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.
Syntax for 2D data types is similar to that for links. You define all 2D plots within >plots< block, with one plot per <plot> block. Within a plot block, you define formatting and data file for the plot, and can insert optional >rules> block that contains multiple <rule> blocks.
There are several 2D data types and the scatter plot is one. The image for this example contains three scatter plots, all derived from the same data file. Each plot is formatted slightly differently. The data are SNP density for windows of 100kb (number of SNPs from dbSNP per base).
Each plot type has default settings which you can find in
etc/tracks. For example,
# etc/tracks/scatter.conf glyph = circle glyph_size = 10 color = grey stroke_color = black stroke_thickness = 0 r1 = 0.79r r0 = 0.7r orientation = out
These settings are applied to every <plot> block of
type=scatter. YOu can undefine a setting using
stroke_color = undef
2D data types share have the same format parameters, with a few exceptions. For the scatter plot, a basic definition might look like this
<plots> <plot> show = yes type = scatter file = data/6/snp.density.txt r1 = 0.75r r0 = 0.90r max = 1.0 min = 0.0 glyph = rectangle glyph_size = 8 color = red stroke_color = dred stroke_thickness = 1 </plot> </plots>
The parameters are
show- as with highlights or links, determines whether to draw the plot or not
type- determines the type of plot and can be one of scatter, line, histogram, heatmap, etc.
file- file that contains plot data
min/max- the range of the plot axis, data outside this range are clipped
r0/r1- the inner and outer radius of the plot track, which may be formatted in absolute or relative (or mix) form, just like for highlights
glyph- shape of glyph to use for the scatter plot and can be one of circle, rectangle, or triangle
glyph_size- size of the glyph, in pixels
color- if used, the the glyph will be solid and of this color
stroke_color- if used, the glyph will have an outline of this color
stroke_thickness- if used, the glyph's outline will have this thickness, in pixels
The data file format for 2D plots is
chr start end value options
Note that a value is associated with an explicit span, and not a single base pair position. For example,
# value 0.005 at span 1000-2000 hs1 1000 2000 0.005 # value 0.010 at span 2001-2001, e.g. a single base position hs1 2001 2001 0.010
The reason why Circos uses start and end positions for the data file is to maintain consistency between data and link files. Glyphs are drawn at the middle of the span. Thus, in the above example, the glyphs would be drawn at positions 1,500 and 2,001.
Points whose values fall outside of the min/max range defined in the plot parameters are not drawn. You do not need to write rules to exclude these points.
r1 parameters define the radial start and end positions
of the plot track. You can optionally add background fill(s) to the track with a
using the following parameters
<backgrounds> <background> color = vvlgrey </background> </backgrounds>
By defining several
<background> blocks, you can stripe and layer the background fills. Use
y0/y1 to define the radial extent of the fill.
<backgrounds> <background> color = vlgrey # absolute fill range y1 = 0.5 y0 = 0 </background> <background> color = vlred # relative fill range y1 = 1r y0 = 0.75r </background> </backgrounds>
You can draw a set of y-axis grid lines within your plot track
<axes> <axis> color = grey thickness = 1 spacing = 0.05r </axis> </axes>
The axes are a series of concentric arcs with a given
spacing. The spacing value can be absolute or relative.
Formatting rules work for plots in the same manner as for
links. Within the condition field, use
var(value) to represent the data
value for a particular point.
<rule> condition = var(value) > 0.5 stroke_color = dgreen color = green glyph = rectangle glyph_size = 6 </rule>
would turn all points whose value is larger than 0.5 to be rectangles of size 6 with a dark green outline and green fill.
You can hide certain data points by setting
show=no within the