN RCircos package

Zhang H, Meltzer P, Davis S 2013 RCircos: an R package for Circos 2D track plots BMC Bioinformatics 14:244.

Circos Interchange Diagrams — Networks and Flow

Zeng et al. introduce a new type of visualization based on Circos, the interchange diagram, in their paper Visualizing Interchange Patterns in Massive Movement Data.

The design is applied to displaying movement data, such as daily trips made by passengers in a city. By incorporating interactivity, this visualization method is helpful to understand interchange patterns at different spatial (between trains, between cities) and time scales (different times of day).

Circos has been used for urban planning before. The town of Caceres in Spain has used Circos to communicate their urban planning strategy.

project website

Zeng W, Fu C-W, Arisona SM et al. 2013 Visualizing Interchange Patterns in Massive Movement Data Computer Graphics Forum 32:271-280

Circos connects to the connectome

Methods to visualize the connectome are reviewed in Craddock et al — Circos is one of them.

Craddock RC, Jbabdi S, Yan C-G et al. 2013 Imaging human connectomes at the macroscale Nat Meth 10:524-539.

The use of Circos for showing the connectome was introduced by Irimia et al. in Circular representation of human cortical networks for subject and population-level connectomic visualization.

A good layman description of the work can be found at the neurosceptic blog.

Irimia A, Chambers MC, Torgerson CM et al. 2012 Circular representation of human cortical networks for subject and population-level connectomic visualization NeuroImage, Irimia A, Chambers MC, Torgerson CM et al. 2012 Patient-tailored connectomics visualization for the assessment of white matter atrophy in traumatic brain injury Frontiers in Neurology 3

Circos is the Method for Visualizing Translocations

Genomic rearrangements can cause disease and are implicated in many cancers. Being able to see the patterns in these changes across samples and patients is important.

In the review article End-joining, Translocations and Cancer, Bunting and Nussenzweig demonstrate how compositing the genome circularly adds value and clarity to the presentation.

Bunting SF, Nussenzweig A 2013 End-joining, translocations and cancer Nat Rev Cancer

From Degree to Job — Circos Visualizes Workforce Transitions

Finding the relationship between a student's major and career field is the topic of "Measuring Transitions Into The Workforce As A Form Of Accountability". The diagrams connect the flow of students from one of 17 fields of study (left) to job sectors (right).

Schenk TL, Jr. 2011 Measuring Transitions into the Workforce as a Form of Accountability SSRN eLibrary ID 1831967

Satyan L Devadoss from Williams College performed a similar analysis of Impact of Major on Career Path for 15600 Williams College Alums.

Circos tackles the connectome

Irimia et al. introduce circular representation of cortical networks in Circular representation of human cortical networks for subject and population-level connectomic visualization. The scalability of this circular visualization approach is demonstrated by lucid aggregate visualizations using cortical networks of 50 individuals.

The UCLA group also used the circular connectome visualization to assess differences in brain injury in patients Patient-tailored connectomics visualization for the assessment of white matter atrophy in traumatic brain injury in Frontiers in Neurotrauma.

A good layman description of the work can be found at the neurosceptic blog.

Irimia A, Chambers MC, Torgerson CM et al. 2012 Circular representation of human cortical networks for subject and population-level connectomic visualization NeuroImage, Irimia A, Chambers MC, Torgerson CM et al. 2012 Patient-tailored connectomics visualization for the assessment of white matter atrophy in traumatic brain injury Frontiers in Neurology 3

Hemolytic–Uremic Syndrome Outbreak

Rasko et al. use Circos to show how the E. coli strain implicated in the German outbreak of hemolytic-uremic syndrome varies from other strains in their New England Journal of Medicine paper, where they find that "the genome of the German outbreak strain can be distinguished from those of other O104:H4 strains because it contains a prophage encoding Shiga toxin 2 and a distinct set of additional virulence and antibiotic-resistance factors."

NEJM created an animation that explains the visualizations. The paper was blogged by Pacific Biosciences.

Rasko DA, Webster DR, Sahl JW et al. 2011 Origins of the E. coli Strain Causing an Outbreak of Hemolytic-Uremic Syndrome in Germany The New England journal of medicine published ahead of print:-.

Circos Maps Cancer Landscapes

Nature features an article by Heidi Ledford, The Cancer Genome Challenge, which discusses the progress and challenges of identifying structural variation signatures in cancer genomes.

Circos images are used throughout the piece, taken from the COSMIC project (Catalogue of Somatic Mutations in Cancer).

Ledford H 2010 Big science: The cancer genome challenge Nature 464 (7291) 972-974.

Linux kernel exploration

Răzvan Musăloiu-E. explored the Linux file system and used Circos to relate the systems (disk-based, optical mediums, flash-based, network-based, cluster-based, memory-based, ancient) to kernel symbols.

Circular Worle

Jonathan Feinberg (IBM) created this perfectly circular wordle for me, using content from the Circos site.

As far as I know, this is the only circular wordle.

