
################################################################
# Sample Circos configuration for multiple-alignments. The data
# files required are generated by tools/clustal2link/
#
# In addition to the data files produced by clustal2link
#
#   highlight.*.txt
#   links.txt
#   karyotype.txt
#
# you need to provide the following
#
# sequences.conf  - order of sequences for highlight tracks (all sequences except for reference)
# seq.colors.conf - RGB colors for each sequence

<<include sequences.conf>>

<colors>
<<include seq.colors.conf>>
</colors>

karyotype = karyotype.txt

chromosomes_units           = 1000
chromosomes_display_default = yes

# set this at command line
# > circos -param refseq=hsa8K
refseq = hsa8K

# reverse everything, except ID that matches /8/ (hsa8K).
chromosomes_reverse         = /./,-/conf(refseq)/

# order of chromosomes.
chromosomes_order           = hsa8K,celA,dmeA,dreB,dreA,ggaB,ggaA,rnoB,rnoA,hsaD,hsaA

# make hsa8K (e.g. reference sequence) to occupy 50% of the circle
chromosomes_scale           = conf(refseq):0.5r

# make segments of all sequences equal size
#chromosomes_scale           = /./=1rn

# crop out regions of the reference sequence
#chromosomes_breaks         = -hsa8K:4.2-7.8

<links>

<link>

ribbon = yes
file   = data/links.txt
radius = 0.99r
color  = black
bezier_radius = 0r
crest         = 0.2

<rules>
<rule>
# 1. color each link by its originating sequence color
# 2. set the z-value (depth) of the link to be proportional to 
#      negative of originating size. Small links (larger z-value) will therefore
#      be drawn on top of larger links (smaller z-value)
condition = 1
color     = eval(sprintf("%s_a2",lc var(chr1)))
radius2   = 0.79r
z         = eval(-var(size1))
</rule>
</rules>

</link>
</links>

# initial radius, width and padding of highlight tracks.

h_0     = 0.80
h_width = 0.015
h_pad   = 0.005

<plots>

<<include highlight.conf>>
<<include highlight.conf>>
<<include highlight.conf>>
<<include highlight.conf>>
<<include highlight.conf>>

<<include highlight.conf>>
<<include highlight.conf>>
<<include highlight.conf>>
<<include highlight.conf>>
<<include highlight.conf>>

</plots>

<image>
<<include etc/image.conf>>
angle_orientation = counterclockwise
</image>

<<include etc/colors_fonts_patterns.conf>>

<<include ideogram.conf>>
<<include ticks.conf>>

<<include etc/housekeeping.conf>>
