Circos > Documentation > Tutorials > Recipes > Link Geometry
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Circos at the EMBO NGS workshop in Tunis, Sept 15–25.

Use the latest version of Circos and read Circos best practices—these list recent important changes and identify sources of common problems.
If you are having trouble, post your issue to the Circos Google Group and include all files and detailed error logs. Please do not email me directly unless it is urgent—you are much more likely to receive a timely reply from the group.
Don't know what question to ask? Read Points of View: Visualizing Biological Data by Bang Wong, myself and invited authors from the Points of View series.

8 — Recipes

2. Link Geometry - Detailed Bezier Control

circos.conf


<colors>
<<include etc/colors.conf>>
</colors>

<fonts>
<<include etc/fonts.conf>>
</fonts>

<<include ideogram.conf>>
<<include ticks.conf>>

karyotype   = data/karyotype.human.txt

<image>
dir = /tmp
file  = circos-tutorial.png
# radius of inscribed circle in image
radius         = 1500p
background     = white
# by default angle=0 is at 3 o'clock position
angle_offset   = -90
</image>

chromosomes_units = 1000000
chromosomes       = hs1;hs2;hs3;hs4
chromosomes_display_default = no

<links>

radius = 0.98r

crest         = 2.5
bezier_radius = 0.5r

<link segdup>
show         = yes
color        = grey
thickness    = 2p
file         = data/5/segdup.txt

<rules>
<rule>
importance = 110
condition  = _CHR1_ eq _CHR2_ 
show       = no
</rule>
# the next two rules must contain flow=continue because it 
# always matches and you do not want it to terminate
# the rule chain (otherwise the color rule would
# never be checked)
<rule>
importance = 100
condition  = 1
thickness  = eval(max(1,min(6,exp(_SIZE1_/50000))))
flow       = continue
</rule>

<rule>
importance = 90
condition  = (_CHR1_ eq "hs2" && _CHR2_ eq "hs4" && abs(_START1_ - 90Mb) < 30Mb) || (_CHR2_ eq "hs2" && _CHR1_ eq "hs4" && abs(_START2_ - 100Mb) < 20Mb)
color      = red
thickness  = eval(_thickness_*2)
z          = 5

crest         = 2
bezier_radius = 0.5r

</rule>

<rule>
importance = 90
condition  = (_CHR1_ eq "hs1" && _CHR2_ eq "hs3" && abs(_START1_ - 160Mb) < 20Mb) || (_CHR2_ eq "hs1" && _CHR1_ eq "hs3" && abs(_START2_ - 160Mb) < 20Mb)
color      = blue
thickness  = eval(_thickness_*2)
z          = 10
crest         = 4
bezier_radius = 0.75r

</rule>

<rule>
importance = 90
condition  = (_CHR1_ eq "hs1" && _CHR2_ eq "hs2" && abs(_START1_ - 10Mb) < 20Mb) || (_CHR2_ eq "hs1" && _CHR1_ eq "hs2" && abs(_START2_ - 10Mb) < 20Mb)
color      = orange
thickness  = eval(_thickness_*2)
z          = 15
crest         = 5
bezier_radius = 0.8r

</rule>

</rules>

</link>

</links>

anglestep       = 0.5
minslicestep    = 10
beziersamples   = 40
debug           = no
warnings        = no
imagemap        = no

# don't touch!
units_ok        = bupr
units_nounit    = n

circos.image-01.conf


<colors>
<<include etc/colors.conf>>
</colors>

<fonts>
<<include etc/fonts.conf>>
</fonts>

<<include ideogram.conf>>
<<include ticks.conf>>

karyotype   = data/karyotype.human.txt

<image>
dir = /tmp
file  = circos-tutorial.png
# radius of inscribed circle in image
radius         = 1500p
background     = white
# by default angle=0 is at 3 o'clock position
angle_offset   = -90
</image>

chromosomes_units = 1000000
chromosomes       = hs1;hs2;hs3;hs4
chromosomes_display_default = no