Circos Citation Themes

A wordle created from the words of the over 100 scientific articles that cite Circos.

All Your Genes Are Belong To Us

Remembering one of the most viral internet memes.

Circos is catching on, too.

Circos at VIZBI 2011

Circos was one of the community visualization tool tutorials at VIZBI 2011, at the Broad Institute in Boston.

Circos Helps with Urban Planning

The town of Caceres, Spain, a UNESCO World Heritage Site, used Circos to illustrate the relationships between businesses in their urban planning strategy.

Hive Plots - Linear Layout for Network Visualization

Visualizing large networks is hard. Nobody wants to see another hairball, but you want to show your data.

What do you do?

Try our new linear layout for network visualization, introducing the hive plot. This plot takes a fresh approach to drawing networks. It scales well, shows topology, and makes the network layout based on meaningful properties.

Power of Round

Circular data tracks naturally support display of information at various resolutions.

Compared to a track at a radius r, a pixel in a track at r/4 will span a region 4x larger. Tracks in the interior of the figure are therefore useful to display low-resolution or summary information.

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.

NYT Article - Mapping the Epigenome

In collaboration with Jonathan Corum from the NYT, Martin Krzywinski created an illustration of data showing methylation on chromosome 22 in a variety of tissues.

The illustration accompanies the article Now: The Rest of the Genome, by Carl Zimmer.

Installation

If you experience problems during installation, please refer to the following resources before contacting me. The answers are out there and you're likely to find them much faster than I can respond to your query.

And don't forget to open your googles!

UNIX vs Windows

If you are a Windows users, read how how Circos differes on UNIX and Windows.

Perl

For a more detailed set of instructions, see the Installation Tutorial

Linux, *NIX, Mac OS X

First, check if you have perl. You probably do. At the terminal,

> which perl
/usr/bin/perl

If you see this, you have perl. On the other hand, if 'which' does not return anything

> which perl
>

you don't have Perl, or the Perl binary is not in your path (which is not likely).

I won't go into the details of installing perl - there are too many ways to do it. Chances are a package (bundle, or whatever your operating system calls precompiled distributions) is available. Check at www.perl.org.

Unless you have an excellent reason, you don't want to compile your own Perl from the source code. There is nothing to be gained.

Windows

I suggest Strawberry Perl. If it's good enough for Larry, it's good enough for you.

Installing on Windows should be relatively painless.

Perl Modules

Perl comes with a large number of workhorse modules. In addition, a few other modules are required to run Circos (see requirements). All these modules are available from CPAN, the Comprehensive Perl Archive Network.

If you attempt to run Circos without having a required module, you'll see an error like this

Can't locate Missing/Module.pm in @INC (@INC contains:
/home/martink/perl/5.10.0/lib/5.10.0/x86_64-linux
/home/martink/perl/5.10.0/lib/5.10.0
/home/martink/perl/5.10.0/lib/site_perl/5.10.0/x86_64-linux
/home/martink/perl/5.10.0/lib/site_perl/5.10.0 .).
BEGIN failed--compilation aborted.

This error tells you Missing::Module is missing. Note that the module name uses :: to encode the directory of the module file. For example, if an error indicates that Set/IntSpan.pm is missing, the corresponding module name is Set::IntSpan.

Linux, *NIX, Mac OS X

To install the missing module, use the perl CPAN shell. At the terminal,

> perl -MCPAN -e shell
...
cpan[1]> install Missing::Module
...
... lengthy output here, should end with a message like
...
... /usr/bin/make install  -- OK
...
cpan[2]> exit
>

If you attempt to install a module you already have an up-to-date version for CPAN will duly inform you.

cpan[1]> install Already::Installed::Module
Already::Installed::Module is up to date (1.00)

Except for GD, installing the modules should cause you no problems.

On Mac OS X you will need to install the XCode tools (which, among others, provide 'make') in order to compile modules like GD. These tools are available on the Mac OS X distribution DVD as an extra installation package.

Windows

Your Perl distribution comes with a package manager. Use it to install modules.

GD

Installing GD can be tricky, since it depends on your system's C libgd library, among others. Getting all the dependency ducks in a row ranges across the full scale of pain, from "wow that was fast" to "omg omg we're all going to die".

Many problems can arise when compiling perl's GD module. Any problem you encounter has likely been solved by others, so here's where a good Google will help.

You should compile GD with TrueType font (TTF) support (requires freetype library) as well as PNG support. It's a good idea to also include JPEG, although this software does not use that output format.

If you are not seeing any text in your output images, but expect to, this is invariably due to lack of TTF support in your GD compilation. You'll need to reinstall the module, making sure that TTF support is activated.

Circos

Because Perl is interpreted, you don't need to compile anything. That should make you happy.

To install Circos, the only thing you need to do is unpack the archive, which you've downloaded.

Linux, *NIX, Mac OS X

> tar xvfz circos-0.55.tgz
...watch files unpack...
> cd circos-0.52

Windows

Use WinZip, WinRAR or whatever your favourite archive manager may be.