1 — Quick Start

9. Automation & Macros

circos.conf

# 1.9 MODULAR CONFIGURATION, MACROS

karyotype = data/karyotype/karyotype.human.txt
chromosomes_units = 1000000

chromosomes_display_default = no
chromosomes                 = /hs[1234]$/
chromosomes_radius          = hs4:0.9r

<colors>
chr1* = red
chr2* = orange
chr3* = green
chr4* = blue
</colors>

chromosomes_reverse = /hs[234]/
chromosomes_scale   = hs1=0.5r,/hs[234]/=0.5rn

<plots>

<plot>
type  = text
file  = data/6/genes.labels.txt
r1    = 0.8r
r0    = 0.6r
label_font = light
label_size = 12p
rpadding   = 5p
show_links     = no
link_dims      = 0p,2p,5p,2p,2p
link_thickness = 2p
link_color     = black

<rules>
<<include rule.exclude.hs1.conf>>
<rule>
condition  = var(value) =~ /a/i
label_font = bold
flow       = continue
</rule>
<rule>
condition  = var(value) =~ /b/i
color      = blue
</rule>
</rules>

</plot>

# By using counters and automatic track placement, we can
# create 4 heatmaps with identical configurations (heatmap.conf).
# The conf() function is used within heatmap.conf to reference
# configuration parameters.

h0 = 0.88 # start of heatmap tracks 
hw = 0.01 # width of heatmap track (-'ve if tracks progress inward)
hp = 0    # padding between heatmap tracks

# Look in heatmap.conf for explanation.

<plot>
<<include heatmap.conf>>
</plot>

<plot>
<<include heatmap.conf>>
</plot>

<plot>
<<include heatmap.conf>>
</plot>

<plot>
<<include heatmap.conf>>
</plot>

<plot>
type = histogram
file = data/5/segdup.hs1234.hist.txt
r1   = 0.88r
r0   = 0.81r
fill_color = vdgrey
extend_bin = no
<rules>
<<include rule.exclude.hs1.conf>>
</rules>
<<include backgrounds.conf>>
</plot>

<plot>
type = histogram
file = data/5/segdup.hs1234.stacked.txt
r1   = 0.99r
r0   = 0.92r
fill_color  = hs1,hs2,hs3,hs4
orientation = in
extend_bin  = no
<rules>
<<include rule.exclude.hs1.conf>>
</rules>
<<include axes.conf>>
</plot>

</plots>

<links>
<link>
file          = data/5/segdup.txt
radius        = 0.6r
bezier_radius = 0r
color         = black_a4
thickness     = 2
<rules>
<<include rules.link.conf>>
</rules>

</link>

</links>

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

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

<<include etc/colors_fonts_patterns.conf>> 
<<include etc/housekeeping.conf>> 
data_out_of_range* = trim

axes.conf

<axes>
# Show axes only on ideograms that have data for this track
show = data

thickness = 1
color     = lgrey
<axis>
spacing   = 0.1r
</axis>
<axis>
spacing   = 0.2r
color     = grey
</axis>
<axis>
position  = 0.5r
color     = red
</axis>
<axis>
position  = 0.85r
color     = green
thickness = 2
</axis>

</axes>

backgrounds.conf

<backgrounds>
# Show the backgrounds only for ideograms that have data
show  = data
<background>
color = vvlgrey
</background>
<background>
color = vlgrey
y0    = 0.2r
y1    = 0.5r
</background>
<background>
color = lgrey
y0    = 0.5r
y1    = 0.8r
</background>
<background>
color = grey
y0    = 0.8r
</background>

</backgrounds>

heatmap.conf

type           = heatmap
file           = data/5/segdup.hs1234.heatmap.txt

# The 'c' parameter (arbitrarily named) is referenced
# within heatmap.conf as conf(.,c). conf(x) retrieves
# the value of parameter 'x' in the current block and
# conf(.,x) looks up the configuration tree until
# it finds x.

c = eval(sprintf("hs%d",counter(heatmap)+1))

# track_r0(counter,start,width,padding) 
# track_r1(counter,start,width,padding) 
# are helper functions that return the start/end radius of a track
# formatted as float+"r", e.g. 0.925r
# 
# r0 = start + counter * (width + padding) 
# r1 = start + counter * (width + padding) + width
#
# The calls to conf(.,x) reference the <plot> block's h0, hw and hp
# parameters. The counter(heatmap) is an 0-start automatically incremented
# index, which is incremented by 1 for each type=heatmap plot.
#
r1    = eval(track_r1(counter(heatmap),conf(.,h0),conf(.,hw),conf(.,hp)))
r0    = eval(track_r0(counter(heatmap),conf(.,h0),conf(.,hw),conf(.,hp)))

# conf(.,c) references the <plot> block's 'c' parameter
color          = conf(.,c)_a5,conf(.,c)_a4,conf(.,c)_a3,conf(.,c)_a2,conf(.,c)_a1,conf(.,c)
scale_log_base = 0.25

<rules>
<<include rule.exclude.hs1.conf>>
<rule>
condition = var(id) ne "conf(.,c)"
show      = no
</rule>
</rules>

ideogram.conf

<ideogram>

<spacing>
default = 0.005r
</spacing>

# Ideogram position, fill and outline
radius           = 0.90r
thickness        = 20p
fill             = yes
stroke_color     = dgrey
stroke_thickness = 2p

# Minimum definition for ideogram labels.

show_label       = yes
# see etc/fonts.conf for list of font names
label_font       = default 
label_radius     = 1.075r  # if ideogram radius is constant, and you'd like labels close to image edge, 
                           # use the dims() function to access the size of the image
                           # label_radius  = dims(image,radius) - 60p
label_size       = 30
label_parallel   = yes

</ideogram>

rule.exclude.hs1.conf

<rule>
condition = on(hs1)
show      = no
</rule>

rules.link.conf

<rule>
condition     = var(intrachr)
show          = no
</rule>
<rule>
condition     = 1
color         = eval(var(chr2))
flow          = continue
</rule>
<rule>
condition     = from(hs1)
radius1       = 0.99r
</rule>
<rule>
condition     = to(hs1)
radius2       = 0.99r
</rule>

ticks.conf

show_ticks          = yes
show_tick_labels    = yes

<ticks>
radius           = 1r
color            = black
thickness        = 2p

# the tick label is derived by multiplying the tick position
# by 'multiplier' and casting it in 'format':
#
# sprintf(format,position*multiplier)
#

multiplier       = 1e-6

# %d   - integer
# %f   - float
# %.1f - float with one decimal
# %.2f - float with two decimals
#
# for other formats, see http://perldoc.perl.org/functions/sprintf.html

format           = %d

<tick>
spacing        = 5u
size           = 10p
</tick>

<tick>
spacing        = 25u
size           = 15p
show_label     = yes
label_size     = 20p
label_offset   = 10p
format         = %d
</tick>

</ticks>