circos-Session 1 Lesson8 Ordering Ideogram Regions

axis breaks helps split an ideogram into two or more pieces. To change the order of these pieces,  use  --tags--

Tags defined by [] and are defined in the chromosomes parameter.

chromosome 4 is associated with two ideogram.  The first ideogram ,named ' a ' ,  represents the region 0-11Mb . The second ideogram , named  ' b ', represents the region 19-31Mb

chromosome = chr3:0-11; chr4[4a]:0-11;chr4[4b]:19-31;chr5[5a]:9-21;chr5[5b]:29-41

Once ideograms of a chromosome are assigned tags, the tags can be used to reorder the ideograms using the savme method as we’ve seen previously (using the chromosomes_order parameter), except now instead of chromosome names, tags are used.

chromosomes_order = ^,chr1,4a,chr3,4b,-,5b,5a

the ^  character, represents the start of the ideogram circle.

Figure 23

 

 

 scale , using the tag name of the ideogram

chromosomes_scale = 5a =2 , 5b =2 

FIgure 24