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.
# Define a parameter that will be used in <rules> block to # globally toggle rules on/off. This can be convenient if you # have many <rules> blocks and want to turn them all off using # one parameter. use_rules = yes <<include etc/colors_fonts_patterns.conf>> <<include ideogram.conf>> <<include ticks.conf>> <image> <<include etc/image.conf>> </image> karyotype = data/karyotype/karyotype.human.txt chromosomes_units = 1000000 chromosomes_display_default = yes #chromosomes = hs1;hs2;hs3;hs4;hs5;hs6 <plots> type = histogram file = data/8/histogram.txt color = black thickness = 2 extend_bin = no <plot> r0 = 0.3r r1 = 0.975r min = -0.6 max = 0.6 # define background colors and cutoffs bgy1 = 0.2 bgy2 = 0.5 bgc1 = orange bgc2 = blue <backgrounds> <background> color = lconf(.,bgc2) # reference the background cutoffs using conf(.,PARAM) y0 = conf(.,bgy2) </background> <background> color = vlconf(.,bgc2) y1 = conf(.,bgy2) y0 = conf(.,bgy1) </background> <background> color = vvlconf(.,bgc2) y1 = conf(.,bgy1) y0 = 0 </background> <background> color = vvlconf(.,bgc1) y1 = 0 y0 = -conf(.,bgy1) </background> <background> color = vlconf(.,bgc1) y1 = -conf(.,bgy1) y0 = -conf(.,bgy2) </background> <background> color = lconf(.,bgc1) y1 = -conf(.,bgy2) </background> </backgrounds> <axes> <axis> color = grey_a1 thickness = 2 spacing = 0.25r </axis> <axis> color = grey_a3 thickness = 1 spacing = 0.05r </axis> <axis> color = grey_a1 thickness = 5 position = 0 </axis> # at each background cutoff, draw a white line <axis> color = white thickness = 5 position = -conf(.,bgy2),-conf(.,bgy1),conf(.,bgy1),conf(.,bgy2) </axis> </axes> <rules> use = conf(use_rules) # remap the histogram value from the range [-0.6,0.6] onto the index [0,5], then # use the index to select the color from the list # dorange orange lorange lblue blue dblue # # Perl syntax for referencing an element of a list is qw(a b c d)[index] # where index starts at 0. <rule> condition = 1 fill_color = eval(qw(dorange orange lorange lblue blue dblue)[remap_round(var(value),-0.6,0.6,0,5)]) </rule> </rules> </plot> </plots> <<include etc/housekeeping.conf>> data_out_of_range* = trim
show_bands = yes fill_bands = yes band_stroke_thickness = 2 band_stroke_color = white band_transparency = 3
<ideogram> <spacing> default = 0.005r break = 0.5r axis_break_at_edge = yes axis_break = yes axis_break_style = 2 <break_style 1> stroke_color = black fill_color = blue thickness = 0.25r stroke_thickness = 2 </break> <break_style 2> stroke_color = black stroke_thickness = 2 thickness = 1.5r </break> </spacing> <<include ideogram.position.conf>> <<include ideogram.label.conf>> <<include bands.conf>> </ideogram>
show_label = yes label_font = default label_radius = dims(image,radius) - 50p label_size = 36 label_parallel = yes label_case = lower label_format = eval(sprintf("chr%s",var(label)))
radius = 0.90r thickness = 30p fill = yes fill_color = black stroke_thickness = 2 stroke_color = black
show_ticks = yes show_tick_labels = yes <ticks> tick_separation = 3p label_separation = 5p radius = dims(ideogram,radius_outer) multiplier = 1e-6 color = black size = 20p thickness = 4p label_offset = 5p format = %d <tick> spacing = 1u show_label = yes label_size = 16p </tick> <tick> spacing = 5u show_label = yes label_size = 18p </tick> <tick> spacing = 10u show_label = yes label_size = 20p </tick> <tick> spacing = 20u show_label = yes label_size = 24p </tick> </ticks>