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

4. Ordering

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;hs2;hs3;hs4;hs5;hs6;hs7;hs8

# absolute order - specify the order for all ideograms
chromosomes_order           = hs2,hs3,hs1,hs5,hs4,hs8,hs7,hs6

# relative order - 1 2 3 6 5 4 7 8
# why does hs6 appear before hs5? The order requires that hs4 
# come after hs5. In turn, the position of hs5 is its original position 
# (i.e. 5th ideogram). Since the position of hs4 has been reserved
# to come after hs5, the next unordered ideogram (hs6) is placed before
# hs5 to make hs5 the 5th ideogram.
#chromosomes_order = hs5,hs4

# relative order - 1 2 3 5 4 6 8 7
#chromosomes_order = hs3,hs5,hs4,hs6,hs8

# relative order 4 2 3 5 6 7 8 1
# chromosomes_order = ^,hs4,|,hs1,$

# relative order 4 2 6 7 5 3 8 1
#chromosomes_order = ^,hs4,|,hs5,hs3,|,hs1,$

# line below will give an error because there are more entries (9)
# in this ordered list than ideograms (8)
# chromosomes_order = ^,-,hs5,hs2,|,hs4,-,-,-,hs3,|,hs7,$

<<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 = 0.0025r
break   = 0.5r

</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>