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>> # specify the karyotype file here; try also # data/2/karyotype.dog.txt # data/2/karyotype.rat.txt # data/2/karyotype.mouse.txt # data/2/karyotype.all.txt (human+dog+rat+mouse) # but reduce frequency of ticks when increasing the # number of ideograms karyotype = data/karyotype.human.txt <image> dir = /tmp file = circos-tutorial.png # radius of inscribed circle in image radius = 1500p background = white # by default angle=0 is at 3 o'clock position angle_offset = -90 #angle_orientation = counterclockwise </image> chromosomes_units = 1000000 #chromosomes_display_default = yes chromosomes = hs1;hs2;hs3 anglestep = 0.5 minslicestep = 10 beziersamples = 40 debug = no warnings = no imagemap = no units_ok = bupr units_nounit = n
<<include etc/colors_fonts_patterns.conf>> <<include ideogram.conf>> <<include ticks.conf>> <image> <<include etc/image.conf>> </image> chromosomes_units = 1000000 chromosomes_display_default = yes ### single genomes # specify the karyotype file here - try other karyotypes in data/karyotype karyotype = data/karyotype/karyotype.human.txt #karyotype = data/karyotype/karyotype.drosophila.txt #karyotype = data/karyotype/karyotype.mouse.txt #karyotype = data/karyotype/karyotype.rat.txt ### multiple genomes # to draw chromosomes from multiple karyotypes, # provide comma-separated list of files #karyotype = data/karyotype/karyotype.human.txt,data/karyotype/karyotype.mouse.txt,data/karyotype/karyotype.rat.txt # adjust color using regular expressions matching chromosome names #chromosomes_color = /hs/:red;/mm/:green;/rn/:blue <<include etc/housekeeping.conf>>
show_bands = yes fill_bands = yes band_stroke_thickness = 2 band_stroke_color = white band_transparency = 4
<ideogram> <spacing> default = 0.0025r break = 0.5r </spacing> <<include ideogram.position.conf>> <<include ideogram.label.conf>> <<include bands.conf>> <rules> use = no <rule> # hide every other ideogram condition = var(display_idx) % 2 show = no </rule> <rule> condition = var(chr) eq "hs3" show_ticks = no </rule> <rule> condition = var(chr) eq "hs5" show_bands = no </rule> <rule> condition = var(chr) eq "hs7" color = vdpurple </rule> <rule> condition = var(chr) eq "hs9" stroke_thickness = 0 </rule> </rules> </ideogram>
show_label = yes label_font = default label_radius = 0.95r label_with_tag = yes label_size = 36 label_parallel = yes label_case = lower # you can format the label by using properties # of the ideogram, accessible with var(PROPERTY): # # chr, chr_with_tag, chrlength, display_idx, end, idx, # label, length, reverse, scale, size, start, tag label_format = eval(sprintf("chr%s",var(label)))
radius = 0.90r thickness = 75p fill = yes fill_color = black stroke_thickness = 2 stroke_color = black
show_ticks = yes show_tick_labels = yes <ticks> skip_first_label = no skip_last_label = no radius = dims(ideogram,radius_outer) tick_separation = 2p label_separation = 5p multiplier = 1e-6 color = black thickness = 4p size = 20p <tick> spacing = 1u show_label = no thickness = 2p color = dgrey </tick> <tick> spacing = 5u show_label = no thickness = 3p color = vdgrey </tick> <tick> spacing = 10u show_label = yes label_size = 20p label_offset = 10p format = %d grid = yes grid_color = dgrey grid_thickness = 1p grid_start = 0.5r grid_end = 0.999r </tick> </ticks>