2 — Drawing Ideograms

1. Ideograms

circos.conf

# MINIMUM CIRCOS CONFIGURATION 
#
# The 'hello world' Circos tutorial. Only required
# configuration elements are included.
#
# Common optional elements are commented out.

# Defines unit length for ideogram and tick spacing, referenced
# using "u" prefix, e.g. 10u
#chromosomes_units           = 1000000

# Show all chromosomes in karyotype file. By default, this is
# true. If you want to explicitly specify which chromosomes
# to draw, set this to 'no' and use the 'chromosomes' parameter.
# chromosomes_display_default = yes

# Chromosome name, size and color definition
karyotype = data/karyotype/karyotype.human.txt

<ideogram>

<spacing>
# spacing between ideograms
default = 0.005r
</spacing>

# ideogram position, thickness and fill
radius           = 0.90r
thickness        = 10p
fill             = yes

#stroke_thickness = 1
#stroke_color     = black

# ideogram labels
# <<include ideogram.label.conf>>

# ideogram cytogenetic bands, if defined in the karyotype file
# <<include bands.conf>>

</ideogram>

# image size, background color, angular position
# of first ideogram, transparency levels, output
# file and directory
#
# it is best to include these parameters from etc/image.conf
# and override any using param* syntax
#
# e.g.
# <image>
# <<include etc/image.conf>>
# radius* = 500
# </image>
<image>
<<include etc/image.conf>> # included from Circos distribution 
</image>

# RGB/HSV color definitions, color lists, location of fonts,
# fill patterns
<<include etc/colors_fonts_patterns.conf>> # included from Circos distribution

# debugging, I/O an dother system parameters
<<include etc/housekeeping.conf>> # included from Circos distribution

# <ticks> blocks to define ticks, tick labels and grids
#
# requires that chromosomes_units be defined
#
# <<include ticks.conf>>

bands.conf

# optional

show_bands            = yes
fill_bands            = yes
band_transparency     = 4

ideogram.label.conf

# optional

show_label       = yes
label_radius     = dims(ideogram,radius) + 0.075r
label_size       = 24
label_parallel   = yes

ticks.conf

# ticks are optional

show_ticks          = yes
show_tick_labels    = yes

<ticks>
radius           = dims(ideogram,radius_outer)
multiplier       = 1e-6
color            = black
thickness        = 2p
size             = 15p

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

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

</ticks>