<links>

radius = 0.98r
#crest  = 0.25
#bezier_radius        = 0.9r
#bezier_radius_purity = 0.5

<link segdup>
show         = yes
color        = vdgrey
thickness    = 2p
file         = data/5/segdup.txt
#record_limit = 500

<rules>
<rule>
importance = 110
condition  = _SIZE1_ < 1.5kb || _SIZE2_ < 1.5kb
show       = no
</rule>
# the next rule must contain flow=continue because it 
# always matches and you do not want it to terminate
# the rule chain (otherwise the next color rule would
# never be checked)
<rule>
importance = 100
condition  = 1
thickness  = eval(max(1,min(6,exp(_SIZE1_/50000))))
flow       = continue
</rule>
<rule>
importance = 90
condition  = (_CHR1_ eq "hs2" && abs(_START1_ - 100Mb) < 20Mb) || (_CHR2_ eq "hs2" && abs(_START2_ - 100Mb) < 20Mb)
color      = red
</rule>
</rules>

</link>

</links>

anglestep       = 0.5
minslicestep    = 10
beziersamples   = 40
debug           = no
warnings        = no
imagemap        = no

# don't touch!
units_ok        = bupr
units_nounit    = n

circos.image-02.conf


<colors>
<<include etc/colors.conf>>
</colors>

<fonts>
<<include etc/fonts.conf>>
</fonts>

<<include ideogram.conf>>
<<include ticks.conf>>

karyotype   = data/karyotype.human.txt

<image>
dir = /tmp
file  = circos-tutorial.png
# radius of inscribed circle in image
radius         = 1500p
background     = white
# by default angle=0 is at 3 o'clock position
angle_offset   = -90
</image>

chromosomes_units = 1000000
chromosomes       = hs1;hs2;hs3;hs4
chromosomes_display_default = no

<links>

radius = 0.98r

#bezier_radius         = 0r
#bezier_radius         = 0.25r
bezier_radius         = 0.5r
#bezier_radius         = 0.75r

<link segdup>
show         = yes
color        = vdgrey
thickness    = 2p
file         = data/5/segdup.txt

<rules>
<rule>
importance = 110
condition  = _SIZE1_ < 1.5kb || _SIZE2_ < 1.5kb
show       = no
</rule>
# the next rule must contain flow=continue because it 
# always matches and you do not want it to terminate
# the rule chain (otherwise the next color rule would
# never be checked)
<rule>
importance = 100
condition  = 1
thickness  = eval(max(1,min(6,exp(_SIZE1_/50000))))
flow       = continue
</rule>
<rule>
importance = 90
condition  = (_CHR1_ eq "hs2" && abs(_START1_ - 100Mb) < 20Mb) || (_CHR2_ eq "hs2" && abs(_START2_ - 100Mb) < 20Mb)
color      = red
</rule>
</rules>

</link>

</links>

anglestep       = 0.5
minslicestep    = 10
beziersamples   = 40
debug           = no
warnings        = no
imagemap        = no

# don't touch!
units_ok        = bupr
units_nounit    = n

circos.image-03.conf


<colors>
<<include etc/colors.conf>>
</colors>

<fonts>
<<include etc/fonts.conf>>
</fonts>

<<include ideogram.conf>>
<<include ticks.conf>>

karyotype   = data/karyotype.human.txt

<image>
dir = /tmp
file  = circos-tutorial.png
# radius of inscribed circle in image
radius         = 1500p
background     = white
# by default angle=0 is at 3 o'clock position
angle_offset   = -90
</image>

chromosomes_units = 1000000
chromosomes       = hs1;hs2;hs3;hs4
chromosomes_display_default = no

<links>

radius = 0.98r

bezier_radius         = 0.5r

<link segdup>
show         = yes
color        = vdgrey
thickness    = 2p
file         = data/5/segdup.txt

<rules>
<rule>
importance = 110
condition  = _SIZE1_ < 1.5kb || _SIZE2_ < 1.5kb
show       = no
</rule>
# the next two rules must contain flow=continue because it 
# always matches and you do not want it to terminate
# the rule chain (otherwise the color rule would
# never be checked)
<rule>
importance = 100
condition  = 1
thickness  = eval(max(1,min(6,exp(_SIZE1_/50000))))
flow       = continue
</rule>

