
# 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 etc/colors.conf>>
<<include data/colors.conf>>
<<include data/colors_percentile.conf>>
</colors>

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

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

karyotype = data/karyotype.txt

<image>
dir   = img
file  = tableview.png
24bit = yes
svg   = yes
png   = 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>

chromosomes_units              = 10
chromosomes_display_default    = yes
chromosomes_order_by_karyotype = yes

<highlights>

show = yes

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

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

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

<highlight>
file = data/cap.col.txt
r0   = 0.999r-30p
r1   = 0.999r-10p
stroke_color = black
stroke_thickness = 1
</highlight>

<highlight>
file = data/cap.row.txt
r0   = 0.999r-20p
r1   = 0.999r
stroke_color = black
stroke_thickness = 1
</highlight>

</highlights>

<plots>

<plot>
type = text
file = data/segmentlabel.txt
label_font = condensedbold
color = black
label_size = 48p
r0   = 1r+100p
r1   = 1r+1000p
rpadding = 0p
padding = 0p

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

label_snuggle             = yes
# shift label up to its height in pixels in the angular direction
max_snuggle_distance      = 10r
snuggle_sampling          = 10
snuggle_tolerance         = 0.25r

</plot>

</plots>

<links>

<link cellvalues>
ribbon        = yes
flat          = yes
file          = data/cells.txt
bezier_radius = 0.0r
radius        = 0.999r-30p
thickness     = 1
color         = grey
stroke_color     = black
stroke_thickness = 1
<rules>

<rule>
importance = 95
condition  = 1
radius1    = 0.999r-20p
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

