1. Introduction of Circos
Yunyun Zhou
03/11/2014

2. Introduction
PRETTY Circular visualization
POPULAR --- APPEARED IN A VARIETY OF PUBLICATIONS

3. Overview
CIRCOS Features
Methods
Applications
Questions
http://circos.ca/

4. Features
 CIRCOS is only a circular visualization tool, no analysis
 Creation of images is controlled through a plain-text
configuration file
Circos can be used to display any kind of information.
---initially, design specific to genomics
---currently, any relationship among data.
i.e. chemical reactivity, tracking transactions…
visualizing tables

5. Typical Circos Image
(A) histogram (B) ideograms (C) histogram (D) heatmap (E) links (F) highlights (G) grid (H) ticks

6. CIRCOS installation
1. System requirement: Unix/Linux/Mac
2. Download & Install circos software
3. Install Required Perl modules
4. Download Tutorial (Best practice examples)

7. Plain Text Input Files
> circos -conf etc/circos.conf

8. Configuration file (circos.conf)
<ticks>
<<include ../etc/ticks.conf>>
<ticks>
ticks.conf

9. Genome to Genome link

10. Clickable image
• Associate areas of the image with web links.
• Any element in the image (ideogram, tick, band, highlight, ribobn, etc) can
have an associated URL.
FEATURES:
 MAKING IDEOGRAMS CLICKABLE
<ideogram>
ideogram_url = http://www.google.com/search?q=[chr]
……
<ideogram>
chr - hs1 1 0 247249719 chr1 url=special_script?chr=[chr]
chr - hs2 2 0 242951149 chr2 url=another_special_script?chr=[chr]
chr - hs3 3 0 199501827 chr3
 DEFINING URLS SPECIFIC TO INDIVIDUAL IDEOGRAMS
METHODS:

11. Image map

12. 1. Microbial Genome
2. Link Geometry - Detailed Bezier Control
3. Labeling Karyotype Bands
4. Image Maps
5. Image Transparency and Background
6. Manipulating Histograms
7. Variable Radius Link Ends
8. Stacked Histograms
9. Transparent Links
10. ID Fields
11. Heat Map Links
12. Inverted Links
13. Copy Number Data
14. Directed Links
15. Pattern Fills
16. Automating Tracks
17. Automating Heatmaps
18. Circular Stacked Bar Plots
19. Cortical Maps — Connectograms
20. Cell Cycle — Part 1
21. Cell Cycle — Part 2
22. Nature Cover Encode Diagram
23. Naming Names
Recipes
• Configuration files
• Input data file
• Output images
Provided files:

13. Copy number variation scatter plot
chrom start end logFC
hs3 7683536 8465787 1.43
hs11 465784 756867 -0.65
gc.txt

14. track for [0,3]
CNV data range [-3,3]
Different background for the positive and negative CNV values
<plot>
type = scatter
file = data/8/13/data.cnv.txt
r0 = 0.6r
r1 = 0.75r
min = -3
max = 0
glyph = circle
glyph_size = 8
color = red
<axes>
<axis>
color = lred
thickness = 2
spacing = 0.1r
</axis>
</axes>
<backgrounds>
<background>
color = vlred_a5
</background>
</backgrounds>
…..
track for [-3,0]
<plot>
type = scatter
file = data/8/13/data.cnv.txt
r0 = 0.75r
r1 = 0.9r
min = 0
max = 3
glyph = circle
glyph_size = 8
color = green
<axes>
<axis>
color = lgreen
thickness = 2
spacing = 0.1r
</axis>
</axes>
<backgrounds>
<background>
color = vlred_a5
</background>
</backgrounds>
…..

15. Visualizing Biological Data
http://vizbi.org/
Genomic alignments
Phylogenies
macromolecular structures
system biology