Circos > Documentation > Tutorials > 2d Tracks > Connectors
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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.

6 — 2D Data Tracks

11. Connectors

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
24bit = yes
png = yes
svg = yes
# radius of inscribed circle in image
radius         = 3000p
background     = white
# by default angle=0 is at 3 o'clock position
angle_offset   = -90

auto_alpha_colors = yes
auto_alpha_steps  = 5

</image>

chromosomes_units  = 1000000
#chromosomes       = hs6;hs20;hs22
chromosomes        = hs22:14.5-)

chromosomes_display_default = no

<highlights>

stroke_thickness = 0
stroke_color     = white

<highlight>
show       = yes
z          = 10
file       = data/6/epi.tmp.txt
r0         = 0.95r
r1         = 0.8r
</highlight>

</highlights>

<plots>

<plot>

show = yes

type = connector
file = data/6/connectors.txt

r0   = 0.8925r
r1   = 0.999r

#connector_dims = 0,0.3,0.4,0.3,0
connector_dims = 0.05,0.15,0.6,0.1,0.1

thickness = 1
color     = black

</plot>

</plots>

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

units_ok = bupr
units_nounit = n


colors.all.conf

# RGB color definition. Colors are refered to within configuration files
# by their name. In order to use a color, you must define it here. 
# 
# e.g. if you really must use 'bisque', then add
#
# bisque = 255,228,196
#
# Many useful colors are already defined. In general, given a HUE, these
# colors are defined
#
# vlHUE (very light HUE, e.g. vlred)
# lHUE  (light HUE, e.g. red)
# HUE   (e.g. red)
# dHUE  (dark HUE, e.g. dred)
#
# In addition to hues, two other color groups are defined. 
#
# - cytogenetic band colors (e.g. gposNNN, acen, stalk, etc.) which
#   correspond to colors on ideogram bands
# - UCSC chromosome color palette (e.g. chrNN, chrUn, chrNA)

optblue   = 55,133,221
optgreen  = 55,221,125
optyellow = 221,215,55
optorange = 221,164,55
optred    = 221,55,55
optviolet = 145,55,221
optpurple = 219,55,221

white     = 255,255,255
vvvvlgrey = 250,250,250
vvvlgrey  = 240,240,240
vvlgrey   = 230,230,230
vlgrey    = 220,220,220
lgrey     = 210,210,210
grey      = 200,200,200
dgrey     = 170,170,170
vdgrey    = 140,140,140
vvdgrey   = 100,100,100
vvvdgrey  = 70,70,70
vvvvdgrey = 40,40,40
black     = 0,0,0

vlred   = 255,193,200
lred    = 255,122,137
red     = 247,42,66
dred    = 205,51,69

vlgreen = 204,255,218
lgreen  = 128,255,164
green   = 51,204,94
dgreen  = 38,153,71

vlblue  = 128,176,255
lblue   = 64,137,255
blue    = 54,116,217
dblue   = 38,82,153

vlpurple= 242,128,255
lpurple = 236,64,255
purple  = 189,51,204
dpurple = 118,32,128

vlyellow = 255,253,202
lyellow  = 255,252,150
yellow   = 255,255,0
dyellow  = 191,186,48

lime     = 186,255,0

vlorange = 255,228,193
lorange  = 255,187,110
orange   = 255,136,0
dorange  = 221,143,55

# karyotype colors

gpos100 = 0,0,0
gpos    = 0,0,0
gpos75  = 130,130,130
gpos66  = 160,160,160
gpos50  = 200,200,200
gpos33  = 210,210,210
gpos25  = 200,200,200
gvar    = 220,220,220
gneg    = 255,255,255
acen    = 217,47,39
stalk   = 100,127,164

# others

select = 135,177,255

# new york times cmyk-safe

# roygbiv - normal
nyt_blue   = 104,152,178
nyt_green  = 137,129,96
nyt_yellow = 241,221,117
nyt_orange = 230,146,57
nyt_red    = 217,47,39

