1 — Quick Start

3. Ideogram Selection, Scale, Color & Orientation

circos.conf

# 1.3 IDEOGRAM SELECTION, SCALE, COLOR AND ORIENTATION
#
# This tutorial shows you how to select which chromosomes to draw and
# flexibly arrange them in the image by applying custom scaling and
# colors.

karyotype = data/karyotype/karyotype.human.txt
chromosomes_units = 1000000

# The default behaviour is to display all chromosomes defined in the
# karyotype file. In this example, I select only a subset.
#
# The 'chromosomes' parameter has several uses, and selecting which
# chromosomes to show is one of them. You can list them
#
# hs1;hs2;hs3;hs4
#
# or provide a regular expression that selects them based on a successful match
#
# /hs[1-4]$/
#
# The $ anchor is necessary, otherwise chromosomes like hs10, hs11 and
# hs20 are also matched.

chromosomes_display_default = no
chromosomes                 = /hs[1-4]$/

# The size of the ideogram on the figure can be adjusted using an
# absolute or relative magnification. Absolute scaling,
#
# hs1=0.5
#
# shrinks or expands the ideogram by a fixed factor. When the "r"
# suffix is used, the magnification becomes relative to the
# circumference of the figure. Thus, 
#
# hs1=0.5r 
#
# makes hs1 to occupy 50% of the figure. To uniformly distribute
# several ideogram within a fraction of the figure, use a regular
# expression that selects the ideograms and the "rn" suffix (relative
# normalized).
#
# /hs[234]/=0.5rn
#
# Will match hs2, hs3, hs4 and divide them evenly into 50% of the figure. Each ideogram will be about 16% of the figure.

chromosomes_scale   = hs1=0.5r,/hs[234]/=0.5rn

# By default, the scale progression is clockwise. You can set the
# global angle progression using 'angle_orientation' in the <image>
# block (clockwise or counterclockwise). To reverse it for one or
# several ideograms, use 'chromosomes-reverse'

chromosomes_reverse = /hs[234]/

# The color of each ideogram is taken from the karyotype file. To
# change it, use 'chromosomes_color'.

chromosomes_color   = hs1=red,hs2=orange,hs3=green,hs4=blue

# The default radial position for all ideograms is set by 'radius' in
# the <ideogram> block (see ideogram.conf). To change the value for
# specific ideograms, use chromosomes_radius.

chromosomes_radius  = hs4:0.9r

<<include ideogram.conf>>

<<include ticks.conf>>

<image>
<<include etc/image.conf>>                
</image>

<<include etc/colors_fonts_patterns.conf>> 

<<include etc/housekeeping.conf>> 

ideogram.conf

<ideogram>

<spacing>
default = 0.005r
</spacing>

# Ideogram position, fill and outline
radius           = 0.90r
thickness        = 20p
fill             = yes
stroke_color     = dgrey
stroke_thickness = 2p

# Minimum definition for ideogram labels.

show_label       = yes
# see etc/fonts.conf for list of font names
label_font       = default 
label_radius     = 1.075r  # if ideogram radius is constant, and you'd like labels close to image edge, 
                           # use the dims() function to access the size of the image
                           # label_radius  = dims(image,radius) - 60p
label_size       = 30
label_parallel   = yes

</ideogram>

ticks.conf

show_ticks          = yes
show_tick_labels    = yes

<ticks>
radius           = 1r
color            = black
thickness        = 2p

# the tick label is derived by multiplying the tick position
# by 'multiplier' and casting it in 'format':
#
# sprintf(format,position*multiplier)
#

multiplier       = 1e-6

# %d   - integer
# %f   - float
# %.1f - float with one decimal
# %.2f - float with two decimals
#
# for other formats, see http://perldoc.perl.org/functions/sprintf.html

format           = %d

<tick>
spacing        = 5u
size           = 10p
</tick>

<tick>
spacing        = 25u
size           = 15p
show_label     = yes
label_size     = 20p
label_offset   = 10p
format         = %d
</tick>

</ticks>