circos-session 1 Lesson 11 Ideogram，Color，Scale，Order and Orientation

data tracks

manipulate what ideogram are displayed, their order and orientation

Filtering Ideograms

with a "-" prefix, remove several ideograms from the display

e.g.

#./etc/ideogram.conf
chromosomes_display_default = yes
chromosomes = -hs1;-hs2;-mm1;-mm2 

 figure 33

using a regular expression , to remove (hsX, hsY, mmX,  mmY):

 

#./etc/ideogram.conf
chromospmes_display_default = yes
chromosomes = -hsX; -hsY; -mmX; -mmY

#./etc/ideogram.conf
chromosomes_display_default = yes
chromosomes = -/[XY]/

 

 

combine ideogram names with regular expressions to form a complex filter

removed are (hs1,mm1,hsY,mmY) and all chromosomes with two digits in their names  (hs10...hs22,mm10...mm19)

chromosome_display_default = yes
chromosomes = -hs1; -mm1; -/Y/;-/\d\d/

 

 define which ideogram to display by setting <chromosomes_display_default = no > and building the ideogram list using the <chromosomes> parameter. Both ideogram names and regular expressions are supported.

For example to display hs1..hs5,hs10,and mm10-mm15 and mmX,

use

chromosomes_display_default = no 
chromosomes = /hs[1-5]$/ ;hs10; /mm1[0-5]/;mmX

Figure34

Ideogram color

human chromosomes are red, mouse chromosomes are blue, mouse chromosomes are reversed

# all ideograms displayed, except those matching regular expression [xy]
#chromosomes_display_default = yes
#chromosomes         = -/[XY]/

# all ideograms displayed, except those matching regular expression [xy]
#chromosomes_display_default = yes
#chromosomes         = -hs1;-hs2;-/Y/;-/\d\d/;

# only the specified ideograms displayed: hs1-hs5, hs10, mm10-mm15, mmx
#chromosomes_display_default = no
#chromosomes         = /hs[1-5]$/;hs10;/mm1[0-5]/;mmX

# human chromosomes are red, mouse ones are blue
# mouse chromosomes are reversed
chromosomes_display_default = yes
chromosomes_color   = /hs/=reds-5-seq-5,/mm/=blues-5-seq-5
chromosomes_reverse = /mm/

# only human chromosomes are shown, each occupying 1/24th of the image
#chromosomes_display_default = no
#chromosomes = /hs/
#chromosomes_scale = /hs/=1rn

# 5 human (hs1...hs5) and 3 mouse (mm17...mm19) chromosomes are shown
# human chromosomes occupy 50% of the image (each occupies 10%)
# mouse chromosomes occupy 50% of the image (each occupies 16.7%)
#chromosomes_display_default = no
#chromosomes = /hs[1-5]$/;/mm1[7-9]/
#chromosomes_scale = /hs/=0.5rn,/mm/=0.5rn

#chromosomes_display_default = no
#chromosomes         = hs1;hs2;mm1;mm2
#chromosomes_order   = hs1,hs2,mm2,mm1
#chromosomes_reverse = /mm/
#chromosomes_scale   = /./=1rn
#chromosomes_color   = hs1=rdylbu-11-div-2,hs2=rdylbu-11-div-3,mm1=rdylbu-11-div-10,mm2=rdylbu-11-div-9

<<include ideogram.conf>>

<<include ticks.conf>>

<<include ../../etc/image.conf>>
                                                                                                                                            21,0-1        81%

 

 

Ideogram Progression

the orientation of ideograms can be reversed using chromosomes_reverse, which accepts both ideograms names and regular expressions, just like   chromosomes_color. Thus, to reverse all mouse chromosomes

chromosomes_reverse = /mm/

Figure 35

relative ideogram scaling

when the scale was relative , the ideogram was made to occupy a fraction of the image (e.g. chr1=0.5r)

to show only human chromosomes and make each to have the same length in the image

 

chromosomes_display_default = no
chromosomes = /hs/
chromosomes_scale = /hs/=1rn

 assign a different scale to groups of ideograms

50% occupied by 5 human chromosomes and 50% by 3 mouse chromosomes.

chromosomes_display_default = no
chromosomes                 = /hs[1-5]$/;/mm1[7-9]/
chromosomes_scale           = /hs/:0.5rn,/mm/:0.5rn

Figure 37

 

 Symmetric Ideogram Layout

creat symmetric layout , in which 2 human and 2 mouse chromosomes are shown ,each occupying 25% of the image

chromosomes_display_default = no 
Chromosomes                 = hs1;hs2;mm1;mm2
chromosomes_order           = hs1,hs2,mm2,mm1
chromosomes_color           = hs1:rdylbu-11-div-2,hs2:rdylbu-11-div-3,
                              mm1:rdylbu-11-div-10,mm2:rdylbu-11-div-9
Chromosomes_reverse         = /m/
chromosomes_scale           =  /./:1rn

Figure 38