# chromosome color map (UCSC) 

chr1 = 153,102,0
chr2 = 102,102,0
chr3 = 153,153,30
chr4 = 204,0,0
chr5 = 255,0,0
chr6 = 255,0,204
chr7 = 255,204,204
chr8 = 255,153,0
chr9 = 255,204,0
chr10 = 255,255,0
chr11 = 204,255,0
chr12 = 0,255,0
chr13 = 53,128,0
chr14 = 0,0,204
chr15 = 102,153,255
chr16 = 153,204,255
chr17 = 0,255,255
chr18 = 204,255,255
chr19 = 153,0,204
chr20 = 204,51,255
chr21 = 204,153,255
chr22 = 102,102,102
chr23 = 153,153,153
chrX  = 153,153,153
chr24 = 204,204,204
chrY = 204,204,204
chrM = 204,204,153
chr0 = 204,204,153
chrUn = 121,204,61
chrNA = 255,255,255
meth0 = 217,33,33
meth1 = 217,40,33
meth2 = 217,47,33
meth3 = 217,55,33
meth4 = 217,62,33
meth5 = 217,69,33
meth6 = 217,77,33
meth7 = 217,84,33
meth8 = 217,91,33
meth9 = 217,99,33
meth10 = 217,106,33
meth11 = 217,114,33
meth12 = 217,121,33
meth13 = 217,128,33
meth14 = 217,136,33
meth15 = 217,143,33
meth16 = 217,150,33
meth17 = 217,158,33
meth18 = 217,165,33
meth19 = 217,173,33
meth20 = 217,180,33
meth21 = 217,187,33
meth22 = 217,195,33
meth23 = 217,202,33
meth24 = 217,209,33
meth25 = 217,217,33
meth26 = 209,217,33
meth27 = 202,217,33
meth28 = 195,217,33
meth29 = 187,217,33
meth30 = 180,217,33
meth31 = 173,217,33
meth32 = 165,217,33
meth33 = 158,217,33
meth34 = 150,217,33
meth35 = 143,217,33
meth36 = 136,217,33
meth37 = 128,217,33
meth38 = 121,217,33
meth39 = 114,217,33
meth40 = 106,217,33
meth41 = 99,217,33
meth42 = 91,217,33
meth43 = 84,217,33
meth44 = 77,217,33
meth45 = 69,217,33
meth46 = 62,217,33
meth47 = 55,217,33
meth48 = 47,217,33
meth49 = 40,217,33
meth50 = 33,217,33
meth51 = 33,217,40
meth52 = 33,217,47
meth53 = 33,217,55
meth54 = 33,217,62
meth55 = 33,217,69
meth56 = 33,217,77
meth57 = 33,217,84
meth58 = 33,217,91
meth59 = 33,217,99
meth60 = 33,217,106
meth61 = 33,217,114
meth62 = 33,217,121
meth63 = 33,217,128
meth64 = 33,217,136
meth65 = 33,217,143
meth66 = 33,217,150
meth67 = 33,217,158
meth68 = 33,217,165
meth69 = 33,217,173
meth70 = 33,217,180
meth71 = 33,217,187
meth72 = 33,217,195
meth73 = 33,217,202
meth74 = 33,217,209
meth75 = 33,217,217
meth76 = 33,209,217
meth77 = 33,202,217
meth78 = 33,195,217
meth79 = 33,187,217
meth80 = 33,180,217
meth81 = 33,173,217
meth82 = 33,165,217
meth83 = 33,158,217
meth84 = 33,150,217
meth85 = 33,143,217
meth86 = 33,136,217
meth87 = 33,128,217
meth88 = 33,121,217
meth89 = 33,114,217
meth90 = 33,106,217
meth91 = 33,99,217
meth92 = 33,91,217
meth93 = 33,84,217
meth94 = 33,77,217
meth95 = 33,69,217
meth96 = 33,62,217
meth97 = 33,55,217
meth98 = 33,47,217
meth99 = 33,40,217
meth100 = 33,33,217


