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.
<<include 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 = -/hs/;/hs[1-9]$/ <plots> # glyph character mappings # # small # | medium # | | large # | | | # a b c square # d e f rhombus # g h i triangle up # j k l triangle down # m n o circle # # lower case - hollow # upper case - solid type = text label_font = glyph label_size = 20 padding = -0.2r rpadding = -0.2r <plot> file = data/6/genes.glyph.txt r0 = 0.4r r1 = 0.99r <rules> flow = continue <rule> condition = var(value) =~ /cancer/ color = red </rule> <rule> condition = var(value) =~ /omim/ color = green </rule> <rule> condition = var(value) =~ /other/ color = blue </rule> <rule> condition = 1 value = N </rule> </rules> </plot> </plots> <<include etc/housekeeping.conf>>
show_bands = yes fill_bands = yes band_stroke_thickness = 2 band_stroke_color = white band_transparency = 0
<ideogram> <spacing> default = 0.01r break = 0.5r </spacing> <<include ideogram.position.conf>> <<include ideogram.label.conf>> <<include bands.conf>> radius* = 0.825r </ideogram>
show_label = yes label_font = default label_radius = dims(image,radius)-30p label_size = 24 label_parallel = yes label_case = lower label_format = eval(sprintf("chr%s",var(label)))
radius = 0.775r thickness = 30p fill = yes fill_color = black stroke_thickness = 2 stroke_color = black
show_ticks = no show_tick_labels = no show_grid = no grid_start = dims(ideogram,radius_inner)-0.5r grid_end = dims(ideogram,radius_inner) <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> #hide = yes #spacing = 0.01u #size = 3p #thickness = 2p #color = black #show_label = no #label_size = 12p #label_offset = 0p #format = %.2f #grid = no #grid_color = lblue #grid_thickness = 1p #</tick> #<tick> #spacing = 0.1u #size = 5p #thickness = 2p #color = black #show_label = yes #label_size = 12p #label_offset = 0p #format = %.1f #grid = yes #grid_color = lgrey #grid_thickness = 1p #</tick> <tick> spacing = 1u size = 8p thickness = 2p color = black show_label = no label_size = 16p label_offset = 0p format = %.1f grid = yes grid_color = grey grid_thickness = 1p </tick> <tick> spacing = 5u size = 10p thickness = 2p color = black show_label = yes label_size = 24p label_offset = 0p format = %d grid = yes grid_color = grey grid_thickness = 1p </tick> </ticks>