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 ideogram.conf>> chromosomes_units = 100 <<include ticks.conf>> <image> angle_offset* = -87 <<include etc/image.conf>> </image> ### single genomes karyotype = data/segments.txt <<include segment.order.conf>> chromosomes_reverse = /.*-l/ ### # HEATMAPS # If you aren't using heatmaps in your image (you have no measures associated with # parcelation regions), remove this section. Also turn of grids in etc/ticks.conf. hm_r = 0.96 hm_w = 0.025 hm_pad = 0.005 #hm_colors = greys-4-seq,greys-4-seq,greys-4-seq,greys-4-seq,greys-4-seq hm_colors = reds-4-seq,oranges-4-seq,greens-4-seq,blues-4-seq,purples-4-seq # HEATMAPS ### <plots> # Remove these lines if you don't have heatmaps. <<include heatmap.conf>> <<include heatmap.conf>> <<include heatmap.conf>> <<include heatmap.conf>> <<include heatmap.conf>> <plot> type = text file = data/structure.label.txt color = black label_font = default label_size = 20 r0 = 1r r1 = 1.5r rpadding = 10p </plot> </plots> <links> <link> file = data/links.txt # If you don't have heatmaps, change radius to # radius = dims(ideogram,radius_inner) radius = 0.825r # eval(sprintf("%fr",conf(hm_r)-counter(heatmap)*(conf(hm_w)+conf(hm_pad))+conf(hm_w))) bezier_radius = 0r bezier_radius_purity = 0.5 crest = 0.25 thickness = 2 color = black <rules> <rule> # this rule is part of variant #1 # to use it, set use=yes and also adjust radius above to 0.7r use = no condition = var(chr1) eq var(chr2) bezier_radius = 1r radius = 0.71r flow = continue </rule> <rule> condition = 1 thickness = eval(remap_int(var(score),0,1,1,5)) flow = continue </rule> <rule> condition = var(type) == 0 color = eval(sprintf("greys-5-seq-%d",remap_int(var(score),0,1,1,5))) </rule> <rule> condition = var(type) == 1 color = eval(sprintf("reds-5-seq-%d",remap_int(var(score),0,1,1,5))) </rule> </rules> </link> </links> <<include etc/colors_fonts_patterns.conf>> <colors> <<include color.brain.conf>> </colors> restrict_parameter_names* = no <<include etc/housekeeping.conf>>
show_bands = yes fill_bands = yes band_stroke_thickness = 1 band_stroke_color = black band_transparency = 0
trfpogs = 255,153,153 fmargs = 204,0,51 mfs = 255,153,51 lors = 102,0,0 sbors = 255,51,102 ors = 255,204,204 rg = 255,204,153 inffgorp = 153,51,0 mfg = 255,255,51 org = 255,255,153 inffgtrip = 255,0,0 inffs = 153,102,0 medors = 255,102,0 supfg = 255,102,102 supfs = 204,153,0 inffgopp = 255,204,0 infprcs = 255,153,0 supprcs = 255,0,102 prcg = 204,102,0 sbcgs = 255,102,153 cs = 255,51,0 alshorp = 0,255,204 acirins = 102,255,255 alsverp = 0,255,255 shoing = 51,255,204 supcirins = 0,153,153 loingcins = 0,204,204 infcirins = 0,102,102 posls = 204,255,255 acggs = 255,255,180 macggs = 255,240,191 sbcag = 255,153,200 percas = 255,164,200 mposcggs = 255,224,203 cgsmarp = 255,192,201 posdcgg = 255,175,201 posvcgg = 255,208,202 tpo = 255,204,255 popl = 204,153,255 suptglp = 153,51,255 hg = 102,0,102 atrcos = 153,0,204 trts = 255,153,255 mtg = 255,102,204 tpl = 153,0,153 inftg = 255,0,255 infts = 204,0,153 supts = 204,51,255 poscg = 204,255,204 sumarg = 204,255,102 pacls = 204,255,153 poscs = 153,255,0 js = 153,204,0 sbps = 102,153,0 intpstrps = 51,255,51 suppl = 153,255,153 prcun = 204,255,0 angg = 0,255,0 pocs = 204,255,51 pahipg = 204,204,255 coslins = 153,204,255 locts = 153,153,255 fug = 102,102,255 ccs = 102,153,255 ling = 102,204,255 aocs = 51,51,255 infocgs = 51,153,255 supocstrocs = 0,102,255 postrcos = 51,102,255 cun = 0,153,255 mocg = 0,204,244 mocslus = 0,51,255 supocg = 0,0,255 ocpo = 0,0,153 pu = 32,32,32 pal = 64,64,64 can = 96,96,96 nacc = 128,128,128 amg = 159,159,159 tha = 191,191,191 hip = 223,223,223 ceb = 255,64,0 bst = 207,255,48
<plot> type = heatmap file = data/measure.counter(heatmap).txt color = eval((split(",","conf(hm_colors)"))[counter(heatmap)]) r1 = eval(sprintf("%fr",conf(hm_r)-counter(heatmap)*(conf(hm_w)+conf(hm_pad)))) r0 = eval(sprintf("%fr",conf(hm_r)-counter(heatmap)*(conf(hm_w)+conf(hm_pad))+conf(hm_w))) stroke_color = white stroke_thickness = 3 </plot>
<ideogram> <spacing> default = 0.005r <pairwise fro-l fro-r> spacing = 5r </pairwise> </spacing> <<include ideogram.position.conf>> <<include ideogram.label.conf>> <<include bands.conf>> </ideogram>
show_label = yes label_font = default label_radius = dims(image,radius)-30p label_size = 24 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("region %s",var(label)))
radius = 0.85r thickness = 75p fill = no stroke_thickness = 1 stroke_color = black
chromosomes_order = fro-r,ins-r,lim-r,tem-r,par-r,occ-r,sbc-r,ceb-r,bst,ceb-l,sbc-l,occ-l,par-l,tem-l,lim-l,ins-l,fro-l
show_ticks = yes show_tick_labels = yes show_grid = yes <ticks> radius = dims(ideogram,radius_outer) color = black thickness = 2p size = 0 <tick> spacing = 0.5u size = 5p grid = yes grid_color = black grid_thickness = 1p grid_start = 1r-conf(ideogram,thickness) grid_end = 0.825r </tick> <tick> spacing = 1u </tick> </ticks>