colors.conf

# RGB color definition. Colors are refered to within configuration files
# by their name. In order to use a color, you must define it here. 
# 
# e.g. if you really must use 'bisque', then add
#
# bisque = 255,228,196
#
# Many useful colors are already defined. In general, given a HUE, these
# colors are defined
#
# vlHUE (very light HUE, e.g. vlred)
# lHUE  (light HUE, e.g. red)
# HUE   (e.g. red)
# dHUE  (dark HUE, e.g. dred)
#
# In addition to hues, two other color groups are defined. 
#
# - cytogenetic band colors (e.g. gposNNN, acen, stalk, etc.) which
#   correspond to colors on ideogram bands
# - UCSC chromosome color palette (e.g. chrNN, chrUn, chrNA)

optblue   = 55,133,221
optgreen  = 55,221,125
optyellow = 221,215,55
optorange = 221,164,55
optred    = 221,55,55
optviolet = 145,55,221
optpurple = 219,55,221

white     = 255,255,255
vvvvlgrey = 250,250,250
vvvlgrey  = 240,240,240
vvlgrey   = 230,230,230
vlgrey    = 220,220,220
lgrey     = 210,210,210
grey      = 200,200,200
dgrey     = 170,170,170
vdgrey    = 140,140,140
vvdgrey   = 100,100,100
vvvdgrey  = 70,70,70
vvvvdgrey = 40,40,40
black     = 0,0,0

vlred   = 255,193,200
lred    = 255,122,137
red     = 247,42,66
dred    = 205,51,69

vlgreen = 204,255,218
lgreen  = 128,255,164
green   = 51,204,94
dgreen  = 38,153,71

vlblue  = 128,176,255
lblue   = 64,137,255
blue    = 54,116,217
dblue   = 38,82,153

vlpurple= 242,128,255
lpurple = 236,64,255
purple  = 189,51,204
dpurple = 118,32,128

vlyellow = 255,253,202
lyellow  = 255,252,150
yellow   = 255,255,0
dyellow  = 191,186,48

lime     = 186,255,0

vlorange = 255,228,193
lorange  = 255,187,110
orange   = 255,136,0
dorange  = 221,143,55

# karyotype colors

gpos100 = 0,0,0
gpos    = 0,0,0
gpos75  = 130,130,130
gpos66  = 160,160,160
gpos50  = 200,200,200
gpos33  = 210,210,210
gpos25  = 200,200,200
gvar    = 220,220,220
gneg    = 255,255,255
acen    = 217,47,39
stalk   = 100,127,164

# others

select = 135,177,255

# new york times cmyk-safe

# roygbiv - normal
nyt_blue   = 104,152,178
nyt_green  = 137,129,96
nyt_yellow = 241,221,117
nyt_orange = 230,146,57
nyt_red    = 217,47,39

# chromosome color map (UCSC) 

chr1 = 153,102,0
chr2 = 102,102,0
chr3 = 153,153,30
chr4 = 204,0,0
chr5 = 255,0,0
chr6 = 255,0,204
chr7 = 255,204,204
chr8 = 255,153,0
chr9 = 255,204,0
chr10 = 255,255,0
chr11 = 204,255,0
chr12 = 0,255,0
chr13 = 53,128,0
chr14 = 0,0,204
chr15 = 102,153,255
chr16 = 153,204,255
chr17 = 0,255,255
chr18 = 204,255,255
chr19 = 153,0,204
chr20 = 204,51,255
chr21 = 204,153,255
chr22 = 102,102,102
chr23 = 153,153,153
chrX  = 153,153,153
chr24 = 204,204,204
chrY = 204,204,204
chrM = 204,204,153
chr0 = 204,204,153
chrUn = 121,204,61
chrNA = 255,255,255


