1 — Quick Start

7. Heat maps

circos.conf

# 1.7 HEAT MAPS

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>

# Heat maps are used for data types which associate a value with a
# genomic position, or region. As such, this track uses the same data
# format as histograms.
#
# The track linearly maps a range of values [min,max] onto a list of colors c[n], i=0..N.
#
# f = (value - min) / ( max - min )
# n = N * f

<plot>
type  = heatmap
file  = data/5/segdup.hs1234.heatmap.txt
r1    = 0.89r
r0    = 0.88r

# Colors are defined by a combination of lists or CSV. Color lists
# exist for all Brewer palletes (see etc/colors.brewer.lists.conf) as
# well as for N-step hue (hue-sN, e.g. hue-s5 =
# hue000,hue005,hue010,...) and N-color hue (hue-sN, e.g. hue-3 =
# hue000,hue120,hue140).

color = hs1_a5,hs1_a4,hs1_a3,hs1_a2,hs1_a1,hs1

# If scale_log_base is used, the mapping is not linear, but a power law 
#
# n = N * f**(1/scale_log_base)
#
# When scale_log_base > 1 the dynamic range for values close to min is expanded. 
# When scale_log_base < 1 the dynamic range for values close to max is expanded. 

scale_log_base = 0.25

<rules>
<<include rule.exclude.hs1.conf>>
</rules>

</plot>

# The other three heatmap tracks are the same as the one above, except
# that each uses a different color list and var(id) condition to show
# the number of links to/from hs2, hs3 and hs4.

<plot>
type  = heatmap
file  = data/5/segdup.hs1234.heatmap.txt
r1    = 0.90r
r0    = 0.89r
color = hs2_a5,hs2_a4,hs2_a3,hs2_a2,hs2_a1,hs2
scale_log_base = 0.25

<rules>
<<include rule.exclude.hs1.conf>>

# Show only data points that have id=hs2
<rule>
condition = var(id) ne "hs2"
show      = no
</rule>

</rules>

</plot>

<plot>
type  = heatmap
file  = data/5/segdup.hs1234.heatmap.txt
r1    = 0.91r
r0    = 0.90r
color = hs3_a5,hs3_a4,hs3_a3,hs3_a2,hs3_a1,hs3
scale_log_base = 0.25

<rules>
<<include rule.exclude.hs1.conf>>

# Show only data points that have id=hs3 
<rule>
condition = var(id) ne "hs3"
show      = no
</rule>

</rules>

</plot>

<plot>
type  = heatmap
file  = data/5/segdup.hs1234.heatmap.txt
r1    = 0.92r
r0    = 0.91r
color = hs4_a5,hs4_a4,hs4_a3,hs4_a2,hs4_a1,hs4
scale_log_base = 0.25

<rules>
<<include rule.exclude.hs1.conf>>

# Show only data points that have id=hs4
<rule>
condition = var(id) ne "hs4"
show      = no
</rule>

</rules>

</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        = 0.8r
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>

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>