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.
<colors> <<include etc/colors.conf>> </colors> <fonts> <<include etc/fonts.conf>> </fonts> <<include ideogram.conf>> <<include ticks.conf>> karyotype = data/karyotype.human.txt <image> dir = /tmp file = circos-tutorial.png # radius of inscribed circle in image radius = 1500p background = white # by default angle=0 is at 3 o'clock position angle_offset = -90 </image> chromosomes_units = 1000000 chromosomes = hs1 chromosomes_display_default = no <plots> <plot> type = text color = black file = data/6/text.genes.znf.txt # inside circle # r0 = 0.4r # r1 = 0.8r # on tick scale r0 = 1r r1 = 1r+200p show_links = yes link_dims = 0p,0p,50p,0p,10p #link_dims = 4p,4p,8p,4p,4p link_thickness = 2p link_color = red label_size = 24p label_font = condensed padding = 0p rpadding = 0p </plot> </plots> anglestep = 0.5 minslicestep = 10 beziersamples = 40 debug = no warnings = no imagemap = no # don't touch! units_ok = bupr units_nounit = n
<ideogram> <spacing> default = 3u break = 3u 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 = 100p 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 = condensedbold label_radius = dims(ideogram,radius) + 0.075r label_size = 60p # 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>
show_ticks = yes show_tick_labels = yes <ticks> radius = dims(ideogram,radius_outer) multiplier = 1e-6 <tick> spacing = 0.1u size = 3p thickness = 2p color = black show_label = no label_size = 10p label_offset = 0p format = %.1f </tick> <tick> spacing = 1u size = 4p thickness = 2p color = black show_label = yes label_size = 16p label_offset = 0p format = %d </tick> <tick> spacing = 5u size = 6p thickness = 2p color = black show_label = yes label_size = 16p label_offset = 0p format = %d </tick> <tick> spacing = 10u size = 8p thickness = 2p color = black show_label = yes label_size = 20p label_offset = 5p format = %d </tick> </ticks>