circos-Session 1 Lesson 7- Chromosome Breaks

to crop the ideogram of a chromosome to a region, use axis breaks 

don't want to show part of a chromosome, use a chromosome break

A break is defined analogously to a crop, except that the parameter is chromosomes_breaks and the chromosome and region combination to remove is preceded by a “-“.

karyotype = ../data/karyotype.5chr.txt

chromosomes_units           = 1000000
chromosomes_display_default = yes

chromosomes_breaks = -chr5=11-19
#chromosomes_breaks = -chr3=13-17;-chr4=(-9;-chr4=41-);-chr5=11-19

<<include ideogram.conf>>

<<include ../etc/ticks.conf>>

<<include ../../etc/image.conf>>
<<include etc/colors_fonts_patterns.conf>>
<<include etc/housekeeping.conf>>
~                                                                                                                                                             
~                                             

 figure 21

 

The format of the axis break is controlled in the <ideogram><spacing> block. The break parameter defines the size of the break, which, like spacing, can be set to absolute or relative. When the break value is relative, it is relative to the spacing. For example, assuming that chromosomes_units = 1000000 and the total ideogram size is 100 Mb,

spacing                          Break

default = 1u     1 Mb       break = 1u     1 Mb
default = 0.1r   10 Mb     break = 1u     1 Mb
default = 1u     1 Mb         break = 0.5r    0.5 Mb (50% of the spacing)
default = 0.1r   10 Mb     break = 0.25r  2.5 Mb (25% of the spacing)

The appearance of the break is defined by the axis_break_style, which is set to a value for which a corresponding <break_style> block has been defined. For more details about formatting breaks, see the tutorial about spacing and breaks at
http://circos.ca/documentation/tutorials/ideograms/spacing_breaks/

 

 

you can use “(“ and “)” to represent the start (or end) of the chromosome. Thus 0-9 is the same as (-9. This notation is helpful because you do not need to remember the start (or end) value of the chromosome to define a break at its edge.

multiple breaks can be defined for a given chromosome. In this example, chromosome
4 has a break at its start (-9, which removes the first 9 Mb and at its end 41-), which removes
the last 9 Mb.

karyotype = ../data/karyotype.5chr.txt

chromosomes_units           = 1000000
chromosomes_display_default = yes

#chromosomes_breaks = -chr5=11-19
chromosomes_breaks = -chr3=13-17;-chr4=(-9;-chr4=41-);-chr5=11-19

<<include ideogram.conf>>

<<include ../etc/ticks.conf>>

<<include ../../etc/image.conf>>
<<include etc/colors_fonts_patterns.conf>>
<<include etc/housekeeping.conf>>
~                               

figure 22