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Circos > Introduction


WHAT IS CIRCOS?


CIRCULAR VISUALIZATION

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.

▲ Images created with Circos, illustrating links, ribbons, tiles and a variety
of 2D data tracks. If it's round, Circos can probably do it (more images).

Circos is flexible. Although originally designed for visualizing genomic data,
it can create figures from data in any field—from genomics to visualizing
migration to mathematical art. 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).


POPULAR AND PRETTY

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!

▲ Experiments in movies are beautiful.

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 assumptions 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 more 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. publication-logos



My images created with Circos have appeared in a variety of publications. Wired,
New York Times, Conde Nast Portfolio, and American Scientist.

In genomics, scientific journals like Science, Nature, PLoS, Genome Research and
others have published papers that used Circos images (Circos citations).

▲ A sampling of published images from New York Times, Conde Nast Portfolio,
American Scientist, Nature and various books (see more).


SCRIPTABLE AND AUTOMATABLE - GET YOUR *NIX GEEK ON

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.


DYNAMIC FORMATTING WITH RUN-TIME RULES

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.

▲ By using run-time rules, defined in the configuration files, you can control
how elements of the figure are drawn based on data values.

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.




WHO SHOULD CARE?

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.


WHAT IS IT FOR?

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 has features that makes it ideal for drawing genomic information. Shown
here are ChIP-Seq, chr 22 methylation, whole-genome methylation, multi-species
comparison, human genome variation and self-similarity and MLL recombinome (see
more).

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.

▲ Circos has been cited by over 500 scientific articles. This wordle is created
from the words of their titles. The most common words are genome, analysis,
sequence, human, comparative and cancer.



ONLY FOR GENOMICS? NO!

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.

▲ Circos is suitable for showing any kind of relationships among data. Shown
here are car purchase trends, chemical reactivity, and dating trends, among
others (see more).

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.


HOW IS IT DIFFERENT?

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.

▲ Each panel shows the sequence similarity between one dog chromosome, placed at
the bottom half of the circle, with the entire human genome, placed at the top.
These data were combined into a single figure which appeared on the cover of the
American Scientist. The image accompanies the article Genetics and the Shape of
Dogs by Elaine Ostrander (see more).


USEFUL TO YOU?

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.

▲ A collection of images created by users of the online tableviewer utility,
which uses Circos to visualize tabular information. (zoom).

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.

To get your feet wet and hands dirty, download Circos and a read the tutorials,
or dive into a full course on Circos.




BRIEF HISTORY

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.


FUTURE OF CIRCOS

I work on Circos in a passive-aggressive manner - sometimes passive sometimes
aggressive. I welcome your comments.

Visit the Circos forum or contact Martin Krzywinski if you would like to report
a bug, request a feature or share the ways in which you are using, or hope to
use, Circos.


LICENSE AND USE

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.



If you are using Circos, please cite us: Krzywinski, M. et al. Circos: an
Information Aesthetic for Comparative Genomics. Genome Res (2009) 19:1639-1645 |
download citation

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Circos is for visualizing genomic data, creating circular data visualizations
and making things pretty (but not dumb) | who is citing Circos?

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a project by Martin Krzywinski | Canada's Michael Smith Genome Sciences Center

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This page is about: aesthetics / alignment / analysis / bioinformatics / cancer
/ circos / circular / comparative / conservation / data visualization / design /
evolution / evolutionary / gene / genetic / genome / genome sciences centre /
genomic / genomics / graph / graphics / human / human genome / infovis / martin
krzywinski / rearrangement / science / sequence / somatic / structural / synteny