Brain Volume in Epilepsy
Pardoe et al. find that "Sodium valproate use in epilepsy is associated with parietal lobe thinning, reduced total brain volume, and reduced white matter volume."
The cover image shows antiepileptic drug combinations in intractable focal epilepsy cases. Linked drugs were being taken concurrently by an individual. Valproate cases are highlighted in orange.
2013Sodium valproate use is associated with reduced parietal lobe thickness and brain volume Neurology 80(20):1895-1900.
Dr. Tim Ley and Circos
The NYT article Cancers Share Gene Patterns, Studies Affirm, reports on the "most telling evidence yet that cancer will increasingly be seen as a disease defined primarily by its genetic fingerprint rather than just by the organ where it originated."
The photo (by Peter Newcomb for The New York Times) shows Dr. Tim Ley of Washington University in St. Louis with a Circos image on the desktop. "It certainly sets the stage for the next era of therapy."
The two studies referenced in the article are
2013 Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia New England Journal of Medicine.
2013 Integrated genomic characterization of endometrial carcinoma Nature 497:67-73.
Round is peachy
The International Peach Genome Initative has ensured that peach, a diploid Prunus species, is one of the best genetically characterized deciduous trees.
"Rosaceae is the most important fruit-producing clade, and its key commercially relevant genera (Fragaria, Rosa, Rubus and Prunus) show broadly diverse growth habits, fruit types and compact diploid genomes."
No mention of fuzz is made.
Circos in Wired's Best Scientific Figures of 2012
Wired's Best Scientific Figures of 2012 includes an image created with Circos.
"Though it's long been assumed that each cell in a body contains the same basic genomic blueprint, research now suggests that genomes actually vary between cells in the same body. The figure comes from a study of copy number variation, in which stretches of DNA are repeated multiple times. In all 23 chromosomes (arrayed in radial form) researchers found copy number differences unique to each cell's physical origin (color coding). Brain cells, for example, had quite different genomes from lung cells."
2012 Extensive genetic variation in somatic human tissues Proc Natl Acad Sci U S A 109:18018-18023.
Circos swims with fish
Howe et al. report on the zebrafish reference genome.
"Zebrafish have become a popular organism for the study of vertebrate gene function. The virtually transparent embryos of this species, and the ability to accelerate genetic studies by gene knockdown or overexpression, have led to the widespread use of zebrafish in the detailed investigation of vertebrate gene function and increasingly, the study of human genetic disease."
Circos Reveals Buzz in Hive NYC
Students at the Indiana University Information Visualization MOOC course used Circos to visualize the connections within the Hive NYC Learning Network, composed of 40 informal learning organizations, including museums, libraries and community-based organizations across New York City and stewarded by Mozilla.
The goal was "to show in what projects the different organizations are involved, what kind of work they do, and how they collaborate in projects over time."
Gloria Jimenez, Carmen Ng, Chantal Melser, Kristina Simacek, Maria Maza and Elwin Koster. Visualizing HiveNYC Where’s the buzz?
Airbus uses Circos to show migration patterns
The image was originally generated by the UN Population division.
Region definition according to United Nations; Asia including Oceania, countries of the Middle East and countries of CIS, Europe including Russia. Source: United Nations Population division, International Migrant Stock
Circos represents cancer genome visualization for the 2013 EMBL Cancer Genomics conference
Circos has long been used by cancer genomic project like COSMIC and consortia like TCGA. The circle has become a visual motif for representing genomic alterations, recently appearing on the cover of the Nature Reviews Cancer 2013 Calendar.
Recently, Circos appeared on the conference poster of EMBL Cancer Genomics conference, held at the Advanced Training Center in Heidelberg, Germany.
Circos used in Visual Motif for 2013 International Symposium: Systems Biology & the Brain
Not just for genomics, Circos is used to show the connectome in publications associated with the 2013 International Symposium: Systems Biology & the Brain, held in Seattle.
