Circos > Documentation > Tutorials > 2d Tracks > Line Plots
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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

2. Line Plots

circos.conf


<<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       = hs1 # ;hs2;hs3
chromosomes_display_default = no

<plots>

type      = line
thickness = 2

<plot>

max_gap = 1u
file    = data/6/snp.density.250kb.txt
color   = vdgrey
min     = 0
max     = 0.015
r0      = 0.5r
r1      = 0.8r

fill_color = vdgrey_a3

<backgrounds>
<background>
color     = vvlgreen
y0        = 0.006
</background>
<background>
color     = vvlred
y1        = 0.002
</background>
</backgrounds>

<axes>
<axis>
color     = lgrey_a2
thickness = 1
spacing   = 0.025r
</axis>
</axes>

<rules>

<rule>
condition    = var(value) > 0.006
color        = dgreen
fill_color   = dgreen_a1
</rule>

<rule>
condition    = var(value) < 0.002
color        = dred
fill_color   = dred_a1
</rule>

</rules>

</plot>

# outside the circle, oriented out
<plot>

max_gap = 1u
file    = data/6/snp.density.txt
color   = black
min     = 0
max     = 0.015
r0      = 1.075r
r1      = 1.15r
thickness = 1

fill_color = black_a4

<axes>
<axis>
color     = lgreen
thickness = 2
position  = 0.006
</axis>
<axis>
color     = lred
thickness = 2
position  = 0.002
</axis>
</axes>

</plot>

<plot>
z       = 5
max_gap = 1u
file    = data/6/snp.density.1mb.txt
color   = red
fill_color = red_a4
min     = 0
max     = 0.015
r0      = 1.075r
r1      = 1.15r
</plot>

# same plot, but inside the circle, oriented in
<plot>
max_gap = 1u
file    = data/6/snp.density.txt
color   = black
fill_color = black_a4
min     = 0
max     = 0.015
r0      = 0.85r
r1      = 0.95r
thickness   = 1
orientation = in

<axes>
<axis>
color     = lgreen
thickness = 2
position  = 0.01
</axis>
<axis>
color     = vlgreen
thickness = 2
position  = 0.008
</axis>
<axis>
color     = vlgreen
thickness = 2
position  = 0.006
</axis>
<axis>
color     = red
thickness = 2
position  = 0.002
</axis>
</axes>

</plot>

<plot>
z       = 5
max_gap = 1u
file    = data/6/snp.density.1mb.txt
color   = red
fill_color = red_a4
min     = 0
max     = 0.015
r0      = 0.85r
r1      = 0.95r
orientation = in
</plot>

</plots>

<<include etc/housekeeping.conf>>


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>