<rule>
importance = 95
condition  = _CHR1_ eq _CHR2_ && abs(_START1_-_START2_) < 100Mb
#bezier_radius = 0.75r
bezier_radius = eval( (0.5 + 0.4*(1-abs(_START1_-_START2_) / 100Mb)) . "r")
flow = continue
</rule>

<rule>
importance = 90
condition  = (_CHR1_ eq "hs2" && abs(_START1_ - 100Mb) < 20Mb) || (_CHR2_ eq "hs2" && abs(_START2_ - 100Mb) < 20Mb)
color      = red
</rule>
</rules>

</link>

</links>

anglestep       = 0.5
minslicestep    = 10
beziersamples   = 40
debug           = no
warnings        = no
imagemap        = no

# don't touch!
units_ok        = bupr
units_nounit    = n

circos.image-04.conf


<colors>
<<include etc/colors.conf>>
</colors>

<fonts>
<<include etc/fonts.conf>>
</fonts>

<<include ideogram.conf>>
<<include ticks.conf>>

karyotype   = data/karyotype.human.txt

<image>
dir = /tmp
file  = circos-tutorial.png
# radius of inscribed circle in image
radius         = 1500p
background     = white
# by default angle=0 is at 3 o'clock position
angle_offset   = -90
</image>

chromosomes_units = 1000000
chromosomes       = hs1;hs2;hs3;hs4
chromosomes_display_default = no

<links>

radius = 0.98r

crest = 2.5
bezier_radius         = 0.5r

<link segdup>
show         = yes
color        = vdgrey
thickness    = 2p
file         = data/5/segdup.txt

<rules>
<rule>
importance = 110
condition  = _SIZE1_ < 1.5kb || _SIZE2_ < 1.5kb
show       = no
</rule>
# the next two rules must contain flow=continue because it 
# always matches and you do not want it to terminate
# the rule chain (otherwise the color rule would
# never be checked)
<rule>
importance = 100
condition  = 1
thickness  = eval(max(1,min(6,exp(_SIZE1_/50000))))
flow       = continue
</rule>

<rule>
importance = 95
condition  = _CHR1_ eq _CHR2_ && abs(_START1_-_START2_) < 100Mb
#bezier_radius = 0.75r
bezier_radius = eval( (0.5 + 0.4*(1-abs(_START1_-_START2_) / 100Mb)) . "r")
flow = continue
</rule>

<rule>
importance = 90
condition  = (_CHR1_ eq "hs2" && abs(_START1_ - 100Mb) < 20Mb) || (_CHR2_ eq "hs2" && abs(_START2_ - 100Mb) < 20Mb)
color      = red
</rule>
</rules>

</link>

</links>

anglestep       = 0.5
minslicestep    = 10
beziersamples   = 40
debug           = no
warnings        = no
imagemap        = no

# don't touch!
units_ok        = bupr
units_nounit    = n

circos.image-05.conf


<colors>
<<include etc/colors.conf>>
</colors>

<fonts>
<<include etc/fonts.conf>>
</fonts>

<<include ideogram.conf>>
<<include ticks.conf>>

karyotype   = data/karyotype.human.txt

<image>
dir = /tmp
file  = circos-tutorial.png
# radius of inscribed circle in image
radius         = 1500p
background     = white
# by default angle=0 is at 3 o'clock position
angle_offset   = -90
</image>

chromosomes_units = 1000000
chromosomes       = hs1;hs2;hs3;hs4
chromosomes_display_default = no

<links>

radius = 0.98r

<link segdup>
show         = yes
color        = vdgrey
thickness    = 2p
file         = data/5/segdup.txt

<rules>

# adjust thickness for all links
<rule>
importance = 100
condition  = 1
thickness  = eval(max(1,min(6,exp(_SIZE1_/50000))))
flow       = continue
</rule>

