Circos Course

This course grew out of a series of lectures and practical workshop sessions delivered at the Bioinformatics and Comparative Genome Analysis Course given in Paris (2010, 2011), Naples (2012), Athens (2014), Tunis (2014), Izmir (2016), Thessaloniki (2017), Tunis (2018) and San Michele all'Adige (2019).

Many thanks to Fredj Tekaia from the Pasteur Institute (Paris) for organizing these courses.

Practical Sessions

The first three practical sessions focus on the core set of Circos' features. In Session 1 (Ideogram Layout), students learn how to define karyotypes, and how to draw, arrange, crop, order and scale ideograms. Session 2 uses the image created in Session 1 to show how to layer 2D tracks and introduces links and rules. The focus of Session 3 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. (1) Drawing ideograms (2) Drawing data (3) Using dynamic rules (4) Comparative analysis of three Yeast genomes (5) Challenge (6) Gene expression data on one Leishmania genomes (7) Orthologues between two Leishmania genomes.

Sessions 4–7 are applied and more challenging.

Session 5 is based on the example image that is included in the Circos distribution.

▲ 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.

The course is designed to be self-directed. For each session, there is a detailed handout in the handouts/ directory that walks you through the material.

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 Resources
Brewer palettes: Perceptually uniform colors for data displays
Making Data Visible: Limits of Human Visual Acuity and Consequences on Sequence Visualization

Lectures
Session 0 Introduction to Circos and practical visualization principles
Session 1 Ideogram layout
Session 2 Data tracks
Session 3 Links and rules
Session 4 Yeast genome comparison
Session 5 Challenge
Session 6 Drawing data on one genome
Session 7 Drawing data on multiple genomes
Configuration and data files
circos-course.tgz

Installing Session Files

Refer to the handout/*preamble* document for each course for details about file setup.

To install, unpack the tarball somewhere convenient and create images in session/. In the example below, I assume you want to unpack the files in your home directory.

# Make sure you are in the home directory (if not, cd ~)
[username@host ~]$ pwd
/home/username

# Got the file?
[username@host ~]$ ls -l
...
-rw-r--r--  1 martink users 246710242 Sep 26 14:16 circos-course.tgz
[username@host ~]$ tar xvfz circos-course.tgz
[username@host ~]$ cd circos-course
[username@host ~]$ cat README
[username@host ~]$ cd session

# Now you're ready to do a lesson - switch to Session 1 Lesson 1
[username@host ~]$ cd 1/1

# Run circos using either "circos -conf etc/circos.conf"
# or just "circos". The file must be in your PATH
[username@host ~]$ circos
debuggroup summary 0.19s welcome to circos v0.67-pre8 24 Sep 2014
debuggroup summary 0.19s guessing configuration file
debuggroup summary 0.19s found conf file /home/martink/work/conference/tunis/session/1/1/etc/circos.conf
debuggroup summary 0.41s debug will appear for these features: summary
debuggroup summary 0.41s bitmap output image ./circos.png
debuggroup summary 0.41s parsing karyotype and organizing ideograms
debuggroup summary 0.44s applying global and local scaling
debuggroup summary 0.46s allocating image, colors and brushes
debuggroup summary 1.29s drawing highlights and ideograms
debuggroup summary,output 2.22s generating output
debuggroup summary,output 2.57s created PNG image ./circos.png (331 kb)
# image is ready!

# follow the slides for this session to proceed through remaining lessons
[username@host ~]$