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.
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) and Thessaloniki (2017).
Many thanks to Fredj Tekaia from the Pasteur Institute (Paris) for organizing these courses.
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.
Sessions 4–7 are applied and more challenging.
Session 5 is based on the example image that is included in the Circos distribution.
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.
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.
|Brewer palettes: Perceptually uniform colors for data displays|
|Making Data Visible: Limits of Human Visual Acuity and Consequences on Sequence Visualization|
Introduction to Circos and practical visualization principles
Links and rules
Yeast genome comparison
Drawing data on one genome
Drawing data on multiple genomes
|Configuration and data files||circos-course.tgz|
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 ~]$