# 1.1 MINIMUM CIRCOS CONFIGURATION 
#
# This is a 'hello world' Circos tutorial. 
#
# Only required configuration elements are included.
#
# Subsequent tutorials in this section build on this example to
# generate a representative image with common elements found in Circos
# figures in the literature.

# Chromosome name, size and color definition
karyotype = fusiondata.txt

<links>
<link>
file          = fusionLinks.txt
radius        = 0.99r
color         = black_a4
ribbon = yes
stroke_color     = vdgrey
stroke_thickness = 2
flat = yes

# Curves look best when this value is small (e.g. 0.1r or 0r)
bezier_radius = 0r
thickness     = 1

# These parameters have default values. To unset them
# use 'undef'
#crest                = undef
#bezier_radius_purity = undef
</link>
</links>

# The <ideogram> block defines the position, size, labels and other
# properties of the segments on which data are drawn. These segments
# are usually chromosomes, but can be any integer axis.

<ideogram>
show_label = yes
label_font       = default
label_radius     = dims(ideogram,radius_outer) + 20p
label_with_tag   = yes
label_size       = 36
label_parallel   = no

<spacing>


# Spacing between ideograms. Suffix "r" denotes a relative value. It
# is relative to circle circumference (e.g. space is 0.5% of
# circumference).
default = 0.012r

# You can increase the spacing between specific ideograms.
#<pairwise hsY;hs1>
#spacing = 20r
#</pairwise>

</spacing>

# Ideogram position, thickness and fill. 
#
# Radial position within the image of the ideograms. This value is
# usually relative ("r" suffix).
radius           = 0.80r

# Thickness of ideograms, which can be absolute (e.g. pixels, "p"
# suffix) or relative ("r" suffix). When relative, it is a fraction of
# image radius.
thickness        = 50p

# Ideograms can be drawn as filled, outlined, or both. When filled,
# the color will be taken from the last field in the karyotype file,
# or set by chromosomes_colors. Color names are discussed in
#
# http://www.circos.ca/documentation/tutorials/configuration/configuration_files
#
# When stroke_thickness=0p or if the parameter is missing, the ideogram is
# has no outline and the value of stroke_color is not used.

fill             = yes  
stroke_color     = dgrey
stroke_thickness = 2p   

</ideogram>

################################################################
# The remaining content is standard and required. It is imported from
# default files in the Circos distribution.
#
# These should be present in every Circos configuration file and
# overridden as required. To see the content of these files, 
# look in etc/ in the Circos distribution.
#
# It's best to include these files using relative paths. This way, the
# files if not found under your current directory will be drawn from
# the Circos distribution. 
#
# As always, centralize all your inputs as much as possible.

<image>
# Included from Circos distribution.
<<include etc/image.conf>>          

# by default angle=0 is at 3 o'clock position
angle_offset = -90
</image>

# RGB/HSV color definitions, color lists, location of fonts, fill
# patterns. Included from Circos distribution.
#
# In older versions of Circos, colors, fonts and patterns were
# included individually. Now, this is done from a central file. Make
# sure that you're not importing these values twice by having
#
# *** DO NOT DO THIS ***
# <colors>
# <<include etc/colors.conf>>
# <colors>
# **********************
<<include etc/colors_fonts_patterns.conf>> 

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