Circos + Chromatin Topology
An organism's B and T lymphocytes — cells that are part of the immune system — continually develop new receptors specific to new threats to the immune system.
These receptor loci are organized into distinct regions that contain multiple variable (V), diversity (D), and/or joining (J) and constant (C) coding elements that are scattered across large genomic regions.
Bossen et al. review the relationship between epigenetics and chromatin and its effect on the diversity of receptors.
2012 Chromatin topology and the regulation of antigen receptor assembly Annual review of immunology 30:337-356.
// circos-chromatin
Circos fruit salad
Circos demonstrates sequence synteny between genomes of peach, apple and strawberry.
Each peach chromosome showed major orthology mostly to one strawberry chromosome, but to more than two apple chromosomes, suggesting that the apple genome went through more chromosomal fissions in addition to the whole genome duplication after the divergence of the three genera.
2012 Whole genome comparisons of Fragaria, Prunus and Malus reveal different modes of evolution between Rosaceous subfamilies BMC Genomics 13:129.
// circos-rosaceae
Circos visualizes a 18.2 Gb metagenome
The genomes of all members in an ecosystem compose the system's metagenome.
In A metagenome of a full-scale microbial community carrying out enhanced biological phosphorus removal, Albertsen et al. use Circos to compare the genome of Accumulibacter, one of the members of the 18.2 Gb metagenome of the bacterial community attached to a EBPR plant, to its reference. The comparison reveals significant differences in gene content and metabolic potential.
2011 A metagenome of a full-scale microbial community carrying out enhanced biological phosphorus removal The ISME journal
// circos-metagenome
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.
2012 Circular representation of human cortical networks for subject and population-level connectomic visualization NeuroImage
2012 Patient-tailored connectomics visualization for the assessment of white matter atrophy in traumatic brain injury Frontiers in Neurology 3
// circos-cortical-network
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).
2011 Measuring Transitions into the Workforce as a Form of Accountability SSRN eLibrary ID 1831967
// workforce
Circle of Cancer
This Circos depiction of a tumor genome provides the cover of 30 November 2011 Science's Transitional Medicine issue in which Roychowdhury et al. describe personalized treatment for patients with colorectal and prostate cancer. By quickly sequencing normal and tumor DNA and RNA, suitable therapies can be tailored for the specific mutations identified.
1 2011 Personalized Oncology Through Integrative High-Throughput Sequencing: A Pilot Study Science Translational Medicine 3:111ra121.
// circleofcancer
Circos Helps Stomach Differences in Gut Bugs
Biggs et al. report on the evolution of Campylobacter jejuni ST-474, an important human enteric pathogen, through a comparison of two flaA SVR-14 isolates and other available C. jejuni isolates and genomes.
2011 Whole-Genome Comparison of Two Campylobacter jejuni Isolates of the Same Sequence Type Reveals Multiple Loci of Different Ancestral Lineage PLoS One 6:e27121.
// campylobacter
Interactive Visualization of Structural Variation
Park et al. use the Circos paradigm to explore predicted structural variation. "Seqeyes is a novel multi-scale visualization that can interactively navigate dozens of genomes down to individual sequencing reads within a web browser."
Park R, Gehlenborg N, Park P. 2011. Seqeyes: A multi-scale interactive visualization tool for structural variations. In 1st IEEE Symposium on Biological Data Visualization, Providence, RI.
// seqeyes
Towards a Human Pan-Genome
As reported in Wired, Li et al. use Circos to visualize the comparison of structural variation in two sequenced human genomes: Asian and Yoruban (African). It's been over 10 years since the first reference genome (comprising DNA from multiple individuals) was reported. Technological advancements have made it possible to now sequence 1000's of human genomes to identify genetic variations for tracing evolution, determining population patterns, and assessing disease susceptibility and other phenotypic traits.
2011 Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly Nature biotechnology 29:723-730.
2010 Building the sequence map of the human pan-genome Nature biotechnology 28:57-63.
// circos-denovovariation
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.
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:-.
// nejm-hemoliticuremic
Circos in Simon Fraser University's AQ magazine (Apr 2011)
A Circos image appears as part of a spread in SFU's biannual AQ Magazine. The composite accompanies my photos of our laboratory and computer equipment.
The image was adapted from Figure 1 of our paper "Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors".
2010 Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors Genome Biol 11:R82.
// circos-aq
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.
// linux-kernel-tux
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.
// circos-caceres
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.
// linnet
Circos Collaborates with Wired
When Wired needed an inforgraphic to illustrate the complex world of relationships on the TV Series Lost, it turned to Circos.
In collaboration with Christy Sheppard, Wired's Art Director, Martin Krzywinski created the illustration for the April 22 2010 issue.
// wired-01
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.
- Strawberry Perl Support (Windows)
- Installing GD with Strawberry Perl (Windows)
- Installing Perl Modules
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.