# closely spaced intrachromosomal links
# go outside ideogram circle

<rule>
importance = 90
condition  = _CHR1_ eq _CHR2_ && abs(_START1_-_START2_) < 40Mb
radius        = 1r+125p
bezier_radius = 1r+225p
crest         = 1
color         = red
</rule>

# all other intrachromosomeal links hidden

<rule>
importance = 80
condition  = _CHR1_ eq _CHR2_
show       = no
</rule>

# interchromosomeal links involving start
# of chromosome are inside circle

<rule>
importance = 70
condition  = _CHR1_ ne _CHR2_ && (_START1_ < 20Mb || _START2_ < 20Mb)
color      = black
radius     = 0.99r
bezier_radius = 0.5r
crest         = 1
</rule>

# all remaining links are hidden

<rule>
importance = 10
condition  = 1
show       = no
</rule>

</rules>

</link>

</links>

anglestep       = 0.5
minslicestep    = 10
beziersamples   = 40
debug           = no
warnings        = no
imagemap        = no

# don't touch!
units_ok        = bupr
units_nounit    = n

circos.image-06.conf


<colors>
<<include etc/colors.conf>>
</colors>

<fonts>
<<include etc/fonts.conf>>
</fonts>

<<include ideogram.conf>>
<<include ticks.conf>>

karyotype   = data/karyotype.human.txt

<image>
dir = /tmp
file  = circos-tutorial.png
# radius of inscribed circle in image
radius         = 1500p
background     = white
# by default angle=0 is at 3 o'clock position
angle_offset   = -90
</image>

chromosomes_units = 1000000
chromosomes       = hs1;hs2;hs3;hs4
chromosomes_display_default = no

<links>

radius = 0.98r

crest = 2.5
bezier_radius         = 0.5r

<link segdup>
show         = yes
color        = vdgrey
thickness    = 2p
file         = data/5/segdup.txt

<rules>
<rule>
importance = 110
condition  = _CHR1_ eq _CHR2_
show       = no
</rule>
# the next two rules must contain flow=continue because it 
# always matches and you do not want it to terminate
# the rule chain (otherwise the color rule would
# never be checked)
<rule>
importance = 100
condition  = 1
thickness  = eval(max(1,min(6,exp(_SIZE1_/50000))))
flow       = continue
</rule>

<rule>
importance    = 95
condition     = _CHR1_ eq _CHR2_ && abs(_START1_-_START2_) < 100Mb
bezier_radius = eval( (0.5 + 0.4*(1-abs(_START1_-_START2_) / 100Mb)) . "r")
flow          = continue
</rule>

<rule>
importance = 90
condition  = (_CHR1_ eq "hs2" && _CHR2_ eq "hs4" && abs(_START1_ - 90Mb) < 30Mb) || (_CHR2_ eq "hs2" && _CHR1_ eq "hs4" && abs(_START2_ - 100Mb) < 20Mb)
color      = red
thickness  = eval(_thickness_*2)
z          = 5
</rule>

<rule>
importance = 90
condition  = (_CHR1_ eq "hs1" && _CHR2_ eq "hs3" && abs(_START1_ - 160Mb) < 20Mb) || (_CHR2_ eq "hs1" && _CHR1_ eq "hs3" && abs(_START2_ - 160Mb) < 20Mb)
color      = blue
thickness  = eval(_thickness_*2)
z          = 10
</rule>

</rules>

</link>

</links>

anglestep       = 0.5
minslicestep    = 10
beziersamples   = 40
debug           = no
warnings        = no
imagemap        = no

# don't touch!
units_ok        = bupr
units_nounit    = n

circos.image-07.conf


<colors>
<<include etc/colors.conf>>
</colors>

<fonts>
<<include etc/fonts.conf>>
</fonts>

<<include ideogram.conf>>
<<include ticks.conf>>

karyotype   = data/karyotype.human.txt

<image>
dir = /tmp
file  = circos-tutorial.png
# radius of inscribed circle in image
radius         = 1500p
background     = white
# by default angle=0 is at 3 o'clock position
angle_offset   = -90
</image>

chromosomes_units = 1000000
chromosomes       = hs1;hs2;hs3;hs4
chromosomes_display_default = no

