Circos > Documentation > Tutorials > 2d Tracks > Scatter 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

1. Scatter 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_reverse = hs2
chromosomes_display_default = no

################################################################
# 
# define 3 scatter plots, using the same data file
#

<plots>

# all are scatter plots

type             = scatter

stroke_thickness = 1

# first plot shows all points and selectively formats points at small/large
# y-axis values to be red/green and triangles/rectangles

<plot>

file             = data/6/snp.density.txt
fill_color       = grey
stroke_color     = black
glyph            = circle
glyph_size       = 10

max   = 0.013
min   = 0
r1    = 0.95r
r0    = 0.65r

# optional y0/y1 values (absolute or relative) in <background> blocks
# define the start/end limits of background color
#
# y0 = 0.006
# y0 = 0.75r

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

<axes>
<axis>
color     = lgreen
thickness = 1
spacing   = 0.05r
y0        = 0.006
</axis>
<axis>
color     = dgreen
thickness = 2
spacing   = 0.1r
y0        = 0.006
</axis>

<axis>
color     = lgrey
thickness = 1
spacing   = 0.05r
y1        = 0.006
y0        = 0.002
</axis>
<axis>
color     = dgrey
thickness = 2
spacing   = 0.1r
y1        = 0.006
y0        = 0.002
</axis>

<axis>
color     = lred
thickness = 1
spacing   = 0.05r
y1        = 0.002
</axis>

<axis>
color     = dred
thickness = 2
spacing   = 0.1r
y1        = 0.002
</axis>

</axes>

<rules>

<rule>
condition    = var(value) > 0.006
stroke_color = dgreen
fill_color   = green
glyph        = rectangle
glyph_size   = 8
</rule>

<rule>
condition    = var(value) < 0.002
stroke_color = dred
fill_color   = red
glyph        = triangle
</rule>

</rules>

</plot>

# the second plot is a crop of the first plot, placed outside
# the ideogram circle, showing only points with large y-values

<plot>

file             = data/6/snp.density.txt
fill_color       = green
stroke_color     = dgreen
glyph            = rectangle
glyph_size       = 8

max   = 0.013
min   = 0.007
r1    = 1.175r
r0    = 1.075r

<backgrounds>
# you can stack backgrounds by using transparent color
<background>
color     = vlgreen_a4
y0        = 0.75r
</background>
<background>
color     = vlgreen_a4
y0        = 0.5r
</background>
<background>
color     = vlgreen_a4
y0        = 0.25r
</background>
<background>
color     = vlgreen_a4
</background>
</backgrounds>

<axes>
<axis>
color     = green_a3
thickness = 2
spacing   = 0.1r
</axis>
</axes>

<rules>

<rule>
condition    = var(value) < 0.007
show         = no
</rule>

</rules>

</plot>

# the third plot is a crop of the first plot, placed closer to the
# center of the circle, showing only points with small y-values

<plot>

file             = data/6/snp.density.txt
fill_color       = red
stroke_color     = dred
glyph            = rectangle
glyph_size       = 8

max   = 0.0015
min   = 0.000
r1    = 0.60r
r0    = 0.35r

<backgrounds>
<background>
color     = vlred_a4
y1        = 0.25r
</background>
<background>
color     = vlred_a4
y1        = 0.5r
</background>
<background>
color     = vlred_a4
y1        = 0.75r
</background>
<background>
color     = vlred_a4
</background>
</backgrounds>

<axes>
<axis>
color     = red_a5
thickness = 1
spacing   = 0.025r
</axis>
<axis>
color     = red_a3
thickness = 2
spacing   = 0.1r
</axis>
</axes>

<rules>
<rule>
condition    = var(value) > 0.002
show         = no
</rule>
</rules>

</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>