Circos > Documentation > Tutorials > 2d Tracks > Stacking Tracks
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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.

6 — 2D Data Tracks

12. Putting It All Together

circos.conf


show_scatter   = yes
show_line      = yes
show_histogram = yes
show_heatmap   = yes
show_tile      = yes
show_highlight = yes
use_rules      = yes

<<include colors_fonts_patterns.conf>>

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

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

karyotype         = data/karyotype/karyotype.human.txt
chromosomes_units = 1000000
chromosomes_display_default = no

# to see how reversing ideograms work - comment out the chromosomes
# line below
chromosomes       = hs2

# and uncomment the two definitions below
# - first split hs2 into three ideograms
# - now reverse the ideogram with tag "b"
#chromosomes       = hs2[a]:0-60;hs2[b]:70-140;hs2[c]:150-)
#chromosomes_reverse = b

#chromosomes        = hs2[a]:0-30;hs2[b]:50-80;hs2[c]:100-130;hs2[d]:150-180;hs2[e]:190-200;hs2[f]:210-)
#chromosomes_radius = a:0.95r;b:0.9r;c:0.85r;d:0.8r;e:0.75r;f:0.7r

<plots>

show = no

<plot>
show             = conf(show_heatmap)
type             = heatmap
color            = spectral-5-div
stroke_thickness = 1
scale_log_base   = 0.25
stroke_color     = black
file             = data/6/snp.number.1mb.txt
r0               = 1.075r
r1               = 1.075r+50p
</plot>

<plot>
show             = conf(show_heatmap)
type             = heatmap
color            = spectral-5-div
file             = data/6/variation.heatmap.txt
stroke_thickness = 0
scale_log_base   = 0.25
r0               = 0.925r
r1               = 0.925r+50p
</plot>

<plot>
show             = conf(show_heatmap)
type             = heatmap
color            = spectral-5-div
file             = data/6/rand.1.txt
r0               = 0.6r
r1               = 0.6r+30p

<rules>
use = conf(use_rules)
<rule>
condition  = rand() < 0.2 || var(value) < 0.5
show       = no
</rule>
</rules>
</plot>

<plot>
show             = conf(show_heatmap)
type             = heatmap
color            = spectral-5-div
file             = data/6/rand.2.txt
r0               = 0.6r+40p
r1               = 0.6r+70p

<rules>
use = conf(use_rules)
<rule>
condition = rand() < 0.2 || var(value) > 0.5
show      = no
</rule>
</rules>
</plot>

<plot>
show             = conf(show_heatmap)
type             = heatmap
color            = spectral-5-div
file             = data/6/rand.3.txt
r0               = 0.6r+80p
r1               = 0.6r+110p

<rules>
use = conf(use_rules)
<rule>
condition  = rand() < 0.2 || (var(value) > 0.25 && var(value) < 0.75)
show       = no
</rule>
</rules>
</plot>

<plot>
show         = conf(show_scatter)
type         = scatter
file         = data/6/conservation.avg.txt
glyph        = circle
glyph_size   = 8
orientation  = out
fill_color   = black
r0           = 0.80r
r1           = 0.90r
z            = 5
</plot>

<plot>
show         = conf(show_line)
type         = line
file         = data/6/conservation.p5.txt
orientation  = out
thickness    = 3
color        = green
r0           = 0.80r
r1           = 0.90r
z = 15
</plot>

<plot>
show         = conf(show_line)
type         = line
file         = data/6/conservation.p95.txt
orientation  = out
thickness    = 3
color        = red
r0           = 0.80r
r1           = 0.90r
z = 15
</plot>

<plot>
show         = conf(show_histogram)
type         = histogram
file         = data/6/snp.number.500kb.txt
thickness    = 2
color        = black
fill_under   = yes
fill_color   = red
r0           = 0.80r
r1           = 0.90r
max_gap      = 5u
z = 10
</plot>

