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.

3 — Drawing Ideograms

5. Cropping

circos.conf


<<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_display_default = no

# to explicitly define what is drawn
#chromosomes                  = hs1:0-100;hs2:50-150;hs3:50-100;hs4;hs5;hs6;hs7;hs8

# use chromosomes_breaks to indicate which regions you want to supress
#chromosomes        = hs1;hs2;hs3;hs4;hs5;hs6;hs7;hs8
#chromosomes_breaks = -hs1:100-200;-hs2:0-50;-hs2:150-);-hs3:0-50

# combine region declarations and breaks
chromosomes = hs1:0-100;hs2:0-100;hs3:0-100;hs4:0-100;hs5;hs6;hs7;hs8
chromosomes_breaks = -hs1:25-75;-hs2:25-75;-hs3:25-75;-hs4:25-75;-hs5:75-);-hs6:0-10,75-);-hs7:75-);-hs8:75-)

<<include etc/housekeeping.conf>>

bands.conf

show_bands            = yes
fill_bands            = yes
band_stroke_thickness = 2
band_stroke_color     = white
band_transparency     = 4

ideogram.conf


<ideogram>

<spacing>

default = 0.005r
break   = 0.5r

axis_break_at_edge = yes
axis_break         = yes
axis_break_style   = 2

<break_style 1>
stroke_color     = black
fill_color       = blue
thickness        = 0.25r
stroke_thickness = 2p
</break>

<break_style 2>
stroke_color     = black
stroke_thickness = 5p
thickness        = 2r
</break>

</spacing>

<<include ideogram.position.conf>>
<<include ideogram.label.conf>>
<<include bands.conf>>

</ideogram>

ideogram.label.conf

show_label       = yes
label_font       = bold
# labels outside circle
#label_radius     = dims(ideogram,radius) + 0.05r
#labels inside circle
label_radius     = dims(ideogram,radius) - 0.15r
label_with_tag   = yes
label_size       = 48
label_parallel   = yes
label_case       = upper

ideogram.position.conf

radius           = 0.90r
thickness        = 100p
fill             = yes
fill_color       = black
stroke_thickness = 2
stroke_color     = black

ticks.conf


show_ticks          = yes
show_tick_labels    = yes

<ticks>
skip_first_label = no
skip_last_label  = no
radius           = dims(ideogram,radius_outer)
tick_separation  = 3p
label_separation = 1p
multiplier       = 1e-6
color            = black
thickness        = 4p
size             = 20p

<tick>
spacing        = 1u
show_label     = no
thickness      = 2p
color          = dgrey
</tick>

<tick>
spacing        = 5u
show_label     = no
thickness      = 3p
color          = vdgrey
</tick>

<tick>
spacing        = 10u
show_label     = yes
label_size     = 20p
label_offset   = 10p
format         = %d
grid           = yes
grid_color     = dgrey
grid_thickness = 1p
grid_start     = 0.5r
grid_end       = 0.999r
</tick>

</ticks>