# 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 /home/ciruvis/public_html//results/result_format_rules_TOXhXJ18/colors.conf>>
<<include /home/ciruvis/public_html//results/result_format_rules_TOXhXJ18/colors_percentile.conf>>
</colors>

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

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

karyotype = /home/ciruvis/public_html//results/result_format_rules_TOXhXJ18/karyotype.txt

<image>
dir   = .
file  = tableview.png
24bit = yes
svg   = yes
png   = no
# radius of inscribed circle in image
radius         = 295p
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 = /home/ciruvis/public_html//results/result_format_rules_TOXhXJ18/row.txt
r0 = 1r+200p
r1 = 1r+220p
stroke_color = black
stroke_thickness = 2
</highlight>

<highlight>
show = no
file = /home/ciruvis/public_html//results/result_format_rules_TOXhXJ18/col.txt
r0 = 1r+230p
r1 = 1r+250p
stroke_color = black
stroke_thickness = 2
</highlight>

<highlight>
show = no
file = /home/ciruvis/public_html//results/result_format_rules_TOXhXJ18/all.txt
r0 = 1r+10p
r1 = 1r+35p
stroke_color = black
stroke_thickness = 2
</highlight>

<highlight>
file = /home/ciruvis/public_html//results/result_format_rules_TOXhXJ18/cap.col.txt
#r0   = 0.999r-30p
#r1   = 0.999r-10p
r0   = 0.999r-20p
r1   = 0.999r
stroke_color = black
stroke_thickness = 1
</highlight>

<highlight>
file = /home/ciruvis/public_html//results/result_format_rules_TOXhXJ18/cap.row.txt
r0   = 0.999r-20p
r1   = 0.999r
stroke_color = black
stroke_thickness = 1
</highlight>

</highlights>

<plots>

#<plot>
#type = text
#file = /home/ciruvis/public_html//results/result_format_rules_TOXhXJ18/segmentlabel.txt
#label_font = condensedbold
#color = black
#label_size = 18p #48p
#r0   = 1r+25p
#r1   = 1r+250p
#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          = /home/ciruvis/public_html//results/result_format_rules_TOXhXJ18/cells.txt
bezier_radius = 0.0r
radius        = 0.999r-20p # -30p
thickness     = 1
color         = grey
stroke_color     = grey
stroke_thickness = 0.5
<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