Circos > Documentation > Tutorials > Quick Start > Selection And Scale
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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.

1 — Quick Start

3. Ideogram Selection, Scale, Color & 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>>

<<include etc/image.conf>>                

<<include etc/colors_fonts_patterns.conf>> 

<<include etc/housekeeping.conf>> 



default = 0.005r

# 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



show_ticks          = yes
show_tick_labels    = yes

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

format           = %d

spacing        = 5u
size           = 10p

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