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.

5 — Tick Marks, Grids and Labels

7. Relative Ticks

circos.conf


<<include 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
# use this to see how relative ticks can be drawn relative to
# the ideograms (use rdivisor=ideogram in the tick blocks)
#chromosomes                 = hs1[a]:0-75;hs1[b]:100-150;hs1[c]:200-)
chromosomes = hs1
chromosomes_display_default = no

<<include etc/housekeeping.conf>>

bands.conf

show_bands            = no
fill_bands            = yes
band_stroke_thickness = 2
band_stroke_color     = white
band_transparency     = 0

ideogram.conf


<ideogram>

<spacing>
default = 0.01r
break   = 2u
</spacing>

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

radius*     = 0.75r

</ideogram>

ideogram.label.conf

show_label     = yes
label_font     = default
label_radius   = (dims(ideogram,radius_inner) + dims(ideogram,radius_outer))/2
label_center   = yes
label_size     = 72
label_with_tag = yes
label_parallel = yes
label_case     = upper

ideogram.position.conf

radius           = 0.90r
thickness        = 100p
fill             = no
fill_color       = black
stroke_thickness = 2
stroke_color     = black

ticks.conf


show_ticks          = yes
show_tick_labels    = yes

<ticks>

radius         = dims(ideogram,radius_outer)
multiplier     = 1/1u
color          = black
force_display  = yes
thickness      = 2p
show_label     = yes
format         = %d

size           = 20p
thicknes       = 4p
label_offset   = 5p

<tick>
show           = yes
spacing        = 1u
rspacing       = 0.02
# this is the default spacing type
spacing_type   = absolute
label_size     = 24p
</tick>

<tick>
# when spacing_type is relative, define
# rspacing to be the increment
show           = yes
rspacing       = 0.01
spacing_type   = relative
color          = red
label_size     = 30p
offset         = 85p
label_relative = yes
rmultiplier    = 100
suffix         = %
# This will make ticks spaced relatively by ideogram,
# and not chromosome. This setting is useful when
# the chromosome is displayed as multiple ideograms
# rdivisor        = ideogram
</tick>

<tick>
show           = yes
rspacing       = 0.1
spacing_type   = relative
thickness      = 3p
color          = blue
label_size     = 36p
offset         = 215p
label_relative = yes
rmultiplier    = 10
suffix         = /10
#rdivisor       = ideogram
</tick>

</ticks>