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.
9 — Recipes
5. Image Transparency and Background
circos.conf
<colors> <<include etc/colors.conf>> </colors> <fonts> <<include etc/fonts.conf>> </fonts> <<include ideogram.conf>> <<include ticks.conf>> karyotype = data/8/karyotype.microbe.txt <image> dir = /tmp file = circos-tutorial.png # radius of inscribed circle in image radius = 1500p # specify a color or image # to make the background transparent, use "transparent" background = data/8/background.png # by default angle=0 is at 3 o'clock position angle_offset = -90 </image> chromosomes_units = 1000 chromosomes_display_default = yes <highlights> <highlight> file = data/8/microbe.highlights.1.txt r0 = 0.95r r1 = 0.98r </highlight> <highlight> file = data/8/microbe.highlights.13.txt r0 = 0.91r r1 = 0.94r </highlight> <highlight> file = data/8/microbe.highlights.14.txt r0 = 0.86r r1 = 0.90r </highlight> <highlight> file = data/8/microbe.highlights.2.txt r0 = 0.82r r1 = 0.85r </highlight> <highlight> file = data/8/microbe.highlights.4.txt r0 = 0.53r r1 = 0.54r </highlight> <highlight> file = data/8/microbe.highlights.5.txt r0 = 0.51r r1 = 0.52r </highlight> <highlight> file = data/8/microbe.highlights.6.txt r0 = 0.46r r1 = 0.47r </highlight> <highlight> file = data/8/microbe.highlights.7.txt r0 = 0.48r r1 = 0.49r </highlight> <highlight> file = data/8/microbe.highlights.8.txt r0 = 0.41r r1 = 0.42r </highlight> <highlight> file = data/8/microbe.highlights.9.txt r0 = 0.43r r1 = 0.44r </highlight> <highlight> file = data/8/microbe.highlights.10.txt r0 = 0.19r r1 = 0.20r </highlight> <highlight> file = data/8/microbe.highlights.19.txt r0 = 0.21r r1 = 0.22r </highlight> <highlight> file = data/8/microbe.highlights.20.txt r0 = 0.23r r1 = 0.24r </highlight> <highlight> file = data/8/microbe.highlights.21.txt r0 = 0.25r r1 = 0.265r </highlight> <highlight> file = data/8/microbe.highlights.22.txt r0 = 0.275r r1 = 0.29r </highlight> <highlight> file = data/8/microbe.highlights.23.txt r0 = 0.30r r1 = 0.32r </highlight> <highlight> file = data/8/microbe.highlights.24.txt r0 = 0.33r r1 = 0.355r </highlight> <highlight> file = data/8/microbe.highlights.25.txt r0 = 0.365r r1 = 0.395r </highlight> <highlight> file = data/8/microbe.highlights.11.txt r0 = 0.17r r1 = 0.18r </highlight> <highlight> file = data/8/microbe.highlights.12.txt r0 = 0.15r r1 = 0.16r </highlight> <highlight> file = data/8/microbe.highlights.15.txt r0 = 0.72r r1 = 0.78r </highlight> <highlight> file = data/8/microbe.highlights.16.txt r0 = 0.56r r1 = 0.60r </highlight> <highlight> file = data/8/microbe.highlights.17.txt r0 = 0.615r r1 = 0.635r </highlight> <highlight> file = data/8/microbe.highlights.18.txt r0 = 0.65r r1 = 0.69r </highlight> <highlight> file = data/8/microbe.highlights.26.txt r0 = 0.65r r1 = 0.69r </highlight> <highlight> file = data/8/microbe.separator.txt r0 = 0.80r r1 = 0.805r fill_color = vvlgrey </highlight> <highlight> file = data/8/microbe.separator.txt r0 = 0.70r r1 = 0.705r fill_color = vvlgrey </highlight> <highlight> file = data/8/microbe.separator.txt r0 = 0.55r r1 = 0.555r fill_color = vvlgrey </highlight> <highlight> file = data/8/microbe.separator.txt r0 = 0.50r r1 = 0.505r fill_color = vvlgrey </highlight> <highlight> file = data/8/microbe.separator.txt r0 = 0.45r r1 = 0.455r fill_color = vvlgrey </highlight> <highlight> file = data/8/microbe.separator.txt r0 = 0.40r r1 = 0.405r fill_color = vvlgrey </highlight> </highlights> anglestep = 0.5 minslicestep = 10 beziersamples = 40 debug = no warnings = no imagemap = no # don't touch! units_ok = bupr units_nounit = n
ideogram.conf
<ideogram> <spacing> default = 0u break = 0u #<pairwise a;b> #spacing = 5u #</pairwise> #<pairwise b;c> #spacing = 10u #</pairwise> #<pairwise c;d> #spacing = 20u #</pairwise> </spacing> # thickness (px) of chromosome ideogram thickness = 20p 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 = no label_font = condensedbold label_radius = dims(ideogram,radius) + 0.05r label_size = 36 # 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 = no grid_start = dims(ideogram,radius_inner)-0.5r grid_end = dims(ideogram,radius_inner) <ticks> skip_first_label = yes skip_last_label = no radius = dims(ideogram,radius_outer) tick_separation = 2p min_label_distance_to_edge = 0p label_separation = 5p label_offset = 2p label_size = 8p multiplier = 0.001 color = black <tick> spacing = 1u size = 3p thickness = 2p color = black show_label = no label_size = 12p label_offset = 0p format = %.2f grid = no grid_color = lblue grid_thickness = 1p </tick> <tick> spacing = 5u size = 5p thickness = 1p color = black show_label = yes label_size = 16p label_offset = 0p format = %s grid = yes grid_color = lgrey grid_thickness = 1p </tick> <tick> spacing = 10u size = 8p thickness = 2p color = black show_label = yes label_size = 16p label_offset = 0p format = %s grid = yes grid_color = grey grid_thickness = 1p </tick> <tick> spacing = 100u size = 8p thickness = 2p color = black show_label = yes suffix = " kb" label_size = 36p label_offset = 5p format = %s grid = yes grid_color = dgrey grid_thickness = 1p </tick> </ticks>