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> karyotype = data/karyotype/karyotype.human.txt chromosomes_units = 1000000 chromosomes = hs1;hs2 chromosomes_breaks = -hs1:120-140 chromosomes_display_default = no track_width = 0.05 track_pad = 0.02 track_start = 0.95 <plots> type = heatmap # default file for all tracks file = data/6/snp.number.1mb.txt # a 9 color diverging spectral palette specified using a color list name color = spectral-9-div # referenced via conf(plots,color_alt) color_alt = black,spectral-8-div,grey # or the reverse list #color = spectral-9-div-rev # or you can even combine lists # color = ylorrd-9-seq-rev,ylgnbu-9-seq stroke_thickness = 1 stroke_color = black min = 1000 max = 5000 <plot> <<include r0r1.conf>> file = data/6/variation.heatmap.txt stroke_thickness = 0 min = 2000 max = 250000 </plot> <plot> <<include r0r1.conf>> scale_log_base = 0.5 </plot> <plot> <<include r0r1.conf>> scale_log_base = 1 # this is the default value </plot> <plot> <<include r0r1.conf>> scale_log_base = 2 </plot> <plot> <<include r0r1.conf>> scale_log_base = 3 </plot> <plot> <<include r0r1.conf>> scale_log_base = 5 </plot> <plot> <<include r0r1.conf>> color = conf(plots,color_alt) file = data/6/heatmap.step.txt pattern = hline,vline color_mapping = 0 # default min = 0 max = 10 stroke_thickness = 0 </plot> <plot> <<include r0r1.conf>> color = conf(plots,color_alt) file = data/6/heatmap.step.txt pattern = hline,solid,vline color_mapping = 1 min = 0 max = 10 stroke_thickness = 0 </plot> <plot> <<include r0r1.conf>> color = conf(plots,color_alt) file = data/6/heatmap.step.txt pattern = hline,solid,vline color_mapping = 2 min = 0 max = 10 stroke_thickness = 0 </plot> <plot> <<include r0r1.conf>> color = conf(plots,color_alt) file = data/6/heatmap.step.txt pattern = hline,checker,vline color_mapping = 2 min = 2 max = 8 stroke_thickness = 0 </plot> </plots> <<include etc/housekeeping.conf>> data_out_of_range* = trim
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
# set track radius values based on track counter
r1 = eval(sprintf("%fr",conf(track_start)-counter(plot)*(conf(track_width)+conf(track_pad))))
r0 = eval(sprintf("%fr",conf(track_start)-counter(plot)*(conf(track_width)+conf(track_pad))-conf(track_width)))
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>