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.
<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
# 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
# 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 = 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
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> <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>
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>