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Circos at the EMBO NGS workshop in Tunis, Sept 15–25.

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.

Circos Courses

Course 1

This course grew out of a series of lectures and practical workshop sessions delivered at the Bioinformatics and Comparative Genome Analysis at the Pasteur Institute given in Paris (2010, 2011), Naples (2012) and Athens (2014).

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.

Learn Circos - Images created during the practical sessions of the Circos course. (950 x 339)
In the practical sessions, you will learn how to create these images.

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

Learn Circos - Images created during the practical sessions of the Circos course. (450 x 454)
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 sixth session uses data from previous lectures in the course (Yeast genome comparisons).

Learn Circos - Images created during the practical sessions of the Circos course. (900 x 227)
Images generated from 3-way Yeast genome comparisons performed in a previous day of the course.

Course 2

Another set of lectures and examples are available from High-throughput next generation sequencing applied to infectious diseases, a course in Tunis (September 15–25, 2014). These require circos-0.67-pre7, or later. The examples in this course are slightly more advanced than for Course 1 and use some new features in Circos.

The course is composed of a lecture, three practical sessions and a challenge session. The data used is Leishmania major and Leishmania mexicana gene expression from four samples.

Learn Circos - Images created during the practical sessions of the Circos course. (950 x 339)
Images from practical sessions for Course 2. (A) Gene expression on a single sample. (B) Gene expression for 4 samples. (C) Gene orthology between Leishmania major and mexicana.

The challenge session asks students to create the mosaic pattern found on the course poster.

Learn Circos - Images created during the practical sessions of the Circos course. (950 x 566)
Creating mosaic patterns with Circos.

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. (902 x 509)
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 Brewer Palettes
Making Data Visible: Limits of Human Visual Acuity and Consequences on Sequence Visualization Making Data Visible: Limits of Human Visual Acuity and Consequences on Sequence Visualization
Lectures—Course 1
Session 1
Practical Visualization Principles
Genome Visualization with Circos - Course, Lessons, Tutorials
Session 1
Introduction to Circos
Genome Visualization with Circos - Course, Lessons, Tutorials Genome Visualization with Circos - Course, Lessons, Tutorials
Session 2
Preamble to Practical Sessions
Genome Visualization with Circos - Course, Lessons, Tutorials Genome Visualization with Circos - Course, Lessons, Tutorials
Session 2
Ideogram Layout
Genome Visualization with Circos - Course, Lessons, Tutorials Genome Visualization with Circos - Course, Lessons, Tutorials
Session 3
Data Tracks
Genome Visualization with Circos - Course, Lessons, Tutorials Genome Visualization with Circos - Course, Lessons, Tutorials
Session 4
Links and Rules
Genome Visualization with Circos - Course, Lessons, Tutorials Genome Visualization with Circos - Course, Lessons, Tutorials
Session 5
Challenge
Genome Visualization with Circos - Course, Lessons, Tutorials Genome Visualization with Circos - Course, Lessons, Tutorials
Session 6
Yeast Genome Comparison
Genome Visualization with Circos - Course, Lessons, Tutorials Genome Visualization with Circos - Course, Lessons, Tutorials
Session Files
circos-course-1-x.xx.tgz Genome Visualization with Circos - Course, Lessons, Tutorials
Lectures—Course 2
Session 0
Introduction to Circos
Genome Visualization with Circos - Course, Lessons, Tutorials
Session 1
Preamble to Practical Sessions
Genome Visualization with Circos - Course, Lessons, Tutorials Genome Visualization with Circos - Course, Lessons, Tutorials
Session 1
Gene expression, one sample
Genome Visualization with Circos - Course, Lessons, Tutorials
Session 2
Gene expression, four samples
Genome Visualization with Circos - Course, Lessons, Tutorials Genome Visualization with Circos - Course, Lessons, Tutorials
Session 3
Gene orthology, 2 genomes
Genome Visualization with Circos - Course, Lessons, Tutorials Genome Visualization with Circos - Course, Lessons, Tutorials
Session 4
Challenge
Genome Visualization with Circos - Course, Lessons, Tutorials Genome Visualization with Circos - Course, Lessons, Tutorials
Session Files
circos-course-2-x.xx.tgz Genome Visualization with Circos - Course, Lessons, Tutorials

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-2-0.67.tgz
[username@host ~]$ tar xvfz circos-course-1-0.67.tgz
[username@host ~]$ cd circos-course-2-0.67
[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 ~]$