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20 imperatives of information design — BioVis 2012

Circos at VIZBI 2011

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

Glyph Tracks

When a text track is rendered using a symbol font, curious results can arise.

Here, a glyph track is created by using the Wingding font to encode sequence using colored dots.

Get Your Learning Organized

The Circos course was presented at the 2010 Bioinformatics and Comparative Genome Analysis workshop at the Paris Pasteur Institute.

The course is composed of four sessions: a theory lecture and three practical sessions. The practical sessions focus on the core set of Circos' features. In Session 2, you learn how to define karyotypes, and how to draw, arrange, crop, order and scale ideograms. Session 3 uses the image created in Session 2 to show how to layer 2D tracks and introduces links and rules. Session 4 demonstrates the use of rules to dynamically format and layer link and scatter plot data.

Bubbles!

When a text track is rendered using a symbol font, curious results can arise.

Here, a bubble track is created by using the Wingding font and applying dynamic rules to scale the glyph size proportionally to local gene density.

Tutorials and Course

The tutorials serve as a walkthrough through Circos. The course is a more structured set of materials that takes you through creating an image from scratch.

The tutorials act as documentation — each lesson presents a specific feature of Circos.

Example Image

Once you download and install Circos,

# install circos
> tar xvfz circos-x.xx.tgz
> cd circos-x.xx

try creating the example image that ships with the Circos core distribution.

> cd example
# on UNIX systems (see README for Windows use)
> ./run

Creating a Tutorial Image

You will need to download the tutorials separately. Follow the installation instructions in the archive file.

> cd tutorials/2/2
# now try tutorial 2.2
> ../../../bin/circos -conf ./circos.conf

In each tutorial directory (e.g. tutorials/2/2), there will be several configuration files (*.conf). There will always be a circos.conf file — this is the central configuration file that you pass to the Circos binary with the -conf flag. There may be other variants of the central configuration file (e.g. circos-2.conf) — these illustrate other aspects of the features discussed in the tutorial.

Creating Your Own Image

The first thing you will need is the karyotype for your genome. The karyotype defines the chromosomes (name, size, color) and, optionally, the cytogenetic band pattern. You can obtain karyotypes for many genomes from the cytoBandIdeo table (UCSC genome browser).

You can download the karyotype from the table browser or directly for human hg19 (Feb 2009) hg18 (Mar 2006), mouse mm9 (Jul 2009) mm8 (Mar 2006), rat rn4 (Nov 2004) rn3 (Jun 2003), or other species.

Once you have decided which ideograms to draw (ideograms are the graphical representation of chromosomes), add highlights, 2D tracks and links.