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 = hs1;hs2;hs3 #chromosomes_reverse = hs2 chromosomes_display_default = no ################################################################ # # define 3 scatter plots, using the same data file # <plots> # all are scatter plots type = scatter stroke_thickness = 1 # first plot shows all points and selectively formats points at small/large # y-axis values to be red/green and triangles/rectangles <plot> file = data/6/snp.density.txt fill_color = grey stroke_color = black glyph = circle glyph_size = 10 max = 0.013 min = 0 r1 = 0.95r r0 = 0.65r # optional y0/y1 values (absolute or relative) in <background> blocks # define the start/end limits of background color # # y0 = 0.006 # y0 = 0.75r <backgrounds> <background> color = vvlgreen y0 = 0.006 </background> <background> color = vlgrey y1 = 0.006 y0 = 0.002 </background> <background> color = vvlred y1 = 0.002 </background> </backgrounds> <axes> <axis> color = lgreen thickness = 1 spacing = 0.05r y0 = 0.006 </axis> <axis> color = dgreen thickness = 2 spacing = 0.1r y0 = 0.006 </axis> <axis> color = lgrey thickness = 1 spacing = 0.05r y1 = 0.006 y0 = 0.002 </axis> <axis> color = dgrey thickness = 2 spacing = 0.1r y1 = 0.006 y0 = 0.002 </axis> <axis> color = lred thickness = 1 spacing = 0.05r y1 = 0.002 </axis> <axis> color = dred thickness = 2 spacing = 0.1r y1 = 0.002 </axis> </axes> <rules> <rule> condition = var(value) > 0.006 stroke_color = dgreen fill_color = green glyph = rectangle glyph_size = 8 </rule> <rule> condition = var(value) < 0.002 stroke_color = dred fill_color = red glyph = triangle </rule> </rules> </plot> # the second plot is a crop of the first plot, placed outside # the ideogram circle, showing only points with large y-values <plot> file = data/6/snp.density.txt fill_color = green stroke_color = dgreen glyph = rectangle glyph_size = 8 max = 0.013 min = 0.007 r1 = 1.175r r0 = 1.075r <backgrounds> # you can stack backgrounds by using transparent color <background> color = vlgreen_a4 y0 = 0.75r </background> <background> color = vlgreen_a4 y0 = 0.5r </background> <background> color = vlgreen_a4 y0 = 0.25r </background> <background> color = vlgreen_a4 </background> </backgrounds> <axes> <axis> color = green_a3 thickness = 2 spacing = 0.1r </axis> </axes> <rules> <rule> condition = var(value) < 0.007 show = no </rule> </rules> </plot> # the third plot is a crop of the first plot, placed closer to the # center of the circle, showing only points with small y-values <plot> file = data/6/snp.density.txt fill_color = red stroke_color = dred glyph = rectangle glyph_size = 8 max = 0.0015 min = 0.000 r1 = 0.60r r0 = 0.35r <backgrounds> <background> color = vlred_a4 y1 = 0.25r </background> <background> color = vlred_a4 y1 = 0.5r </background> <background> color = vlred_a4 y1 = 0.75r </background> <background> color = vlred_a4 </background> </backgrounds> <axes> <axis> color = red_a5 thickness = 1 spacing = 0.025r </axis> <axis> color = red_a3 thickness = 2 spacing = 0.1r </axis> </axes> <rules> <rule> condition = var(value) > 0.002 show = no </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 = yes show_tick_labels = yes <ticks> radius = dims(ideogram,radius_outer) orientation = out label_multiplier = 1e-6 color = black size = 20p thickness = 3p label_offset = 5p format = %d <tick> spacing = 1u show_label = no size = 10p </tick> <tick> spacing = 5u show_label = yes label_size = 20p size = 15p </tick> <tick> spacing = 10u show_label = yes label_size = 24p </tick> </ticks>