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.
4 — Highlights
7. Recipe 2 - Focusing on a Genome Region
circos.conf
<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 # first image #chromosomes = hs1;hs2;hs3 #chromosomes_breaks = -hs1:120-145;-hs1:180-200 #chromosomes_display_default = no # second image chromosomes = hs1;hs2;hs3;hs13;hs14;hs15 <highlights> z = 5 # For the first image, the same highlight set is # drawn both inside and outside the ideogram # circle. Another highlight set is layered # on top of the outer highlight set. #<highlight> #file = data/3/chr.highlights.txt #r0 = 0.5r #r1 = 1r #</highlight> #<highlight> #file = data/3/chr.highlights.txt #stroke_thickness = 2 #stroke_color = black #r0 = 1.1r #r1 = 1.15r #</highlight> #<highlight> #file = data/3/chr.hetero.highlights.txt #stroke_thickness = 2 #stroke_color = black #fill_color = white #r0 = 1.1r #r1 = 1.15r #z = 10 #</highlight> # In the second image, selected regions of the # genome are singled out using several highlights. # Note that highlights do not radially cross the # ideograms. Highlights with r0 < 1 < r1 are not # supported (Circos will not always behave well in # these cases). <highlight> file = data/3/highlights.few.txt r0 = 0.5r r1 = 1r fill_color = lgrey </highlight> <highlight> file = data/3/highlights.few.txt r0 = 1r r1 = 1.10r fill_color = lyellow </highlight> <highlight> file = data/3/highlights.few.txt r0 = 1.10r r1 = 1.15r fill_color = lgrey </highlight> </highlights> anglestep = 0.025 minslicestep = 5 beziersamples = 40 debug = no warnings = no imagemap = no units_ok = bupr units_nounit = n
ideogram.conf
<ideogram> <spacing> default = 3u 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 = 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) + 0.05r label_size = 48 # 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 = yes grid_start = 0.5r grid_end = 1.0r <ticks> skip_first_label = no skip_last_label = no radius = dims(ideogram,radius_outer) tick_separation = 2p min_label_distance_to_edge = 10p label_separation = 5p label_offset = 2p label_size = 8p multiplier = 1e-6 color = black <tick> spacing = 1u size = 6p thickness = 1p color = black show_label = no label_size = 16p label_offset = 0p format = %.2f grid = no grid_color = grey grid_thickness = 1p </tick> <tick> spacing = 5u size = 10p thickness = 1p color = black show_label = yes label_size = 16p label_offset = 0p format = %d grid = yes grid_color = grey grid_thickness = 2p </tick> <tick> spacing = 10u size = 16p thickness = 2p color = black show_label = yes label_size = 16p label_offset = 0p format = %d grid = yes grid_color = vdgrey grid_thickness = 2p </tick> </ticks>