Circos has been previously used to visualize the connectome 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 on Cover of Biotechnology Focus
Circos appears on the cover of the Dec 2012 / Jan 2013 issue of Biotechnology Focus, a magazine about the Life Sciences sector in Canada.
The image is part of an article about epigenomics, which includes other graphics work I've done for the Genome Sciences Center.
"One of the biggest breakthroughs so far in the war on cancer was the realization that it is essentially a genetic disease. However, as we learn more about cancer, it becomes clearer that what’s written in our DNA is only part of the story; there are other factors at work that go beyond genetics."
Circos on Cover of Nature Reviews Cancer Calendar 2013
Circos appears on the cover of Nature Review's 2013 Cancer Calendar in the form of a figure taken from2012 The role of mutations in epigenetic regulators in myeloid malignancies Nat Rev Cancer 12:599-612.
Nature Reviews recognizes the importance of clear and informative figures:
"Indeed, given the adage that 'a picture paints a thousand words', good figures can encapsulate entire fields of cancer research without the need for extensive explanations."
Circos, Lung Cancer and Smoking
Imielinski et al. visualize mutations in the exome and genome sequences of 183 lung adenocarcinomas to reveal recurrent somatic mutations in the splicing factor gene U2AF1 and RBM10 and ARID1A, as well as EGFR and SIK2. Grouping the data revealed clusters that correlated with smoking history.
2012 Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing Cell 150:1107-1120.
Circos and Hive Plots describe regulatory networks
One of the first uses of Circos in the literature was to visualize the grapevine genome. Since then, Circos has gained popularity in the plant literature and has been used to look at poplar, rice and wheat, prairie cord grass, Arabidopsis as well as peach, apple and strawberry.
Here, Cockram et al. describe and visualize the control exerted by genes on the flowering time of members in the true grasses family (Poaceae).
2012 Genome Dynamics Explain the Evolution of Flowering Time CCT Domain Gene Families in the Poaceae PLoS One 7:e45307.
Circos visualizes transitions from fields of study to industry sectors
Schenk addresses the question "Are college graduates employed in sectors related to their major?"
An interactive poster uses Circos to explore the data.
2011 Measuring Transitions into the Workforce as a Form of Accountability SSRN eLibrary ID 1831967.
Circos and Hive Plots describe regulatory networks
Neph et al. use Circos and hive plots visualize how the core human regulatory network varies across 41 cell and tissue types. They find that, "in spite of their inherent diversity, all cell-type regulatory networks independently converge on a common architecture that closely resembles the topology of living neuronal networks."
2012 Circuitry and dynamics of human transcription factor regulatory networks Cell 150:1274-1286.
Microarray QC with Circos
Koch et al. use Circos to assess quality of microarray data in the publication Quality Visualization of Microarray Datasets Using Circos. The method is tuned for the Affymetrix Human Genome platform.
2012 Quality Visualization of Microarray Datasets Using Circos Microarrays 1:84-94.
Bang. That's the genomes, exploding.
Scientific terminology. Longer, harder and more arcane. A Circos illustration accompanies the New York Times article ‘Ome,’ the Sound of the Scientific Universe Expanding.
The age of 'omes' is here. It began with the genome, continued with the proteome, branched out with the memome and reached full flowering with the notion of the omome.
This probably sounds like raw material for nonsense poetry, but it’s a real biological and linguistic trend that makes sense, once you get the idea of just what an 'ome' is.
Circos cancer genome display in NYT article
Photo shows Dr. John Carpten, left, and Dr. David Craig with a cancer genome display. New strategies attack cancer at the genetic level. (Joshua Lott for The New York Times).
"It looked as if two genes had fused to each other in Mrs. McDaniel’s cancer cells. The result was that the cell growth signals in the cancer cells were reversed, like crossed wires. The research team theorized that every time those cancer cells, T cells of her immune system, got a signal to stop growing, they reacted as though they had gotten a signal to grow. And every time they got a signal to grow, they responded by stopping their growth."
