2 — Drawing Ideograms

2. Karyotypes

circos.2.conf

<colors>
<<include etc/colors.conf>>
</colors>

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

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

# specify the karyotype file here; try also
#  data/2/karyotype.dog.txt
#  data/2/karyotype.rat.txt
#  data/2/karyotype.mouse.txt
#  data/2/karyotype.all.txt (human+dog+rat+mouse)
# but reduce frequency of ticks when increasing the 
# number of ideograms
karyotype = data/karyotype.human.txt

<image>
dir = /tmp
file  = circos-tutorial.png
# radius of inscribed circle in image
radius         = 1500p
background     = white
# by default angle=0 is at 3 o'clock position
angle_offset   = -90
#angle_orientation = counterclockwise
</image>

chromosomes_units           = 1000000

#chromosomes_display_default = yes

chromosomes = hs1;hs2;hs3

anglestep       = 0.5
minslicestep    = 10
beziersamples   = 40
debug           = no
warnings        = no
imagemap        = no

units_ok = bupr
units_nounit = n

circos.conf

<<include etc/colors_fonts_patterns.conf>>

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

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

chromosomes_units           = 1000000
chromosomes_display_default = yes

### single genomes

# specify the karyotype file here - try other karyotypes in data/karyotype
karyotype = data/karyotype/karyotype.human.txt
#karyotype = data/karyotype/karyotype.drosophila.txt
#karyotype = data/karyotype/karyotype.mouse.txt
#karyotype = data/karyotype/karyotype.rat.txt

### multiple genomes

# to draw chromosomes from multiple karyotypes, 
# provide comma-separated list of files
#karyotype          = data/karyotype/karyotype.human.txt,data/karyotype/karyotype.mouse.txt,data/karyotype/karyotype.rat.txt

# adjust color using regular expressions matching chromosome names
#chromosomes_color  = /hs/:red;/mm/:green;/rn/:blue

<<include etc/housekeeping.conf>>

bands.conf

show_bands            = yes
fill_bands            = yes
band_stroke_thickness = 2
band_stroke_color     = white
band_transparency     = 4

ideogram.conf

<ideogram>

<spacing>

default = 0.0025r
break   = 0.5r

</spacing>

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

<rules>
use       = no
<rule>
# hide every other ideogram
condition = var(display_idx) % 2
show      = no
</rule>
<rule>
condition = var(chr) eq "hs3"
show_ticks = no
</rule>
<rule>
condition = var(chr) eq "hs5"
show_bands = no
</rule>
<rule>
condition = var(chr) eq "hs7"
color     = vdpurple
</rule>
<rule>
condition = var(chr) eq "hs9"
stroke_thickness = 0
</rule>
</rules>

</ideogram>

ideogram.label.conf

show_label       = yes
label_font       = default
label_radius     = 0.95r
label_with_tag   = yes
label_size       = 36
label_parallel   = yes
label_case       = lower

# you can format the label by using properties
# of the ideogram, accessible with var(PROPERTY):
#
# chr, chr_with_tag, chrlength, display_idx, end, idx, 
# label, length, reverse, scale, size, start, tag

label_format     = eval(sprintf("chr%s",var(label)))

ideogram.position.conf

radius           = 0.90r
thickness        = 75p
fill             = yes
fill_color       = black
stroke_thickness = 2
stroke_color     = black

ticks.conf

show_ticks          = yes
show_tick_labels    = yes

<ticks>
skip_first_label = no
skip_last_label  = no
radius           = dims(ideogram,radius_outer)
tick_separation  = 2p
label_separation = 5p
multiplier       = 1e-6
color            = black
thickness        = 4p
size             = 20p

<tick>
spacing        = 1u
show_label     = no
thickness      = 2p
color          = dgrey
</tick>

<tick>
spacing        = 5u
show_label     = no
thickness      = 3p
color          = vdgrey
</tick>

<tick>
spacing        = 10u
show_label     = yes
label_size     = 20p
label_offset   = 10p
format         = %d
grid           = yes
grid_color     = dgrey
grid_thickness = 1p
grid_start     = 0.5r
grid_end       = 0.999r
</tick>

</ticks>