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 etc/colors_fonts_patterns.conf>> <<include ideogram.conf>> <<include ticks.conf>> <image> <<include etc/image.conf>> </image> chromosomes_units = 10 chromosomes_display_default = yes chromosomes_scale = g1=0.45,s=0.35,g2=0.15,m=0.05 karyotype = phases.txt palette = greys-6-seq <phases> g1 = 3 s = 4 g2 = 5 m = 6 </phases> chromosomes_color = g1=conf(palette)-conf(phases,g1),s=conf(palette)-conf(phases,s),g2=conf(palette)-conf(phases,g2),m=conf(palette)-conf(phases,m) #don't show phase m chromosomes = -m <links> # connections between genes <link> file = links.txt radius = 0.95r bezier_radius = 0r # shorter links will be drawn closer # to the edge of the circle bezier_radius_purity = 0.1 crest = 1 thickness = 3 <rules> <rule> condition = var(type) == 1 color = red </rule> <rule> condition = var(type) == 2 color = blue </rule> </rules> </link> </links> <plots> <plot> # gene labels type = text file = genes.txt r0 = 0.95r r1 = 1.5r label_size = 36 label_font = bold show_links = yes link_dims = 0p,200p,20p,10p,20p link_thickness = 3 link_color = black <rules> <rule> condition = 1 value = eval(var(name)) </rule> </rules> </plot> <plot> # circular glyph at start of gene label type = scatter file = genes.txt r0 = 0.95r r1 = 0.95r glyph = circle glyph_size = 36 color = white stroke_color = black stroke_thickness = 2 <rules> <rule> condition = var(type) == 1 color = blues-5-seq-4 </rule> <rule> condition = var(type) == 2 color = reds-5-seq-4 </rule> </rules> </plot> </plots> <<include etc/housekeeping.conf>> restrict_parameter_names* = no
<ideogram> <spacing> default = 0.005r </spacing> <<include ideogram.position.conf>> <<include ideogram.label.conf>> </ideogram>
show_label = yes label_font = bold label_radius = (dims(ideogram,radius_inner)+dims(ideogram,radius_outer)-conf(ideogram,label_size))/2 label_with_tag = yes label_size = 72 label_color = white label_parallel = yes label_case = upper # you can format the label by using properties # of the ideogram, accessible with var(PROPERTY): # # chr, chr_with_tag, chrlength, display_idx, end, idx, # label, length, reverse, scale, size, start, tag #label_format = eval(sprintf("chr%s",var(label)))
radius = 0.90r thickness = 100p fill = yes fill_color = black stroke_thickness = 2 stroke_color = dgrey
show_ticks = yes show_tick_labels = yes show_grid = yes <ticks> radius = dims(ideogram,radius_outer) color = dgrey thickness = 2p size = 15p grid = yes grid_start = dims(ideogram,radius_outer) grid_end = dims(ideogram,radius_inner) grid_color = white spacing_type = relative label_relative = yes format = %d rmultiplier = 100 suffix = % <tick> rspacing = 0.05 grid_thickness = 1p </tick> <tick> rspacing = 0.10 show_label = yes label_size = 26p label_offset = 5p grid_thickness = 2p </tick> </ticks>