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>