Source: A New Treatment’s Tantalizing Promise Brings Heartbreaking Ups and Downs, New York Times
Circos contributes to Max Planck Science Gallery in Berlin
The Max Planck Science Gallery is a walk-in digital installation of science, art and their intersection.
"The Max Planck Science Gallery explores the significance of the latest scientific and technological transformations – new and complex developments which are just emerging. It not only concerns science, technology and society’s requirements, but also the multifaceted links and interactions between them."
Interactive, multi-touch displays, present all aspects of science and its relationship to society and culture. Circos was used as part of the exhibit on cancer biology.
Circos draws Phineas Gage's brain
In 1848 a railroad worker named Phineas Gage had a meter-long iron rod go through his head. He survived the accident, underwent a dramatic personality change, and became one of the most famous case studies in neuroscience.
The Van Horn group at UCLA used high-resolution CT scans of Gage's skull to reconstruct the extent of damage Gage's brain suffered at the level of neuron connections.
Circos was used to contrast the connectivity in a healthy brain to Gage's brain. The circular 'connectome' diagrams depict the brain's major white matter tracts, showing the major brain regions - the frontal lobe, insula, limbic system, temporal lobe, parietal lobe, occipital lobe, brain stem and cerebellum - as colour-coded segments outside diagram, according to their position from the front.
Phineas Gage's Connectome, theguardian.co.uk.
2012 Mapping connectivity damage in the case of phineas gage PLoS One 7:e37454.
Circos is a software package for visualizing data and information. It visualizes data in a circular layout — this makes Circos ideal for exploring relationships between objects or positions. There are other reasons why a circular layout is advantageous, not the least being the fact that it is attractive.
Circos is ideal for creating publication-quality infographics and illustrations with a high data-to-ink ratio, richly layered data and pleasant symmetries. You have fine control each element in the figure to tailor its focus points and detail to your audience.
Circos is flexible. Although originally designed for visualizing genomic data, it can create figures from data in any field. If you have data that describes relationships or multi-layered annotations of one or more scales, Circos is for you.
Circos can be automated. It is controlled by plain-text configuration files, which makes it easily incorporated into data acquisition, analysis and reporting pipelines (a data pipeline is a multi-step process in which data is analyzed by multiple and typically independent tools, each passing their output as the input to the next step).
Have you noticed how beautifully everyday science and technology is rendered in movies? Information is delivered seamlessly from interfaces oozing with style and function. While others complain that the movie doesn't get the science facts right, I contrarily note that it doesn't get the science look right. No busy scientist is able to make such great design and type face choices!
Sadly, the reality of cutting-edge science reveals a grimmer picture, replete with incomprehensible figures, illegible color combination and awkward type faces. This is due in large part by the fact that the people in charge of the science are too busy with the science to worry about figures. It is therefore important for designers, artists and other visual creatives to continue providing working scientists with tools that are useful, effective and ... pretty. One example of this kind of knowledge transfer are Brewer palettes. The scientists will thank you, the press will thank you, as will the public and policy makers, who are ultimately asked to digest the results.
Circos attempts to bring a different aesthetic to science and strike a balance between flexibility and ease-of-use. Circos makes no assumpmtions about your data, uses extremely simple input data format, and makes image creation and customization easy. It's helping to make science look better, one figure at a time.
Circos has appeared in many publications, both scientific and general. It has changed the way the scientific community visualizes genomic alterations (changes in a genome over time, or differences between two or mor genomes). One timely application of this approach is creating effective figures showing how cancer genomes differ from healthy ones (e.g. COSMIC: Census of Somatic Mutations in Cancer).
The biological scientific community has adopted Circos wholeheartedly. By now, Circos has appeared on the the covers of both Nature and Science publications, which are the world's top scientific journals.
Creation of images is controlled through a plain-text configuration file — there is no interactive user interface. This approach to configuration should be very famililar to you if you have UNIX experience.
