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.
Spacing between ideograms derived from different chromosomes is
controlled by the
default parameter in <ideogram><spacing> block.
This parameter may be set relative to chromosome units (suffixed
u). For example, if
chromosomes_units=1000000 and the spacing
10u, then the actual spacing in the image will be 10Mb.
<ideogram> <spacing> default = 10u </spacing> </ideogram>
You can also set the parameter to be relative to the total size of
ideograms in the image (suffix with
r). This is useful if you
would like to maintain a fixed spacing between ideograms as you
add/remove ideograms from the image.
<ideogram> <spacing> default = 0.01r </spacing> </ideogram>
In this example, the spacing will be 1% of the size of all ideograms. This will be close to 1% of the circumference of the image.
Use the absolute value format (e.g.
10u), when you have created
your ideogram layout and want to adjust the spacing value to be
visually compatible with adjacent tick marks. For example, if you have
major ticks every 5Mb, you may want to set the spacing value to this.
Use the relative value format (e.g.
0.01r), when you anticipate
that you will be adding/removing/cropping ideograms from the image but
do not want the spacing value to fluctuate.
Spacing between specific ideograms can be adjusted in <pairwise> block.
<ideogram> <spacing> default = 10u <pairwise hs1> spacing = 5u </pairwise> <pairwise hs3 hs4> spacing = 0.25r </pairwise> </spacing> </ideogram>
When you specify the name of one ideogram, spacing on either side of it will be affected. The first pairwise block creates
5u spacing around
When you specify the names of two ideograms, the spacing between them is affected. If you use relative spacing, it is interpreted to be relative to the default spacing. Thus,
hs4 will be 2.5u (i.e. 25% of
To make room for a track legend, use the <pairwise> block to adjust spacing between the ideograms at the top of the image and then
angle_offset to rotate the image to center the spacing along the vertical line.
# ideogram.conf <ideogram> <spacing> # spacing between ideograms is 0.1% of image default = 0.001r <pairwise hsY hs1> # spacing between hsY and hs1 is 50x 0.1% of image spacing = 50r </pairwise> </spacing> </ideogram> # circos.conf <image> # override angle_offset defined in etc/image.conf angle_offset* = -82 <<include etc/image.conf>> </image>
This example assumes that
hs1 are the last and first ideograms in your image, flanking the 12 o'clock position.
angle_offset=-90, which makes ideograms start at 12 o'clock position. The image is rotated slightly clockwise by reducing this offset. You'll need to determine this offset yourself—start at
-85 and then vary the value up/down as required.
When only a subregion of a chromosome is drawn, you have the option to place axis breaks on the ideogram to indicate that the chromosome extent is larger than shown in the figure.
There are two axis break styles, with style properties defined in
break_style blocks. The size of the axis break is controlled
by the break parameter and can be defined in absolute units (
relative to the default spacing (
<ideogram> block(spacing> default = 10u break = 2u axis_break = yes axis_break_style = 2 axis_break_at_edge = yes <break_style 1> stroke_color = black fill_color = blue thickness = 0.25r stroke_thickness = 2 </break_style> <break_style 2> stroke_color = black stroke_thickness = 3 thickness = 1.5r </break_style> </spacing> </ideogram>
If an ideogram does not begin at its chromosome start or end, you
can choose to place an axis break at the edge with
The thickness parameter defines the radial extent of the break and
can be expressed relative to the thickness of the ideogram
0.25r) or in in absolute pixel size (e.g.
break style 1 should have a thickness <
1r and style 2 should have a
The axis break defined by style 1 uses a rectangle to join the ideogram across the break. Style 2 uses two radial lines to indicate a break. The size of the break is independent of spacing between two ideograms. Thus, if two neighbouring ideograms have breaks at neighbouring ends, then the total space between them is the sum of break sizes and ideogram spacing.