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.
# 1.9 MODULAR CONFIGURATION, MACROS karyotype = data/karyotype/karyotype.human.txt chromosomes_units = 1000000 chromosomes_display_default = no chromosomes = /hs$/ chromosomes_radius = hs4:0.9r <colors> chr1* = red chr2* = orange chr3* = green chr4* = blue </colors> chromosomes_reverse = /hs/ chromosomes_scale = hs1=0.5r,/hs/=0.5rn <plots> <plot> type = text file = data/6/genes.labels.txt r1 = 0.8r r0 = 0.6r label_font = light label_size = 12p rpadding = 5p show_links = no link_dims = 0p,2p,5p,2p,2p link_thickness = 2p link_color = black <rules> <<include rule.exclude.hs1.conf>> <rule> condition = var(value) =~ /a/i label_font = bold flow = continue </rule> <rule> condition = var(value) =~ /b/i color = blue </rule> </rules> </plot> # By using counters and automatic track placement, we can # create 4 heatmaps with identical configurations (heatmap.conf). # The conf() function is used within heatmap.conf to reference # configuration parameters. h0 = 0.88 # start of heatmap tracks hw = 0.01 # width of heatmap track (-'ve if tracks progress inward) hp = 0 # padding between heatmap tracks # Look in heatmap.conf for explanation. <plot> <<include heatmap.conf>> </plot> <plot> <<include heatmap.conf>> </plot> <plot> <<include heatmap.conf>> </plot> <plot> <<include heatmap.conf>> </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> # 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> # 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>
type = heatmap file = data/5/segdup.hs1234.heatmap.txt # The 'c' parameter (arbitrarily named) is referenced # within heatmap.conf as conf(.,c). conf(x) retrieves # the value of parameter 'x' in the current block and # conf(.,x) looks up the configuration tree until # it finds x. c = eval(sprintf("hs%d",counter(heatmap)+1)) # track_r0(counter,start,width,padding) # track_r1(counter,start,width,padding) # are helper functions that return the start/end radius of a track # formatted as float+"r", e.g. 0.925r # # r0 = start + counter * (width + padding) # r1 = start + counter * (width + padding) + width # # The calls to conf(.,x) reference the <plot> block's h0, hw and hp # parameters. The counter(heatmap) is an 0-start automatically incremented # index, which is incremented by 1 for each type=heatmap plot. # r1 = eval(track_r1(counter(heatmap),conf(.,h0),conf(.,hw),conf(.,hp))) r0 = eval(track_r0(counter(heatmap),conf(.,h0),conf(.,hw),conf(.,hp))) # conf(.,c) references the <plot> block's 'c' parameter color = conf(.,c)_a5,conf(.,c)_a4,conf(.,c)_a3,conf(.,c)_a2,conf(.,c)_a1,conf(.,c) scale_log_base = 0.25 <rules> <<include rule.exclude.hs1.conf>> <rule> condition = var(id) ne "conf(.,c)" show = no </rule> </rules>
<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> condition = on(hs1) show = no </rule>
<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>
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 http://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>