circos- Session 1 Lesson 3 Changing ideogram scale

scale adjustment is defined in the circos.conf  using the chromosomes_scale parameter.  The syntax of the value for this parameter is :   chromosomes_scale = chr1 = 0,2 , chr2 =2 , chr3 = 10 .  which would display chr1 at 0.2x magnification (5x reduction), chr2 at 2x magnification and chr 3 at 10x magnification, respectively.   

the original circos.conf content:

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

chromosomes_units           = 1000000
chromosomes_display_default = yes

#chromosomes_scale = chr1=0.5

# ABSOLUTE SCALE
#
# Multiply the apparent size of an ideogram by a fixed factor.
#
##########################################################
#
# chr1 is magnified 0.5x
# chr2 is magnified   2x
# chr2 is magnified  10x
#chromosomes_scale = chr1=0.5,chr2=2,chr3=10

# RELATIVE SCALE
#
# Scale an ideogram to a fraction of the figure.
#
##########################################################
#
# chr1 occupies 50% of figure
#chromosomes_scale = chr1=0.5r

# chr5 occupies 25% of figure
# chr4 occupies 25% of figure
#chromosomes_scale = chr5=0.25r,chr4=0.25r

# NORMALIZED RELATIVE SCALE
#
Type  :quit<Enter>  to exit Vim                                                                                                    8,0-1         Top

figure output: 

 

uncomment chromosomes_scale = chr1 = 0.5

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

chromosomes_units           = 1000000
chromosomes_display_default = yes

chromosomes_scale = chr1=0.5

# ABSOLUTE SCALE
#
# Multiply the apparent size of an ideogram by a fixed factor.
#
##########################################################
#
# chr1 is magnified 0.5x
# chr2 is magnified   2x
# chr2 is magnified  10x
#chromosomes_scale = chr1=0.5,chr2=2,chr3=10

# RELATIVE SCALE
#
# Scale an ideogram to a fraction of the figure.
#
##########################################################
#
# chr1 occupies 50% of figure
#chromosomes_scale = chr1=0.5r

# chr5 occupies 25% of figure
# chr4 occupies 25% of figure
#chromosomes_scale = chr5=0.25r,chr4=0.25r

# NORMALIZED RELATIVE SCALE
#
"circos.conf" 62L, 1553C                                                                                                           7,1           Top

figure 8  output :

:

 

chr1 0.5x  ,   chr2 2x ,  chr3  10 x

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

chromosomes_units           = 1000000
chromosomes_display_default = yes

#chromosomes_scale = chr1=0.5

# ABSOLUTE SCALE
#
# Multiply the apparent size of an ideogram by a fixed factor.
#
##########################################################
#
# chr1 is magnified 0.5x
# chr2 is magnified   2x
# chr2 is magnified  10x
chromosomes_scale = chr1=0.5,chr2=2,chr3=10

# RELATIVE SCALE
#
# Scale an ideogram to a fraction of the figure.
#
##########################################################
#
# chr1 occupies 50% of figure
#chromosomes_scale = chr1=0.5r

# chr5 occupies 25% of figure
# chr4 occupies 25% of figure
#chromosomes_scale = chr5=0.25r,chr4=0.25r

# NORMALIZED RELATIVE SCALE
#
# Distributes the size of several ideograms equally
"etc/circos.conf" 62L, 1553C                                                                                                       35,1           3%

figure 9 output

 

chr1  occupies 50% of figure

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

chromosomes_units           = 1000000
chromosomes_display_default = yes

#chromosomes_scale = chr1=0.5

# ABSOLUTE SCALE
#
# Multiply the apparent size of an ideogram by a fixed factor.
#
##########################################################
#
# chr1 is magnified 0.5x
# chr2 is magnified   2x
# chr2 is magnified  10x
#chromosomes_scale = chr1=0.5,chr2=2,chr3=10

# RELATIVE SCALE
#
# Scale an ideogram to a fraction of the figure.
#
##########################################################
#
# chr1 occupies 50% of figure
chromosomes_scale = chr1=0.5r