<links>

radius = 0.98r

crest         = 2.5
bezier_radius = 0.5r

<link segdup>
show         = yes
color        = grey
thickness    = 2p
file         = data/5/segdup.txt

<rules>
<rule>
importance = 110
condition  = _CHR1_ eq _CHR2_ 
show       = no
</rule>
# the next two rules must contain flow=continue because it 
# always matches and you do not want it to terminate
# the rule chain (otherwise the color rule would
# never be checked)
<rule>
importance = 100
condition  = 1
thickness  = eval(max(1,min(6,exp(_SIZE1_/50000))))
flow       = continue
</rule>

<rule>
importance = 90
condition  = (_CHR1_ eq "hs2" && _CHR2_ eq "hs4" && abs(_START1_ - 90Mb) < 30Mb) || (_CHR2_ eq "hs2" && _CHR1_ eq "hs4" && abs(_START2_ - 100Mb) < 20Mb)
color      = red
thickness  = eval(_thickness_*2)
z          = 5

crest         = 2
bezier_radius = 0.5r

</rule>

<rule>
importance = 90
condition  = (_CHR1_ eq "hs1" && _CHR2_ eq "hs3" && abs(_START1_ - 160Mb) < 20Mb) || (_CHR2_ eq "hs1" && _CHR1_ eq "hs3" && abs(_START2_ - 160Mb) < 20Mb)
color      = blue
thickness  = eval(_thickness_*2)
z          = 10
crest         = 4
bezier_radius = 0.75r

</rule>

<rule>
importance = 90
condition  = (_CHR1_ eq "hs1" && _CHR2_ eq "hs2" && abs(_START1_ - 10Mb) < 20Mb) || (_CHR2_ eq "hs1" && _CHR1_ eq "hs2" && abs(_START2_ - 10Mb) < 20Mb)
color      = orange
thickness  = eval(_thickness_*2)
z          = 15
crest         = 5
bezier_radius = 0.8r

</rule>

</rules>

</link>

</links>

anglestep       = 0.5
minslicestep    = 10
beziersamples   = 40
debug           = no
warnings        = no
imagemap        = no

# don't touch!
units_ok        = bupr
units_nounit    = n

ideogram.conf


<ideogram>

<spacing>

default = 5u
break   = 1u

axis_break_at_edge = yes
axis_break         = yes
axis_break_style   = 2

<break_style 1>
stroke_color = black
fill_color   = blue
thickness    = 0.25r
stroke_thickness = 2
</break>

<break_style 2>
stroke_color     = black
stroke_thickness = 3
thickness        = 1.5r
</break>

</spacing>

# thickness (px) of chromosome ideogram
thickness        = 100p
stroke_thickness = 2
# ideogram border color
stroke_color     = black
fill             = yes
# the default chromosome color is set here and any value
# defined in the karyotype file overrides it
fill_color       = black

# fractional radius position of chromosome ideogram within image
radius         = 0.85r
show_label     = yes
label_with_tag = yes
label_font     = condensedbold
label_radius   = dims(ideogram,radius) + 0.075r
label_size     = 60p

# cytogenetic bands
band_stroke_thickness = 2

# show_bands determines whether the outline of cytogenetic bands
# will be seen
show_bands            = yes
# in order to fill the bands with the color defined in the karyotype
# file you must set fill_bands
fill_bands            = yes

</ideogram>

ticks.conf


show_ticks          = yes
show_tick_labels    = yes

<ticks>
radius               = dims(ideogram,radius_outer)
multiplier           = 1e-6
<tick>
spacing        = 5u
size           = 5p
thickness      = 2p
color          = black
show_label     = no
label_size     = 16p
label_offset   = 0p
format         = %d
</tick>

<tick>
spacing        = 10u
size           = 8p
thickness      = 2p
color          = black
show_label     = yes
label_size     = 20p
label_offset   = 5p
format         = %d
</tick>

</ticks>