Tutorial for Genomics Data scientists, students at a beginner level who wish to represent their human genomics analysis results in a circular way CIRCOS. These plots can be used for publication purpose too.

1. Genome Visualization: Circos Plots
Samarth Kulshrestha
Data Analyst
sk3@nibmg.ac.in

2. ● Circos Plots: Examples
● Technical Requirements
● Chromosomes & Ideogram
● Points to remember
● Circos Configuration file format
● Circos Distribution.
– Folder Distribution
● Data format
Overview

3. ● Circos is a softare package for visualizing data
and information. It visualize data in circular
layout.
● Circos is ideal for creating publication-quality
infographics, richly layered data and pleasant
symmetries.
● If you are a researcher, analyst,data geek or
visual artist who is seeking to communicate a
dataset, circos is for you.
Circos plots

4. ● The biological scientific community has
adopted circos worldwide. Circos has
appeared in many top scientific journals.

5. Availability @
www.circos.ca
5

6. D
C
B
A
Available Data
Tracks/Display:
D) Stacked Histogram
C) Ideogram
B) Highlights
A) Links
Circos-plot example
6

7. Circos-plot example
Available Data Tracks/Display:
F) Ticks
E) Text
E
F
7

8. 8
Nature Communications 6, Article number: 5973 doi:10.1038/ncomms6973
Circos Plot showing the
count of SNV variants
and copy number
changes.

9. 9
1) A machine with installed perl and additional
perl modules.
2) Karyotype file
3) Configuration file
4) Genomic data files.
To generate Circos, We NEED

10. 9
Technical Requirements

11. Technical Requirements
● Platform: Windows/Linux/Mac OS
● Perl 5.8 or newer version and additional
perl modules
11
..continue

12. 12
..continue
●
Config::General
Font::TTF
GD
List::MoreUtils
Math::Bezier
Math::Vecstat
Param::Validat
e Readonly
.............. And many
more
●
●
●
●
●
●
●
For more information regarding perl
modules installation, please follow the link
http://circos.ca/tutorials/lessons/configurat
ion/perl_and_modules/
Additional Perl Modules

13. ●
To list all the required
modules and check whether
they are installed, use
-modules.
First open a new terminal &
change directory to Circos
folder
●
Now check installed
modules using:
13
perl circos -modules

14. Chromosomes & Ideogram
14

15. vs
Traditional Way vs Circular way

16. The chromosome is the entire sequence structure
as defined in Karyotype file.
Ideogram is the depiction of the chromosome, or
region. Ideogram of hg 19 has been shown in the
image. (22+X,Y chr)
Format of hg19 Karyotype File: (available with
circos package in Workshop/circos/data/karyotype)
16
chr - hs1 1 0 249250621 chr1
chr - hs2 2 0 243199373 chr2
chr - hs3 3 0 198022430 chr3
chr - hs4 4 0 191154276 chr4
chr - hs5 5 0 180915260 chr5
--------------------------------------
--------------------------------------
band hs1 p36.33 p36.33 0 2300000 gneg
band hs1 p36.32 p36.32 2300000 5400000 gpos25
--------------------------------------
Example of Ideogram
Chromosome & Ideogram

17. Points to remember
17

18. ● All input files are text.
● Output image formats are .png and .svg and are
static.
● It requires configuration file(s) to specify Circos
layout and data tracks.
● It does not do any analysis,only for visualization.
● Comment lines starts with a hash “#”
● Run on command-line.
Points To remember

19. Circos Configuration file format
19

20. 20
●
The image generation process is driven by
a central configuration file.
●
Circos configuration (.conf) file is text file with
some parameters that define the image,
including input files, image size, formatting
etc.
●
This file usually imports other
configuration files, such as global color
and font settings.
Circos configuration (.conf) file
format

21. 21
..continue
Configuration file syntax
➢
Blocks
<ideogram> #start of block
thickness = 30p
fill = yes
..........
</ideogram> #end of block
Nested Blocks
<plots>
<plot>
type=line
➢
file = data/file1.txt
.........
</plot>
<plot>
type=line
file = data/file2.txt
..........
</plot>
</plots>
An example of Nested Block
Under <plots> parameter there are 2
line plots, hence Nested plots. We
can add more than 2 plots in a
nested block.
An example of a simple block
This is an example of single
block for an ideogram.

22. Global vs Local parameters
<plots>
type
color
# start of plots block
= line
= grey
<plot> # start of first plot
file = data/file1.txt
..........
</plot>
<plot>
# end of first plot
# start of second plot
file = data/file2.txt
..........
</plot> # end of second plot
<plot>
type
color
file
</plot>
# start of third plot
= scatter
= blue
= data/file3.txt
# end of third plot
Global parameters type and
color. First two plots will be of
grey color line plots.
22</plots> # end of plots block
Local parameters type and
color are specific to third
plot only. So third plot will
be of blue scatterd.

23. Circos Distribution
23

24. Following directories comes with circos package.
bin/
data/
etc/
.........
Circos executable
Contains Karyotype files
Necessary configuration files
24
Circos Distribution

25. circos -conf <configFile>
Configuration file
Circos
Circos.png
Data track files 25
Circos.svg
Command to run
circos:
Simple Circos Process

26. circos -conf <configFile>
Configuration file
Additional conf files
Circos
Circos.svg
Circos.png
Data track files 26
Command to run
circos:

27. 27
●
User Should always import these
additional conf files
# colors, fonts and fill patterns
<<include etc/colors_fonts_patterns.conf>>
# system and debug parameters
<<include etc/housekeeping.conf>>
# image parameters
<<include etc/image.conf>>

28. Data format for circos input
28NIBMG Winter School 2017

29. hs10 60001 134200
hs10 134201 234000
hs10 234001 317600
hs10 317601 445100
...................................
chr10 60001 134200
chr10 134201 234000
chr10 234001 317600
chr10 317601 445100
...................................
Chr Start Stop Values
Data format for different
tracks for Circos plot is 4
column data ie
Chr Start Stop Values
But before creating any
plot “chr” needs to be
change to “hs” and
header should be removed
as shown in the right hand
side image.
Data formats for Circos tracks
..continue

30. hs10
hs10
hs10
hs10
50632 50632 CALY
134201 234000 ------
219699 219699 UNC5B
317601 445100 ------
...................................
hs10
hs10
hs10
hs10
50632 50632
134201 234000
219699 219699
317601 445100
...................................
Chr Start Stop Values
Data format for different
tracks for Circos plot is 4
column data ie
Chr Start Stop Values
But before creating any
plot “chr” needs to be
change to “hs” and
header should be
removed as shown in the
right hand side image.
30

31. <ideogram>
<spacing>
default = 0.005r
</spacing>
radius = 0.90r
thickness = 30p
fill = yes
#Radius of ideogram
# thickness of ideogram
# Color in ideogram
show_label = yes
label_font = default
label_radius
label_size
label_parallel
label_case
label_center
</ideogram>
= dims(ideogram,radius)+50p
= 50
= yes
= upper
= yes
radius=0.90r
31
Parameter Explained for a simple
ideogram

32. Thank You