# chr5 occupies 25% of figure
# chr4 occupies 25% of figure
#chromosomes_scale = chr5=0.25r,chr4=0.25r

# NORMALIZED RELATIVE SCALE
#
# Distributes the size of several ideograms equally
-- INSERT --                                                                                                                       27,1           3%

figure 10 

 

chr4=0,25r  ,   chr5 = 0.25r   

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

chromosomes_units           = 1000000
chromosomes_display_default = yes

#chromosomes_scale = chr1=0.5

# ABSOLUTE SCALE
#
# Multiply the apparent size of an ideogram by a fixed factor.
#
##########################################################
#
# chr1 is magnified 0.5x
# chr2 is magnified   2x
# chr2 is magnified  10x
#chromosomes_scale = chr1=0.5,chr2=2,chr3=10

# RELATIVE SCALE
#
# Scale an ideogram to a fraction of the figure.
#
##########################################################
#
# chr1 occupies 50% of figure
#chromosomes_scale = chr1=0.5r

# chr5 occupies 25% of figure
# chr4 occupies 25% of figure
chromosomes_scale = chr5=0.25r,chr4=0.25r

# NORMALIZED RELATIVE SCALE
#
-- INSERT --                                                                                                                       31,1          Top

figure 11

 normalized  relative scale :

# NORMALIZED RELATIVE SCALE
#
# Distributes the size of several ideograms equally
# within a fraction of the image. Use a regular expression
# to specify the ideograms. Ideograms matching RX will
# be divided into fraction X of the figure
#
# /RX/=Xrn
#
# e.g. if RX matches 5 ideograms and X is 0.5, then each
# ideogram will occupy 0.5/5 = 0.1 of the figure.
#
##########################################################
#
# chr1 chr2 chr3 together occupy 50% of figure, and within
# this region they are equally sized
#
# equivalent to chr1=0.0833r,chr2=0.0833r,chr3=0.0833r
chromosomes_scale = /chr[123]/=0.5rn

# all chromosomes equally sized
#chromosomes_scale = /./=1rn

<<include ideogram.conf>>

-- INSERT --                                                                                                                       51,1          82%

:figure 12

chromosomes_scale = /. / = 1rn  equals with chromosomes_scale = /. / = 0.2 r    for we have five chromosomes defined in the karyotype file.  

# NORMALIZED RELATIVE SCALE
#
# Distributes the size of several ideograms equally
# within a fraction of the image. Use a regular expression
# to specify the ideograms. Ideograms matching RX will
# be divided into fraction X of the figure
#
# /RX/=Xrn
#
# e.g. if RX matches 5 ideograms and X is 0.5, then each
# ideogram will occupy 0.5/5 = 0.1 of the figure.
#
##########################################################
#
# chr1 chr2 chr3 together occupy 50% of figure, and within
# this region they are equally sized
#
# equivalent to chr1=0.0833r,chr2=0.0833r,chr3=0.0833r
#chromosomes_scale = /chr[123]/=0.5rn

# all chromosomes equally sized
chromosomes_scale = /./=1rn

<<include ideogram.conf>>

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

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

figure 13

test :   chromosomes_scale = /./ = 0.2r  

# NORMALIZED RELATIVE SCALE
#
# Distributes the size of several ideograms equally
# within a fraction of the image. Use a regular expression
# to specify the ideograms. Ideograms matching RX will
# be divided into fraction X of the figure
#
# /RX/=Xrn
#
# e.g. if RX matches 5 ideograms and X is 0.5, then each
# ideogram will occupy 0.5/5 = 0.1 of the figure.
#
##########################################################
#
# chr1 chr2 chr3 together occupy 50% of figure, and within
# this region they are equally sized
#
# equivalent to chr1=0.0833r,chr2=0.0833r,chr3=0.0833r
#chromosomes_scale = /chr[123]/=0.5rn

# all chromosomes equally sized
#chromosomes_scale = /./=1rn
chromosomes_scale = /./ = 0.2r
<<include ideogram.conf>>

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

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