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.
9 — Recipes
1. Microbial Genome
circos.conf
<<include etc/colors_fonts_patterns.conf>> <<include ideogram.conf>> <<include ticks.conf>> karyotype = data/8/karyotype.microbe.txt <image> <<include etc/image.conf>> </image> chromosomes_units = 1000 chromosomes_display_default = yes <<include highlights.conf>> <plots> <plot> type = text file = data/8/microbe.labels.txt color = black r1 = 0.95r r0 = 0.85r label_size = 16 label_font = light padding = 5p rpadding = 5p show_links = yes link_dims = 5p,4p,8p,4p,0p link_thickness = 1p link_color = dgrey label_snuggle = yes max_snuggle_distance = 2r snuggle_sampling = 1 snuggle_tolerance = 0.25r snuggle_link_overlap_test = yes snuggle_link_overlap_tolerance = 2p snuggle_refine = yes </plot> <plot> type = text file = data/8/microbe.labels.2.txt color = black r1 = 0.4r r0 = 0.2r label_size = 10p label_font = default padding = 1p rpadding = 1p show_links = yes link_dims = 1p,2p,3p,2p,1p link_thickness = 1p link_color = red label_snuggle = yes max_snuggle_distance = 2r snuggle_sampling = 1 snuggle_tolerance = 0.25r snuggle_link_overlap_test = yes snuggle_link_overlap_tolerance = 2p snuggle_refine = yes </plot> <plot> type = tile file = data/8/microbe.tile.txt r1 = 0.78r r0 = 0.72r layers = 5 margin = 0.2u thickness = 12 padding = 6 layers_overflow = hide orientation = out stroke_thickness = 1 stroke_color = grey color = orange <rules> <rule> condition = var(size) < 5kb color = lgrey </rule> </rules> </plot> <plot> type = histogram file = data/8/microbe.plot.1.txt r1 = 0.68r r0 = 0.65r min = 0 max = 1 extend_bin = no fill_color = lblue color = blue thickness = 0 orientation = out </plot> <plot> type = histogram file = data/8/microbe.plot.2.txt r1 = 0.65r r0 = 0.63r max = 1 min = 0 extend_bin = no fill_color = orange orientation = in <rules> <rule> condition = var(start) % 2000 show = no </rule> </rules> </plot> <plot> type = histogram file = data/8/microbe.plot.3.txt color = black thickness = 2 r1 = 0.62r r0 = 0.57r max = 1 min = 0 orientation = out <rules> <rule> condition = var(value) > 0.9 color = red </rule> <rule> condition = var(value) < 0.1 color = green </rule> </rules> </plot> </plots> <<include etc/housekeeping.conf>>
highlights.conf
<highlights> <highlight> init_counter = highlight:1 file = data/8/microbe.highlights.counter(highlight).txt r1 = conf(.,r0)+0.03r r0 = 0.95r </highlight> <highlight> file = data/8/microbe.highlights.counter(highlight).txt r1 = conf(.,r0)+0.03r r0 = 0.82r </highlight> <highlight> file = data/8/microbe.highlights.counter(highlight).txt r1 = conf(.,r0)+0.01r r0 = 0.53r </highlight> <highlight> file = data/8/microbe.highlights.counter(highlight).txt r1 = conf(.,r0)+0.01r r0 = 0.51r </highlight> <highlight> file = data/8/microbe.highlights.counter(highlight).txt r1 = conf(.,r0)+0.01r r0 = 0.46r </highlight> <highlight> file = data/8/microbe.highlights.counter(highlight).txt r1 = conf(.,r0)+0.01r r0 = 0.48r </highlight> <highlight> file = data/8/microbe.highlights.counter(highlight).txt r1 = conf(.,r0)+0.01r r0 = 0.41r </highlight> <highlight> file = data/8/microbe.highlights.counter(highlight).txt r1 = conf(.,r0)+0.01r r0 = 0.43r </highlight> <highlight> file = data/8/microbe.highlights.counter(highlight).txt r1 = conf(.,r0)+0.01r r0 = 0.19r </highlight> <highlight> file = data/8/microbe.highlights.counter(highlight).txt r1 = conf(.,r0)+0.01r r0 = 0.17r </highlight> <highlight> file = data/8/microbe.highlights.counter(highlight).txt r1 = conf(.,r0)+0.01r r0 = 0.15r </highlight> <highlight> file = data/8/microbe.separator.txt r1 = conf(.,r0)+0.005r r0 = 0.80r fill_color = vvlgrey </highlight> <highlight> file = data/8/microbe.separator.txt r1 = conf(.,r0)+0.005r r0 = 0.70r fill_color = vvlgrey </highlight> <highlight> file = data/8/microbe.separator.txt r1 = conf(.,r0)+0.005r r0 = 0.55r fill_color = vvlgrey </highlight> <highlight> file = data/8/microbe.separator.txt r1 = conf(.,r0)+0.005r r0 = 0.50r fill_color = vvlgrey </highlight> <highlight> file = data/8/microbe.separator.txt r1 = conf(.,r0)+0.005r r0 = 0.45r fill_color = vvlgrey </highlight> <highlight> file = data/8/microbe.separator.txt r1 = conf(.,r0)+0.005r r0 = 0.40r fill_color = vvlgrey </highlight> </highlights>
ideogram.conf
<ideogram> <spacing> default = 0u break = 0u </spacing> # thickness (px) of chromosome ideogram thickness = 20p stroke_thickness = 2 # ideogram border color stroke_color = black fill = yes # the default chromosome color is set here and any value # defined in the karyotype file overrides it fill_color = black # fractional radius position of chromosome ideogram within image radius = 0.85r show_label = no label_font = default label_radius = dims(ideogram,radius) + 0.05r label_size = 36 label_parallel = yes label_case = upper # cytogenetic bands band_stroke_thickness = 2 # show_bands determines whether the outline of cytogenetic bands # will be seen show_bands = yes # in order to fill the bands with the color defined in the karyotype # file you must set fill_bands fill_bands = yes </ideogram>
ticks.conf
show_ticks = yes show_tick_labels = yes show_grid = no grid_start = dims(ideogram,radius_inner)-0.5r grid_end = dims(ideogram,radius_inner) <ticks> skip_first_label = yes skip_last_label = no radius = dims(ideogram,radius_outer) tick_separation = 2p min_label_distance_to_edge = 0p label_separation = 5p label_offset = 5p label_size = 8p multiplier = 0.001 color = black thickness = 3p size = 20p <tick> size = 10p spacing = 1u color = black show_label = no label_size = 12p format = %.2f grid = no grid_color = lblue grid_thickness = 1p </tick> <tick> size = 15p spacing = 5u color = black show_label = yes label_size = 16p format = %s grid = yes grid_color = lgrey grid_thickness = 1p </tick> <tick> size = 18p spacing = 10u color = black show_label = yes label_size = 16p format = %s grid = yes grid_color = grey grid_thickness = 1p </tick> <tick> spacing = 100u color = black show_label = yes suffix = " kb" label_size = 36p format = %s grid = yes grid_color = dgrey grid_thickness = 1p </tick> </ticks>