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

cc1 = 245,13,11,.3
cc2 = 153,28,32,.3
cc3 = 151,42,102,.3
cc4 = 110,57,139,.3
cc5 = 132,102,152,.3
cc6 = 83,86,165,.3
cc7 = 51,162,209,.3
cc8 = 100,188,206,.3
cc9 = 76,132,145,.3
cc10 = 121,193,127,.3
cc11 = 34,124,62,.3
cc12 = 82,185,87,.3
cc13 = 132,160,61,.3
cc14 = 187,181,50,.3
cc15 = 243,234,19,.3
cc16 = 239,145,33,.3
cc99 = 197,74,7,.3
ic = 118,117,119

# 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