Circos > Documentation > Tutorials > Recipes > Cortical Maps
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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

19. Cortical Maps

circos.conf


<<include ideogram.conf>>

chromosomes_units = 100
<<include ticks.conf>>

<image>
angle_offset* = -87
<<include etc/image.conf>>
</image>

### single genomes

karyotype = data/segments.txt

<<include segment.order.conf>>

chromosomes_reverse = /.*-l/

###
# HEATMAPS
# If you aren't using heatmaps in your image (you have no measures associated with
# parcelation regions), remove this section. Also turn of grids in etc/ticks.conf.

hm_r      = 0.96
hm_w      = 0.025
hm_pad    = 0.005

#hm_colors = greys-4-seq,greys-4-seq,greys-4-seq,greys-4-seq,greys-4-seq
hm_colors = reds-4-seq,oranges-4-seq,greens-4-seq,blues-4-seq,purples-4-seq

# HEATMAPS
###

<plots>

# Remove these lines if you don't have heatmaps.
<<include heatmap.conf>>
<<include heatmap.conf>>
<<include heatmap.conf>>
<<include heatmap.conf>>
<<include heatmap.conf>>

<plot>
type       = text
file       = data/structure.label.txt
color      = black
label_font = default
label_size = 20
r0         = 1r
r1         = 1.5r
rpadding   = 10p
</plot>

</plots>

<links>

<link>
file          = data/links.txt

# If you don't have heatmaps, change radius to
# radius = dims(ideogram,radius_inner) 

radius        = 0.825r # eval(sprintf("%fr",conf(hm_r)-counter(heatmap)*(conf(hm_w)+conf(hm_pad))+conf(hm_w)))
bezier_radius = 0r
bezier_radius_purity = 0.5
crest         = 0.25
thickness     = 2
color         = black

<rules>
<rule>
# this rule is part of variant #1
# to use it, set use=yes and also adjust radius above to 0.7r
use       = no
condition = var(chr1) eq var(chr2)
bezier_radius = 1r
radius    = 0.71r
flow      = continue
</rule>
<rule>
condition = 1
thickness = eval(remap_int(var(score),0,1,1,5)) 
flow      = continue
</rule>
<rule>
condition = var(type) == 0 
color     = eval(sprintf("greys-5-seq-%d",remap_int(var(score),0,1,1,5)))
</rule>
<rule>
condition = var(type) == 1
color     = eval(sprintf("reds-5-seq-%d",remap_int(var(score),0,1,1,5)))
</rule>
</rules>

</link>

</links>

<<include etc/colors_fonts_patterns.conf>>
<colors>
<<include color.brain.conf>>
</colors>

restrict_parameter_names* = no
<<include etc/housekeeping.conf>>


bands.conf

show_bands            = yes
fill_bands            = yes
band_stroke_thickness = 1
band_stroke_color     = black
band_transparency     = 0


color.brain.conf

trfpogs = 255,153,153
fmargs = 204,0,51
mfs = 255,153,51
lors = 102,0,0
sbors = 255,51,102
ors = 255,204,204
rg = 255,204,153
inffgorp = 153,51,0
mfg = 255,255,51
org = 255,255,153
inffgtrip = 255,0,0
inffs = 153,102,0
medors = 255,102,0
supfg = 255,102,102
supfs = 204,153,0
inffgopp = 255,204,0
infprcs = 255,153,0
supprcs = 255,0,102
prcg = 204,102,0
sbcgs = 255,102,153
cs = 255,51,0
alshorp = 0,255,204
acirins = 102,255,255
alsverp = 0,255,255
shoing = 51,255,204
supcirins = 0,153,153
loingcins = 0,204,204
infcirins = 0,102,102
posls = 204,255,255
acggs = 255,255,180
macggs = 255,240,191
sbcag = 255,153,200
percas = 255,164,200
mposcggs = 255,224,203
cgsmarp = 255,192,201
posdcgg = 255,175,201
posvcgg = 255,208,202
tpo = 255,204,255
popl = 204,153,255
suptglp = 153,51,255
hg = 102,0,102
atrcos = 153,0,204
trts = 255,153,255
mtg = 255,102,204
tpl = 153,0,153
inftg = 255,0,255
infts = 204,0,153
supts = 204,51,255
poscg = 204,255,204
sumarg = 204,255,102
pacls = 204,255,153
poscs = 153,255,0
js = 153,204,0
sbps = 102,153,0
intpstrps = 51,255,51
suppl = 153,255,153
prcun = 204,255,0
angg = 0,255,0
pocs = 204,255,51
pahipg = 204,204,255
coslins = 153,204,255
locts = 153,153,255
fug = 102,102,255
ccs = 102,153,255
ling = 102,204,255
aocs = 51,51,255
infocgs = 51,153,255
supocstrocs = 0,102,255
postrcos = 51,102,255
cun = 0,153,255
mocg = 0,204,244
mocslus = 0,51,255
supocg = 0,0,255
ocpo = 0,0,153
pu = 32,32,32
pal = 64,64,64
can = 96,96,96
nacc = 128,128,128
amg = 159,159,159
tha = 191,191,191
hip = 223,223,223
ceb = 255,64,0
bst = 207,255,48


heatmap.conf

<plot>
type         = heatmap
file         = data/measure.counter(heatmap).txt
color        = eval((split(",","conf(hm_colors)"))[counter(heatmap)])
r1           = eval(sprintf("%fr",conf(hm_r)-counter(heatmap)*(conf(hm_w)+conf(hm_pad))))
r0           = eval(sprintf("%fr",conf(hm_r)-counter(heatmap)*(conf(hm_w)+conf(hm_pad))+conf(hm_w)))

stroke_color = white
stroke_thickness = 3
</plot>


ideogram.conf


<ideogram>

<spacing>
default = 0.005r
<pairwise fro-l fro-r>
spacing = 5r
</pairwise>
</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)-30p
label_size       = 24
label_parallel   = yes
label_case       = upper

# 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("region %s",var(label)))


ideogram.position.conf

radius           = 0.85r
thickness        = 75p
fill             = no
stroke_thickness = 1
stroke_color     = black


segment.order.conf

chromosomes_order = fro-r,ins-r,lim-r,tem-r,par-r,occ-r,sbc-r,ceb-r,bst,ceb-l,sbc-l,occ-l,par-l,tem-l,lim-l,ins-l,fro-l


ticks.conf


show_ticks          = yes
show_tick_labels    = yes
show_grid           = yes

<ticks>

radius           = dims(ideogram,radius_outer)
color            = black
thickness        = 2p
size             = 0

<tick>
spacing        = 0.5u
size           = 5p
grid           = yes
grid_color     = black
grid_thickness = 1p
grid_start     = 1r-conf(ideogram,thickness)
grid_end       = 0.825r
</tick>

<tick>
spacing        = 1u
</tick>

</ticks>