circos- Session 1 Lesson 6 - Drawing Ideogram Regions

Axis Breaks

to draw 9-21Mb of chromosome 5 

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

chromosomes_units           = 1000000
chromosomes_display_default = yes

chromosomes  = chr5=9-21
#chromosomes = chr3=8-12;chr4=4-11;chr5=9-21

<<include ideogram.conf>>

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

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

figure 19 

notice that unlike in the previous lesson in which a subset of chromosomes was selected for display, in this case chromosomes_display_default=yes. The yes value of this parameter results in all chromosomes being drawn.

In this case, the chromosomes parameter is used to adjust the region of one or more chromosomes. Chromosomes 1-4 are drawn in their entirety (chromosomes_display_default=yes ensures that all chromosomes that are not explicitly removed from display are drawn) and chromosome 5 is cropped.

crop chromosomes3 .chr4 , chr 5

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

chromosomes_units           = 1000000
chromosomes_display_default = yes

#chromosomes  = chr5=9-21
chromosomes = chr3=8-12;chr4=4-11;chr5=9-21

<<include ideogram.conf>>

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

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

 

figure 20