circos- Session 1 Lesson 2 relative ideogram spacing

relative ideogram spacing

u  ,  absolute value ,  relative to the value of chromosomes_units

r   ,  relative to the total size(size/number of chromosomes) of all displayed ideograms. can keep the same visual spacing layout  in the figure.

<ideogram>

<spacing>

#default = 2u

# When spacing unit is "r", the fraction is calculated
# relative to the total size of all ideograms.
# e.g. if all ideograms total 185 Mb, 0.1r spacing is 18.5Mb

default = 0.1r

#<pairwise chr1 chr2>
#spacing = 0u # no space
#</pairwise>

#<pairwise chr2 chr3>
#spacing = 2u # 2Mb space
#</pairwise>

#When pairwise spacing is relative, the space is calculated
# relative to the default spacing. Here chr3-chr4 spacing will
# be 2x normal spacing, defined as 0.1r above (10% of circle).

#<pairwise chr3 chr4>
#spacing = 2r # 2x the default space
#</pairwise>

</spacing>

<<include ../../etc/ideogram.conf>>

</ideogram>

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"ideogram.conf" 35L, 665C                                                                                                                   12,1          All

default 2u to 0.1r , pairwise commented

figure  6

<ideogram>

<spacing>

#default = 2u

# When spacing unit is "r", the fraction is calculated
# relative to the total size of all ideograms.
# e.g. if all ideograms total 185 Mb, 0.1r spacing is 18.5Mb

default = 0.1r

<pairwise chr1 chr2>
spacing = 0u # no space
</pairwise>

<pairwise chr2 chr3>
spacing = 2u # 2Mb space
</pairwise>

#When pairwise spacing is relative, the space is calculated
# relative to the default spacing. Here chr3-chr4 spacing will
# be 2x normal spacing, defined as 0.1r above (10% of circle).

<pairwise chr3 chr4>
spacing = 2r # 2x the default space
</pairwise>

</spacing>

<<include ../../etc/ideogram.conf>>

</ideogram>

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"ideogram.conf" 35L, 656C                                                                                                                   35,0-1        All

default = 0.1r ,  pairwise uncomment  , 

when spacing is defined relatively , it is relative to the default spacing.

<pairwise ch2 ch3>

spacing = 2u  # 1u=1M so 2u = 2M ,  default = 2u has been commented , which has no effect here ?

</pairwise>

<pairwise ch3 ch4>

spacing = 2r  # total size 185M ,  default = 0.1 r ,  so 2r = 0.2r = 37M

</pairwise>

figure 7

 

Benefits of relative spacing

 Relative spacing is usefu when you don't know the size of ideograms., or are changing their scale . Absolute spacing , on the other hand,  is useful when the size of ideogram is known . you can mix and match these spacing types freely.

suggestions :  display human whole genome: 

      (1)  approximately 25%  of the ideogram circle's circumference  to spacing  . default = 0.01r  , set spacing between each ideogram to 1% 

      (2)  put the equivalent of 20Mb of space between each ideogram. default = 20 u , assuming chromosomes_units = 1000000