<plot>
show         = conf(show_histogram)
type         = histogram
file         = data/6/snp.number.250kb.txt
orientation  = in
thickness    = 1
color        = black
fill_under   = yes
fill_color   = red
r0           = 0.65r
r1           = 0.75r
max_gap      = 5u
z = 10
</plot>

<plot>
show         = conf(show_heatmap)
type         = heatmap
file         = data/6/snp.number.1mb.txt
scale_log_base = 0.25
min          = 1500
color        = spectral-5-div
r0           = 0.75r
r1           = 0.80r
</plot>

<plot>
show         = conf(show_tile)
type         = tile
file         = data/6/variation.txt
color        = orange
stroke_color = black
stroke_thickness = 0
r0           = 0.50r
r1           = 0.65r
orientation  = out
layers       = 11
margin       = 0.25u
padding      = 4
thickness    = 10
z = 10

<rules>
use = conf(use_rules)
<rule>
condition  = var(size) < 25000
show = no
</rule>
</rules>
</plot>

<plot>
show         = conf(show_tile)
type         = tile
file         = data/6/tiles.rand.1.txt
color        = black
r0           = 0.05r
r1           = 0.35r
orientation  = center
layers       = 11
margin       = 0.25u
padding      = 4
thickness    = 10
z = 10

<rules>
use = conf(use_rules)
<rule>
condition  = abs(var(start) - 20Mb) < 10Mb
color      = red
</rule>
<rule>
condition  = abs(var(start) - 60Mb) < 10Mb
color      = orange
</rule>
<rule>
condition  = abs(var(start) - 160Mb) < 10Mb
color      = green
</rule>
<rule>
condition  = rand() < 0.1
color      = blue
</rule>
<rule>
condition  = rand() < 0.1
show = no
</rule>
<rule>
condition  = rand() < 0.1
color      = orange
</rule>
</rules>

</plot>

<plot>
show         = conf(show_tile)
type         = tile
file         = data/6/assembly.txt
color        = black
stroke_thickness = 1
r0           = 0.30r
r1           = 0.49r
orientation  = in
layers       = 11
margin       = 0.25u
padding      = 4
thickness    = 10
z = 10

<rules>
use = conf(use_rules)
<rule>
condition = var(size) < 50000
show = no
</rule>
</rules>

</plot>

<plot>
show = conf(show_highlight)
type = highlight
file = data/6/highlights.txt
r0   = 0.98r
r1   = 0.0r
z    = 2

<rules>
use = conf(use_rules)
<rule>
condition  = 1
fill_color = eval(var(fill_color)."_a4")
</rule>
</rules>
</plot>

</plots>

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

bands.conf

show_bands            = yes
fill_bands            = yes
band_stroke_thickness = 2
band_stroke_color     = white
band_transparency     = 0

ideogram.conf


<ideogram>

<spacing>
default = 0.01r
break   = 0.5r
</spacing>

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

radius*       = 0.825r

</ideogram>

ideogram.label.conf

show_label       = yes
label_font       = default
label_radius     = dims(image,radius)-30p
label_size       = 24
label_parallel   = yes
label_case       = lower
label_format     = eval(sprintf("chr%s",var(label)))

ideogram.position.conf

radius           = 0.775r
thickness        = 30p
fill             = yes
fill_color       = black
stroke_thickness = 2
stroke_color     = black

ticks.conf


show_ticks          = yes
show_tick_labels    = yes

<ticks>

radius           = dims(ideogram,radius_outer)
orientation      = out
label_multiplier = 1e-6
color            = black
size             = 20p
thickness        = 3p
label_offset     = 5p
format           = %d

<tick>
spacing        = 1u
show_label     = no
size           = 10p
</tick>

<tick>
spacing        = 5u
show_label     = yes
label_size     = 20p
size           = 15p
</tick>

<tick>
spacing        = 10u
show_label     = yes
label_size     = 24p
</tick>

</ticks>