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>> <ideogram> band_url* = undef </ideogram> <<include ticks.conf>> karyotype = data/karyotype/karyotype.human.txt <image> <<include etc/image.conf>> ################################################################ # Here are the new image map parameters image_map_use = yes image_map_missing_parameter = removeurl #image_map_name = circos #image_map_file = circos-tutorial.html #image_map_protocol = http #image_map_xshift = 0 #image_map_yshift = 0 # original image is 3000 x 3000, resized for web at 800 x 800 image_map_xfactor = 0.266667 image_map_yfactor = 0.266667 image_map_overlay = yes #image_map_overlay_fill_color = lred_a5 image_map_overlay_stroke_color = red image_map_overlay_stroke_thickness = 2 </image> chromosomes_units = 1000000 #chromosomes = hs1:0-50 chromosomes_display_default = yes <<include etc/housekeeping.conf>>
show_bands = yes fill_bands = yes band_stroke_thickness = 2 band_stroke_color = white band_transparency = 3
<ideogram> <spacing> default = 0.005r break = 0.5r </spacing> <<include ideogram.position.conf>> <<include ideogram.label.conf>> <<include bands.conf>> #ideogram_url = http://www.google.com #ideogram_url = http://www.google.com/search?q=[chr] #ideogram_url = script?type=ideogram&start=[start]&end=[end]&length=[chrlength]&chr=[chr]&tag=[tag]&label=[label]&idx=[idx]&display_idx=[display_idx]&scale=[scale] #ideogram_url = script?chr=[chr] band_url = script?start=[start]&end=[end]&label=[label] </ideogram>
show_label = yes label_font = default label_radius = dims(image,radius) - 70p label_size = 48 label_parallel = yes label_case = upper
radius = 0.85r thickness = 100p fill = yes fill_color = black stroke_thickness = 2 stroke_color = black
show_ticks = yes show_tick_labels = yes show_grid = no <ticks> radius = dims(ideogram,radius_outer) label_offset = 10p multiplier = 1e-6 color = black <tick> spacing = 25u size = 10p thickness = 3p color = black show_label = yes label_size = 30p label_offset = 0p format = %d grid = yes grid_color = grey grid_thickness = 2p url = script?type=tick&chr=chr[label]&start=[start]&end=[end] map_size = 100p #map_radius_inner = 0.5r #map_radius_outer = 1.2r </tick> <tick> show = no spacing = 5u spacing_type = relative rspacing = 0.25 size = 10p radius = 0.9r thickness = 3p color = black show_label = yes label_size = 30p label_relative = yes label_offset = 0p format = %.0f rmultiplier = 100 suffix = % grid = yes grid_color = grey grid_thickness = 2p url = script?type=tick&chr=chr[label]&start=[start]&end=[end] map_size = -100p #map_radius_inner = 0.5r #map_radius_outer = 1.2r </tick> </ticks>