# This is the main configuration file for the Circos tableviewer. This file also
# depends on colors.conf (definition on basic colors), ideogram.conf (size and spacing of
# row/cell segments), and ticks.conf (tick spacing and label definitions - these are turned
# off by default).
#
# In addition to these configuration files, the bin/make-conf script creates 
# colors.conf (colors of row/col segments) and colors_percentile.conf (colors based on
# cell percentile values). These configuration files are also included via the <<include>> directive.
#
# Some elements of the output image are toggled off by default (e.g. row and column highlights, 
# anchor links to segment labels, tick marks).

<colors>
<<include DATA_DIR/etc_colors.conf>>
<<include DATA_DIR/colors.conf>>
<<include DATA_DIR/colors_percentile.conf>>
</colors>

<fonts>
<<include DATA_DIR/fonts.conf>>
</fonts>

<<include DATA_DIR/ideogram.conf>>
<<include DATA_DIR/ticks.conf>>

karyotype = DATA_DIR/karyotype.txt

<image>
dir   = DATA_DIR
file  = circos.png
24bit = yes
svg   = no
png   = yes
pdf   = yes
# radius of inscribed circle in image
radius         = 1500p
background     = white
# by default angle=0 is at 3 o'clock position
angle_offset   = -180
auto_alpha_colors = yes
auto_alpha_steps  = 5
</image>

chromosomes_units              = 10
chromosomes_display_default    = yes
chromosomes_order_by_karyotype = yes

<highlights>

show = yes

<highlight>
show = no
file = DATA_DIR/row.txt
r0 = 1r+200p
r1 = 1r+220p
stroke_color = black
stroke_thickness = 2
</highlight>

<highlight>
show = no
file = DATA_DIR/col.txt
r0 = 1r+230p
r1 = 1r+250p
stroke_color = black
stroke_thickness = 2
</highlight>

<highlight>
show = no
file = DATA_DIR/all.txt
r0 = 1r+10p
r1 = 1r+35p
stroke_color = black
stroke_thickness = 2
</highlight>

</highlights>

<plots>

<plot>
type = text
file = DATA_DIR/segmentlabel.txt
label_font = condensedbold
color = black
label_size = 30p
r0   = 1r+50p
r1   = 1r+500p
rpadding = 0p
padding = 0p

show_links     = no
link_dims      = 0p,10p,32p,10p,5p
link_thickness = 3p
link_color     = black

label_snuggle             = no
# shift label up to its height in pixels in the angular direction
max_snuggle_distance      = 2r
snuggle_sampling          = 2
snuggle_tolerance         = 0.25r

</plot>

</plots>

<links>

<link cellvalues>
ribbon        = yes
flat          = yes
file          = DATA_DIR/cells.txt
bezier_radius = 0.0r
radius        = 0.999r-15p
thickness     = 1
color         = grey
stroke_color     = black
stroke_thickness = 1
<rules>

<rule>
importance = 95
condition  = 1
radius1    = 0.999r+2p
flow       = continue
</rule>

</rules>

</link>

</links>

#anglestep       = 0.5
#minslicestep    = 10
#beziersamples   = 40
#debug           = no
#warnings        = no
#imagemap        = no

#units_ok = bupr
#units_nounit = n

<<include DATA_DIR/housekeeping.conf>>