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.
2 — Quick Start
8. Text
circos.conf
# 1.8 TEXT TRACKS karyotype = data/karyotype/karyotype.human.txt chromosomes_units = 1000000 chromosomes_display_default = no chromosomes = /hs[1234]$/ chromosomes_radius = hs4:0.9r <colors> chr1* = red chr2* = orange chr3* = green chr4* = blue </colors> chromosomes_reverse = /hs[234]/ chromosomes_scale = hs1=0.5r,/hs[234]/=0.5rn <plots> <plot> type = text file = data/6/genes.labels.txt # Like with other tracks, text is limited to a radial range by setting # r0 and r1. # # Individual labels can be repositioned automatically with in a # position window to fit more labels, without overlap. This is an # advanced feature - see the 2D Track text tutorials. r1 = 0.8r r0 = 0.6r # For a list of fonts, see etc/fonts.conf in the Circos distribution. label_font = light label_size = 12p # padding - text margin in angular direction # rpadding - text margin in radial direction rpadding = 5p # Short lines can be placed before the label to connect them to the # label's position. This is most useful when the labels are # rearranged. show_links = no link_dims = 0p,2p,5p,2p,2p link_thickness = 2p link_color = black <rules> <<include rule.exclude.hs1.conf>> # Text can be tested with var(value). <rule> condition = var(value) =~ /a/i label_font = bold flow = continue </rule> <rule> condition = var(value) =~ /b/i color = blue </rule> </rules> </plot> <plot> type = heatmap file = data/5/segdup.hs1234.heatmap.txt r1 = 0.89r r0 = 0.88r color = hs1_a5,hs1_a4,hs1_a3,hs1_a2,hs1_a1,hs1 scale_log_base = 0.25 <rules> <<include rule.exclude.hs1.conf>> </rules> </plot> <plot> type = heatmap file = data/5/segdup.hs1234.heatmap.txt r1 = 0.90r r0 = 0.89r color = hs2_a5,hs2_a4,hs2_a3,hs2_a2,hs2_a1,hs2 scale_log_base = 0.25 <rules> <<include rule.exclude.hs1.conf>> <rule> condition = var(id) ne "hs2" show = no </rule> </rules> </plot> <plot> type = heatmap file = data/5/segdup.hs1234.heatmap.txt r1 = 0.91r r0 = 0.90r color = hs3_a5,hs3_a4,hs3_a3,hs3_a2,hs3_a1,hs3 scale_log_base = 0.25 <rules> <<include rule.exclude.hs1.conf>> <rule> condition = var(id) ne "hs3" show = no </rule> </rules> </plot> <plot> type = heatmap file = data/5/segdup.hs1234.heatmap.txt r1 = 0.92r r0 = 0.91r color = hs4_a5,hs4_a4,hs4_a3,hs4_a2,hs4_a1,hs4 scale_log_base = 0.25 <rules> <<include rule.exclude.hs1.conf>> <rule> condition = var(id) ne "hs4" show = no </rule> </rules> </plot> <plot> type = histogram file = data/5/segdup.hs1234.hist.txt r1 = 0.88r r0 = 0.81r fill_color = vdgrey extend_bin = no <rules> <<include rule.exclude.hs1.conf>> </rules> <<include backgrounds.conf>> </plot> <plot> type = histogram file = data/5/segdup.hs1234.stacked.txt r1 = 0.99r r0 = 0.92r fill_color = hs1,hs2,hs3,hs4 orientation = in extend_bin = no <rules> <<include rule.exclude.hs1.conf>> </rules> <<include axes.conf>> </plot> </plots> <links> <link> file = data/5/segdup.txt radius = 0.6r bezier_radius = 0r color = black_a4 thickness = 2 <rules> <<include rules.link.conf>> </rules> </link> </links> <<include ideogram.conf>> <<include ticks.conf>> <image> <<include etc/image.conf>> </image> <<include etc/colors_fonts_patterns.conf>> <<include etc/housekeeping.conf>> data_out_of_range* = trim
axes.conf
<axes> # Show axes only on ideograms that have data for this track show = data thickness = 1 color = lgrey <axis> spacing = 0.1r </axis> <axis> spacing = 0.2r color = grey </axis> <axis> position = 0.5r color = red </axis> <axis> position = 0.85r color = green thickness = 2 </axis> </axes>
backgrounds.conf
<backgrounds> # Show the backgrounds only for ideograms that have data show = data <background> color = vvlgrey </background> <background> color = vlgrey y0 = 0.2r y1 = 0.5r </background> <background> color = lgrey y0 = 0.5r y1 = 0.8r </background> <background> color = grey y0 = 0.8r </background> </backgrounds>
ideogram.conf
<ideogram> <spacing> default = 0.005r </spacing> # Ideogram position, fill and outline radius = 0.90r thickness = 20p fill = yes stroke_color = dgrey stroke_thickness = 2p # Minimum definition for ideogram labels. show_label = yes # see etc/fonts.conf for list of font names label_font = default label_radius = 1.075r # if ideogram radius is constant, and you'd like labels close to image edge, # use the dims() function to access the size of the image # label_radius = dims(image,radius) - 60p label_size = 30 label_parallel = yes </ideogram>
rule.exclude.hs1.conf
<rule> condition = on(hs1) show = no </rule>
rules.link.conf
<rule> condition = var(intrachr) show = no </rule> <rule> condition = 1 color = eval(var(chr2)) flow = continue </rule> <rule> condition = from(hs1) radius1 = 0.99r </rule> <rule> condition = to(hs1) radius2 = 0.99r </rule>
ticks.conf
show_ticks = yes show_tick_labels = yes <ticks> radius = 1r color = black thickness = 2p # the tick label is derived by multiplying the tick position # by 'multiplier' and casting it in 'format': # # sprintf(format,position*multiplier) # multiplier = 1e-6 # %d - integer # %f - float # %.1f - float with one decimal # %.2f - float with two decimals # # for other formats, see https://perldoc.perl.org/functions/sprintf.html format = %d <tick> spacing = 5u size = 10p </tick> <tick> spacing = 25u size = 15p show_label = yes label_size = 20p label_offset = 10p format = %d </tick> </ticks>