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> <patterns> <<include etc/pattern.conf>> </patterns> <<include ideogram.conf>> <<include ticks.conf>> karyotype = data/karyotype/karyotype.human.hg18.txt <image> <<include etc/image.conf>> </image> chromosomes_units = 1000000 chromosomes_display_default = yes <highlights> <highlight> file = data/3/chr.highlights.txt r0 = 0.99r r1 = 0.995r </highlight> </highlights> <links> <link linkexample> file = data/8/15/tmp.1 ribbon = yes flat = yes radius = 0.95r bezier_radius = 0r crest = 0.2 color = black <rules> <rule> importance = 100 condition = rand() < 0.5 pattern = eval((qw(hline vline checker dot))[rand(4)]) color = eval((qw(red orange yellow green blue purple))[rand(6)]) z = 10 </rule> </rules> </link> </links> <<include etc/housekeeping.conf>>
<ideogram> <spacing> default = 10u </spacing> # thickness (px) of chromosome ideogram thickness = 20p 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_font = condensedbold label_radius = dims(ideogram,radius) + 0.05r label_size = 36 label_parallel = no # 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 band_transparency = 0 </ideogram>
show_ticks = yes show_tick_labels = yes grid_start = dims(ideogram,radius_inner)-0.5r grid_end = dims(ideogram,radius_outer)+100 <ticks> skip_first_label = no skip_last_label = no radius = dims(ideogram,radius_outer) tick_separation = 2p min_label_distance_to_edge = 0p label_separation = 5p label_offset = 2p label_size = 8p multiplier = 1e-6 color = black <tick> spacing = 5u size = 5p thickness = 2p color = black show_label = no label_size = 8p label_offset = 0p format = %d grid = yes grid_color = grey grid_thickness = 1p </tick> <tick> spacing = 10u size = 8p thickness = 2p color = black show_label = yes label_size = 12p label_offset = 0p format = %d grid = yes grid_color = dgrey grid_thickness = 1p </tick> </ticks>