1 — Quick Start

4. Links & Rules

circos.conf

# 1.4 LINKS AND RULES
#
# The first data track we will add are links. By using rules, which
# are expressions that are evaluated for every link, the formatting
# can be dynamically changed based on data values.
#
# I will also show you how to change the definition of colors, if you
# would like to assign different chromosome color scheme to your
# figure.

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

chromosomes_display_default = no
chromosomes                 = /hs[1-4]$/
chromosomes_reverse         = /hs[234]/
chromosomes_scale           = hs1=0.5r,/hs[234]/=0.5rn
chromosomes_radius          = hs4:0.9r

# In the previous tutorial (1.3), I used chromosomes_colors to change
# the color of the ideograms. This approach works well when the only
# thing you want to do is change the color of the segments. 
#
# Another way to achieve this is to actually redefine the colors which
# are used to color the ideograms. The benefit of doing this is that
# whenever you refer to the color (which you can use by using the name
# of the chromosome), you get the custom value.
#
# If you look in the human karyotype file linked to above, you'll see
# that each chromosome's color is chrN where N is the number of the
# chromosome. Thus, hs1 has color chr1, hs2 has color chr2, and so
# on. For convenience, a color can be referenced using 'chr' and 'hs'
# prefixes (chr1 and hs1 are the same color).
#
# Colors are redefined by overwriting color definitions, which are
# found in the <colors> block. This block is included below from the
# colors_fonts_patterns.conf file, which contains all the default
# definitions. To overwrite colors, use a "*" suffix and provide a new
# value, which can be a lookup to another color.

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

# Links are defined in <link> blocks enclosed in a <links> block. The
# links start at a radial position defined by 'radius' and have their
# control point (adjusts curvature) at the radial position defined by
# 'bezier_radius'. In this example, I use the segmental duplication
# data set, which connects regions of similar sequence (90%+
# similarity, at least 1kb in size).

<links>

<link>
file          = data/5/segdup.txt
radius        = 0.8r
bezier_radius = 0r
color         = black_a4
thickness     = 2

# Rule blocks can be added to any <link> or <plot> block and form a
# decision chain that changes how data points (e.g. links, histogram
# bins, scatter plot glyphs, etc) are formatted.

<rules>

# The decision chain is composed of one or more <rule> blocks.

<rule>

# Each rule has a condition, formatting statements and an optional
# 'flow' statement. If the condition is true, the rule is applied to
# the data point and no further rules are checked (unless
# flow=continue). If the condition is false, the next rule is checked.
#
# var(X) referrs to the value of variable X for the data point. Here 'intrachr' means intra-chromosomal.

condition     = var(intrachr)

# Any links that are intra-chromosomal will not be shown. Further rules are not tested.

show          = no

</rule>

<rule>

# This rule is applied to all remaining links, since its condition is always true.

condition     = 1

# The color of the link is set to the 2nd chromosome in the link
# coordinate (link's end). Here eval() is required so that the
# expression var(chr2) is evaluated (we want the result of var(chr2),
# not the color named "var(chr2)"). Note that for conditions,
# evaluation is automatic, but required for all other parameters.

color         = eval(var(chr2))

# After this rule is applied, the rule chain continues.

flow          = continue
</rule>

<rule>

# If the link's start is on hs1...

condition     = from(hs1)

# ...set the radial position of the link's start to be close to the ideogram.

radius1       = 0.99r
</rule>

<rule>

# Same as the rule above, but applies to the end of the link.

condition     = to(hs1)

# 'radius2' (like chr2, start2, end2) refers to the variable 'radius' of the end of the link.

radius2       = 0.99r

</rule>

</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>> 

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     = dims(image,radius) - 60p
label_size       = 30
label_parallel   = yes

</ideogram>

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>