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
3. Labeling Karyotype Bands
circos.conf
<<include etc/colors_fonts_patterns.conf>> <<include ideogram.conf>> <<include ticks.conf>> karyotype = data/karyotype/karyotype.human.txt <image> <<include etc/image.conf>> </image> chromosomes_units = 1000000 chromosomes = /hs([1-9]|10)$/ chromosomes_display_default = no <plots> <plot> type = text color = red file = data/8/text.bands.txt r0 = 1r r1 = 1r+300p label_size = 12 label_font = condensed show_links = yes link_dims = 0p,2p,6p,2p,5p link_thickness = 2p link_color = black label_snuggle = yes max_snuggle_distance = 1r snuggle_tolerance = 0.25r snuggle_sampling = 2 snuggle_refine = yes <rules> <rule> condition = on(hs1) color = blue flow = continue </rule> <rule> condition = var(start) > 50mb && var(end) < 100mb color = green flow = continue </rule> <rule> condition = var(value) =~ /[.]\d\d/ color = grey </rule> </rules> </plot> </plots> <<include etc/housekeeping.conf>>
ideogram.conf
<ideogram> <spacing> default = 5u break = 1u 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 = 3 thickness = 1.5r </break> </spacing> # thickness (px) of chromosome ideogram thickness = 30p 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 = yes label_with_tag = yes label_font = default label_radius = dims(ideogram,radius) + 175p label_size = 30p 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 <ticks> radius = dims(ideogram,radius_outer)+120p multiplier = 1e-6 <tick> spacing = 0.5u size = 3p thickness = 1p color = black show_label = no label_size = 16p label_offset = 0p format = %d </tick> <tick> spacing = 5u size = 5p thickness = 2p color = black show_label = no label_size = 16p label_offset = 0p format = %d </tick> <tick> spacing = 10u size = 8p thickness = 2p color = black show_label = yes label_size = 12p label_offset = 5p format = %d </tick> </ticks>