Circos > Documentation > Tutorials > Recipes > Copy Number Data
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Circos at the EMBO NGS workshop in Tunis, Sept 15–25.

Use the latest version of Circos and read Circos best practices—these list recent important changes and identify sources of common problems.
If you are having trouble, post your issue to the Circos Google Group and include all files and detailed error logs. Please do not email me directly unless it is urgent—you are much more likely to receive a timely reply from the group.
Don't know what question to ask? Read Points of View: Visualizing Biological Data by Bang Wong, myself and invited authors from the Points of View series.

8 — Recipes

13. Copy Number Data

circos.conf


<<include etc/colors_fonts_patterns.conf>>

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

<image>
<<include etc/image.conf>>
</image>

karyotype = data/karyotype/karyotype.human.txt

chromosomes_units           = 1000000
chromosomes                 = -hsX;-hsY
chromosomes_display_default = yes

<plots>

# Data out of bounds should be hidden. Otherwise the
# default is to clip the data to range min/max.
range = hide

# scatter plot for values [-3,0]
<plot>
type = scatter
file = data/8/13/data.cnv.txt
r0   = 0.6r
r1   = 0.75r
min  = -3
max  = 0
glyph = circle
glyph_size = 8
color = red

<axes>
<axis>
color     = lred
thickness = 2
spacing   = 0.1r
</axis>
</axes>

<backgrounds>
<background>
color = vlred_a5
</background>
</backgrounds>

<rules>
<rule>
condition  = 1
glyph_size = eval( 6 + 4*abs(var(value)))
flow       = continue
</rule>
<rule>
condition  = var(value) < -2
stroke_color = black
stroke_thickness = 2
</rule>
</rules>
</plot>

# scatter plot for values [0,3]
<plot>
type = scatter
file = data/8/13/data.cnv.txt
r0   = 0.75r
r1   = 0.9r
min  = 0
max  = 3
glyph = circle
glyph_size = 8
color = green

<axes>
<axis>
color     = lgreen
thickness = 2
spacing   = 0.1r
</axis>
</axes>

<backgrounds>
<background>
color = vlgreen_a5
</background>
</backgrounds>

<rules>
<rule>
condition  = 1
glyph_size = eval( 6 + 4*abs(var(value)))
flow       = continue
</rule>
<rule>
condition    = var(value) > 2
stroke_color = black
stroke_thickness = 2
</rule>
</rules>

</plot>

# scatter plot for values [-3,3] turned into a heat map
# by using r0=r1
<plot>
type = scatter
file = data/8/13/data.cnv.txt
r0   = 0.935r
r1   = 0.935r
min  = -3
max  = 0
glyph = square
glyph_size = 8
fill_color = red

<rules>
<rule>
condition  = 1
fill_color = eval( "red_a" . remap_int(var(value),-3,3,1,5) )
</rule>
</rules>

</plot>

# scatter plot for values [0,3] turned into a heat map
# by using r0=r1
<plot>
type = scatter
file = data/8/13/data.cnv.txt
r0   = 0.955r
r1   = 0.955r
min  = 0
max  = 3
glyph = square
glyph_size = 8
fill_color = green

<rules>
<rule>
condition  = 1
fill_color = eval( "green_a" . remap_int(var(value),0,3,1,5) )
</rule>
</rules>

</plot>

</plots>

<<include etc/housekeeping.conf>>



bands.conf

show_bands            = yes
fill_bands            = yes
band_stroke_thickness = 2
band_stroke_color     = white
band_transparency     = 3


ideogram.conf


<ideogram>

<spacing>
default = 0.005r
break   = 0.5r

axis_break_at_edge = yes
axis_break         = yes
axis_break_style   = 2

<break_style 1>
stroke_color = black
fill_color   = blue
thickness    = 0.25r
stroke_thickness = 2
</break>

<break_style 2>
stroke_color     = black
stroke_thickness = 2
thickness        = 1.5r
</break>

</spacing>

<<include ideogram.position.conf>>
<<include ideogram.label.conf>>
<<include bands.conf>>

</ideogram>



ideogram.label.conf

show_label       = yes
label_font       = default
label_radius     = dims(image,radius) - 50p
label_size       = 36
label_parallel   = yes
label_case       = lower
label_format     = eval(sprintf("chr%s",var(label)))



ideogram.position.conf

radius           = 0.90r
thickness        = 30p
fill             = yes
fill_color       = black
stroke_thickness = 2
stroke_color     = black


ticks.conf


show_ticks          = yes
show_tick_labels    = yes

<ticks>
tick_separation      = 3p
label_separation     = 5p
radius               = dims(ideogram,radius_outer)
multiplier           = 1e-6
color          = black
size           = 20p
thickness      = 4p
label_offset   = 5p
format         = %d

<tick>
spacing        = 1u
show_label     = yes
label_size     = 16p
</tick>

<tick>
spacing        = 5u
show_label     = yes
label_size     = 18p
</tick>

<tick>
spacing        = 10u
show_label     = yes
label_size     = 20p
</tick>

<tick>
spacing        = 20u
show_label     = yes
label_size     = 24p
</tick>

</ticks>