Circos Course

This course grew out of a series of lectures delivered at the EMBO Bioinformatics and Comparative Genome Analysis at the Pasteur Institute in Paris. This year (2012) the course will take place in Naples.

2012 EMBO Practical course: Bioinformatics and Comparative Genome Analyses
Stazione Zoologica Anton Dohrn - Naples - Italy
May 7 - May 19, 2012 (Circos covered on May 9)

Lecture

The course is composed of a lecture (Introduction to Circos), in which Circos is introduced, along with its use in the field of genomics. The lecture is followed by three interactive practical sessions, in which students follow lessons to create a Circos image.

Practical Sessions

The practical sessions focus on the core set of Circos' features. In Session 2 (Ideogram Layout), students 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. The focus of Session 4 is the use of rules to dynamically format and layer link and scatter plot data.

▴ In the practical sessions, you will learn how to create these images.

There is a self-directed fifth session — Circos challenge — in which you create the image below on your own, using what you have learned in the previous sessions.

▴ This year, I have organized a challenge session. Here, you work on your own to create this image. You get data and configuration templates to start. (A) Scatter plot track with data values mapped onto glyph size. (B) Opposing histograms summarizing high-resolution scatter plot data, shown on top. (C) Automated heat maps with transparency mapped onto data values. (D) Heatmaps showing data at various resolutions. (E) Link bundles (F) Several layers of absolute and relative tick marks, each with grid. (G) Scatter plot corresponding to heatmap in (C) with data values mapped onto glyph size.

I've added a brief sixth session that shows how to depict sequence comparisons between multiple genomes, based on data analyzed by the students from the previous day (May 8) of the 2012 course.

Visualization Seminar

If you are interested in data visualization, you will find my seminar on data visualization in genomics useful.

Using examples of figures from literature, I provide reworked versions to illustrate common problems such as lack of consistency, redundancy, excess ink, poor color choice and cart junk.

The seminar is independent of the Circos lessons. Some of the examples from the seminar are also found in the handout for Session 1.

▴ Learn Genome Visualization - Practical and effective techniques for visualizing complex data, with examples from the literature.

Course Files

Visualization Seminar
Visualization of Genomic Data: Creating information-rich, informative and appealing genome data graphics
Making Data Visible: Limits of Human Visual Acuity and Consequences on Sequence Visualization
Lectures
Session 1 Practical Visualization Principles
Session 1 Introduction to Circos
Session 2 Preamble to Practical Sessions
Session 2 Ideogram Layout
Session 3 Data Tracks
Session 4 Links and Rules
Session 5 Challenge
Session 6 Yeast Genome Comparison
Session Files
circos-course-x.xx.tgz

Installing Session Files

To install, copy the tarball to your home directory (e.g. ~username), then run

# Make sure you are in the home directory (if not, cd ~)
[username@host ~]$ pwd
/home/username
# Got the file?
[username@host ~]$ ls -l
total 83208
-rw-r--r-- 1 username users 266991988 Feb 6 17:44 circos-course-0.03.tgz
[username@host ~]$ tar xvfz circos-course-0.03.tgz
[username@host ~]$ cd circos-course-0.03
[username@host ~]$ cat README
[username@host ~]$ cd workstation
# Now you're ready to do a lesson - switch to Session 2 Lesson 1
[username@host ~]$ cd 2/1
# Run circos using either "circos -conf etc/circos.conf"
# or just "circos". The file must be in your PATH

[username@host ~]$ circos
debuggroup conf 0.11s welcome to circos v0.60 23 Apr 2012
debuggroup conf 0.11s guessing configuration file
debuggroup conf 0.12s looking for conf file /home/martink/work/circos/course/workstation/2/1/etc/circos.conf
debuggroup conf 0.12s found conf file /home/martink/work/circos/course/workstation/2/1/etc/circos.conf
debuggroup summary 0.37s debug will appear for these features: summary
debuggroup summary 0.37s parsing karyotype and organizing ideograms
debuggroup summary 0.44s applying global and local scaling
debuggroup summary 0.45s allocating image, colors and brushes
debuggroup summary 1.35s drawing highlights and ideograms
debuggroup summary,output 1.47s generating output
debuggroup summary,output 1.56s created PNG image ./circos.png (62 kb)
# image is ready!
# follow the slides for this session to proceed through remaining lessons
[username@host ~]$