circos.conf.template

#####circos configure template for viewFusion.pl#####
#####Use system configures by circos at etc/#####
<<include etc/housekeeping.conf>>
#####define colors and fonts#####
<colors>
<<include etc/colors.conf>>
</colors>

<fonts>
<<include etc/fonts.conf>>
</fonts>


#####Define IDEOGRAM#####
<ideogram>
<spacing>
default = 10u
break   = 5u
</spacing>
# thickness (px) of chromosome ideogram
thickness        = 100p
stroke_thickness = 2
# ideogram border color
stroke_color     = black
fill             = yes
# the default chromosome color is set here and any value
# defined in the karyotype file overrides it
fill_color       = black

# fractional radius position of chromosome ideogram within image
radius         = 0.75r
show_label     = yes
label_with_tag = yes
label_font     = condensedbold
label_radius   = dims(ideogram,radius) - 0.2r
label_size     = 60p

# cytogenetic bands
band_stroke_thickness = 2
band_transparency     = 2

# show_bands determines whether the outline of cytogenetic bands
# will be seen
show_bands            = yes
# in order to fill the bands with the color defined in the karyotype
# file you must set fill_bands
fill_bands            = yes

</ideogram>


#####ticks configure######
show_ticks          = yes
show_tick_labels    = yes

<ticks>
skip_first_label = no
skip_last_label  = no
radius           = dims(ideogram,radius_outer)
tick_separation  = 3p
label_separation = 1p
#multiplier       = 1e-6
multiplier        =1/1u
color            = black
thickness        = 4p
size             = 20p

<tick>
spacing        = 1u
show_label     = no
thickness      = 2p
color          = dgrey
</tick>

<tick>
spacing        = 5u
show_label     = no
thickness      = 3p
color          = vdgrey
</tick>

<tick>
spacing        = 10u
show_label     = yes
label_size     = 20p
label_offset   = 10p
format         = %d
grid           = yes
grid_color     = dgrey
grid_thickness = 1p
grid_start     = 0.5r
grid_end       = 0.999r
#suffix         = Mb
</tick>

</ticks>

#Do not modify here, the viewFusion.pl will replace it according to $species and $build
karyotype=replacekaryotype

chromosomes_units           = 1000000
chromosomes_display_default = yes


#####Define image output#####
#####Both output png and svg format#####
<image>
dir = .
file  = circos-fusion.png
png = yes
svg = yes
# radius of inscribed circle in image
radius         = 1500p
background     = white
# by default angle=0 is at 3 o'clock position
angle_offset   = -90

auto_alpha_colors = yes
auto_alpha_steps  = 5
</image>


########Define link##################
# Links (bezier curves or straight lines) are defined in <links> blocks.
# Each link data set is defined within a <link>.
# As with highlights, parameters defined
# in the root of <links> affect all data sets and are considered
# global settings. Individual parameters value can be refined by
# values defined within <link> blocks, or additionally on each
# data line within the input file.

<links>
z      = 0
radius = 0.99r

bezier_radius = 0.05r

<link segdup>
show         = yes
color        = vvdgrey
thickness    = 5
#Do not modify here, the viewFusion.pl will generate the file named fusion-link.txt
file         = fusion-link.txt
#record_limit = 500

</link>

</links>


<plots>
<plot>
show=yes
type=text

#Do not modify here, the viewFusion.pl will generate the file named as fusion-gene.txt
file=fusion-gene.txt
color=black

r0=1r
r1=1r+400p

show_links     = yes
#link_dims      = 1p,1p,2p,1p,1p
link_dims      = 1p,1p,50p,1p,10p
link_thickness = 2p
link_color     = red

padding        = 0p
rpadding       = 0p

label_snuggle         = yes
max_snuggle_distance  = 4r
snuggle_tolerance     = 0r
snuggle_sampling      = 2
snuggle_link_overlap_test = yes
snuggle_link_overlap_tolerance = 0p
snuggle_refine        = yes
label_rotate = yes
label_size   = 30p
label_font   = condensed

</plot>
</plots>