If you're used to pointing (and clicking), you're in for both a surprise and a treat and, initially, perhaps for a little bit of frustration. It's ok, don't worry. Although Circos' barrier to entry is higher than most applications you may have used, once you become comfortable with Circos and gain experience in its use, you will see benefits from Circos' approach and will be able to convert the time you invested into learning Circos into great-looking figures.
Image creation can be completely automated — you can write scripts to generate both data and configuration file and make a call to Circos to generate the image — making Circos suitable for incorporation into data analysis pipelines and applications. In this way, Circos is similar to gnuplot.
Most aspects of the output image can be adjusted using dynamic rules, which format elements of the figure based on data values. This feature allows a variety of images to be created without changing the input data or configuration file.
This feature is extremely powerful and uniquely suited for visual analytics. For example, for a given data track (e.g. histogram) you can ask that all bins with values >10 are colored blue, or more generally you can color the bins by value using your own color scheme. Rules can be chained. For example, later in the rule chain, you can ask that any blue bins that fall within a specific position range be hidden.
If you are a researcher, analyst, data geek, art director, illustrator or visual artist who is seeking to explore or communicate a data set, or to think outside the box (and inside a circle), Circos is worth looking into.
Circos can be used to display any kind of information. It's particularly suitable for layering different data sets to create highly informative infographics with texture and visual appeal. Circos can make low-resolution bitmaps, suitable for basic web-based reporting, as well as publication-quality images with a lot of bling (but I mean legible, clear and informative bling!).
Circos was initially designed for displaying genomic data (particularly cancer genomics and comparative genomics) and molecular biology. It has specific features that address typical challenges in drawing these kind of data, which tend to be very sparse and encompass a large number of length scales.
Data is data. Circos is flexible. There is nothing about Circos that is specific to genomics — it just happens that I work in genomics and therefore the tool has been applied to this field.
Circos can illustrate genomic rearrangements, where a relationship between two elements (genomic positions) represents a structural fusion. Circos can also visually represent the flow of refugees, where a relationship between two elements (countries) represents the extent of ingress and egress.
To name a few, Circos has been used to visualize customer flow in the auto industry, volume of courier shipments, database schemas, and presidential debates.
My purpose in creating Circos was not as much to create yet another way to draw data, but rather to create a tool which can help make data look beautiful. The compactness of the circular form is inherently more appealing than a linear layout. Although some figures are ideally suited for a square layout, most of the time a circular figure can match or exceed efficiency in delivering information, have a higher ink-to-data ratio and sit more tightly on the page.
It is easy to plot, format and layer your data with Circos. A large variety of plot and feature parameters are customizable, helping you make the image that best communicates your data. You supply your data to Circos as plain-text files, tell Circos what you want plotted using the configuration file, and then create the image.
How do you know whether Circos can be useful to you? First, look at published images and see what others are doing with Circos (for other images, see sample image archive). For examples of Circos' capabilities, see the tutorial images. These image sets will give you an idea of the types of data visualizations that Circos can create.
For quick exposure to Circos, try the online tableviewer, which is an instance of Circos designed to visualize tabular data. You can upload a table (e.g. exported from a spreadsheet) and have it drawn à la Circos. If you don't have any data (who these days doesn't?), you can choose to use pre-generated or random tabular data.
To learn how Circos can be used in specific applications, browse the walkthrough guides which spend some time telling you about features and applications, use in genomics and application to table visualization.
Circos was originally conceived for visualizing genomic data such as alignments and structural variation. Over time, support was added for 2D data tracks such as line, scatter, heatmap and histogram plots.
As Circos' popularity grew — sparked by a New York Times full-page infographic — it started to be used for visualizing other data, not just genomics.
I work on Circos in a passive-aggressive manner - sometimes passive sometimes aggressive. I welcome your comments.
Circos is free software, licensed under GPL.
Circos is written in Perl, can be deployed on any operating system for which Perl is available (e.g. Windows, Mac OS X, Linux and other UNIX flavours) and produces bitmap (PNG) and vector (SVG) images using plain text configuration and input files.