circos- Session 1 Lesson 5 Ideogram Order

 to draw a subset of chromosomes , need to change chromosomes_display_default to no .  all of the chromosomes that were defined in the karyotype were shown. this is the default behaviour.

to change  the ideogram order , use the parameter : chromosomes_order

default order defined in the karyotype is chr1、chr2  、chr3、 chr4 、 chr5

here we use parameter : chromosomes_order = chr1, chr2, chr5, chr4, chr3

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

chromosomes_units           = 1000000
chromosomes_display_default = yes

# explicitly define order
chromosomes_order = chr1,chr2,chr5,chr4,chr3

# relative order
#chromosomes_order = chr3,chr5

# relative order
#chromosomes_order = chr1,chr4,-,-,chr2

<<include ideogram.conf>>

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

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

 figure 16

 

 

 ajust the order of a few ideograms

the former is anchor ,  others following

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

chromosomes_units           = 1000000
chromosomes_display_default = yes

# explicitly define order
#chromosomes_order = chr1,chr2,chr5,chr4,chr3

# relative order
chromosomes_order = chr3,chr5

# relative order
#chromosomes_order = chr1,chr4,-,-,chr2

<<include ideogram.conf>>

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

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

 

figure 17

reorder several subsets of ideograms by separating the order of subsets by “-“, one for each unordered ideogram

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

chromosomes_units           = 1000000
chromosomes_display_default = yes

# explicitly define order
#chromosomes_order = chr1,chr2,chr5,chr4,chr3

# relative order
#chromosomes_order = chr3,chr5

# relative order
chromosomes_order = chr1,chr4,-,-,chr2

<<include ideogram.conf>>

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

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

 figure 18