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>>
50,1 Bot
figure