colors.values.conf

meth0 = 230,230,0
meth1 = 222,228,1
meth2 = 214,227,2
meth3 = 206,226,3
meth4 = 199,225,4
meth5 = 191,224,4
meth6 = 184,223,5
meth7 = 177,222,6
meth8 = 170,221,7
meth9 = 163,220,8
meth10 = 156,219,9
meth11 = 149,218,10
meth12 = 143,217,10
meth13 = 136,216,11
meth14 = 130,215,12
meth15 = 124,214,13
meth16 = 117,213,14
meth17 = 111,212,14
meth18 = 105,211,15
meth19 = 99,210,16
meth20 = 94,209,17
meth21 = 88,208,17
meth22 = 82,207,18
meth23 = 77,206,19
meth24 = 72,205,20
meth25 = 66,204,20
meth26 = 61,203,21
meth27 = 56,202,22
meth28 = 51,201,23
meth29 = 46,200,23
meth30 = 41,199,24
meth31 = 37,198,25
meth32 = 32,197,25
meth33 = 28,196,26
meth34 = 26,195,30
meth35 = 27,194,35
meth36 = 28,193,41
meth37 = 28,192,46
meth38 = 29,191,52
meth39 = 30,190,57
meth40 = 30,189,62
meth41 = 31,188,67
meth42 = 31,187,72
meth43 = 32,186,77
meth44 = 32,185,81
meth45 = 33,184,86
meth46 = 34,183,90
meth47 = 34,182,95
meth48 = 35,181,99
meth49 = 35,180,103
meth50 = 36,179,107
meth51 = 36,177,111
meth52 = 37,176,115
meth53 = 37,175,119
meth54 = 38,174,122
meth55 = 38,173,126
meth56 = 39,172,130
meth57 = 39,171,133
meth58 = 40,170,136
meth59 = 40,169,140
meth60 = 40,168,143
meth61 = 41,167,146
meth62 = 41,166,149
meth63 = 42,165,152
meth64 = 42,164,154
meth65 = 42,163,157
meth66 = 43,162,160
meth67 = 43,160,161
meth68 = 44,155,160
meth69 = 44,151,159
meth70 = 44,147,158
meth71 = 45,142,157
meth72 = 45,138,156
meth73 = 45,134,155
meth74 = 46,130,154
meth75 = 46,126,153
meth76 = 46,122,152
meth77 = 46,119,151
meth78 = 47,115,150
meth79 = 47,111,149
meth80 = 47,108,148
meth81 = 48,104,147
meth82 = 48,101,146
meth83 = 48,97,145
meth84 = 48,94,144
meth85 = 49,91,143
meth86 = 49,88,142
meth87 = 49,85,141
meth88 = 49,82,140
meth89 = 49,79,139
meth90 = 50,76,138
meth91 = 50,73,137
meth92 = 50,70,136
meth93 = 50,68,135
meth94 = 50,65,134
meth95 = 50,63,133
meth96 = 51,60,132
meth97 = 51,58,131
meth98 = 51,56,130
meth99 = 51,53,129
meth100 = 51,51,128


fonts.conf


default       = /home/martink/work/circos/dev/fonts/LTe50046.ttf
normal        = /home/martink/work/circos/dev/fonts/LTe50046.ttf
bold          = /home/martink/work/circos/dev/fonts/LTe50048.ttf
condensed     = /home/martink/work/circos/dev/fonts/LTe50050.ttf
condensedbold = /home/martink/work/circos/dev/fonts/LTe50054.ttf
mono          = /home/martink/work/circos/dev/fonts/pragmata.ttf
glyph         = /home/martink/work/circos/dev/fonts/wingding.ttf


ideogram.conf


<ideogram>

<spacing>

default = 0.1u

</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     = no
label_with_tag = yes
label_font     = condensedbold
label_radius   = dims(ideogram,radius) + 0.05r
label_size     = 48

# 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)
offset     = 0p
label_size = 16p
multiplier = 1e-6
color      = black

<tick>
spacing        = .1u
size           = 4p
thickness      = 3p
color          = black
show_label     = no
</tick>

<tick>
spacing        = 1u
size           = 6p
thickness      = 3p
color          = black
show_label     = yes
label_size     = 32p
format         = %d
</tick>

<tick>
spacing        = 5u
size           = 10p
thickness      = 3p
color          = black
show_label     = yes
label_size     = 32p
format         = %d
</tick>

<tick>
spacing        = 10u
size           = 16p
thickness      = 3p
color          = black
show_label     = yes
label_size     = 32p
format         = %d
</tick>
</ticks>