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.
This series of tutorials focuses on adjusting ideogram scale, both globally and locally. By scale I mean the quantity
scale = size/degree
which defines the magnification factor of each ideogram on the image.
By default, if you draw all (or some) of the ideograms using
chromosomes_display_default = yes
all ideograms will have the same magnification. This means that the angles they subtend are proportional to the length of the ideogram. Unless you change the scale locally, this proportionality factor is constant across the entire image.
The first image in this example shows the entire human genome—about 3Gb— fit in 360 degrees. This gives a scale of about 8 Mb/degree. The circumference of the ideogram circle for an 800 x 800 pixel image (the resolution of the images in this example) is about 2000 pixels. When expressed in terms of pixels, the scale is 1.5 Mb/pixel at the radius of the ideograms.
The simplest way to make everything larger is to increase the size of the output image. The best way to do this is to override the
radius parameter in the <image> block.
<image> <<include etc/image.conf>> radius* = 3000p </image>
The default value is
radius = 1500p, which creates images 3,000 x 3,000 pixels in size. This is generally sufficient (>300 dpi) for images printed at 10 inches or less.
Within an image you can adjust the magnification factor of individual ideograms, or groups of ideograms. This is useful to do because genomes tend to be interesting in spots.
You can adjust the length scale for each ideogram using the
chromosomes_scale parameter. The parameter associates a magnification with each
ideogram. For example,
chromosomes_scale = hs1:0.2;hs2:0.2;hs3:0.2;hs8:5;hs9:5;hs10:5
would result in chromosomes 1, 2, and 3 drawn at 0.2x their size and chromosomes 8, 9, and 10 drawn at 5x. All other ideograms are scaled appropriately so that all elements fit within the circle.
You can individually enumerate the ideograms for which scale should be adjusted, as shown above, or use a regular expression to select more than one ideogram.
For example, to shrink all ideograms matching the regular expression
chromosomes_scale = /rn/:0.5
You can combine regular expressions with lists. This will apply a scale of 2x to
rn5, with all other
rn ideograms shown at 0.5x.
chromosomes_scale = /rn/:0.5;rn5:2
By defining the
parameters in the <ticks> block, you can supress the display of
ticks and their labels in areas where they appear densely. This is
useful to help avoid micro-managing tick and label
Another parameter that helps manage tick labels is
min_label_distance_to_edge, which controls the display of labels which are too
close to the edge of an ideogram. This parameter is useful if
ideograms are closely spaced and their edge tick labels start to
overlap. You can also use this parameter to effectively hide the first
tick label (typically 0).
<ticks> tick_separation = 3p label_separation = 10p min_label_distance_to_edge = 10p ... </ticks>
When changing the scale of ideograms, you may need to toggle the display of ticks for specific ideograms to keep the image clean. One use case is to show ticks only for the first ideogram, to establish the scale for the image, and then only for subsequent ideograms for which scale changes.
To hide ticks for specific ideograms (e.g. chr9), use
chromosomes parameter in the <tick> block
<tick> chromosomes = -hs9 spacing = 0.5u ... </tick>
To display ticks on specific ideograms (e.g. chr9),
<tick> chromosomes_display_default = no chromosomes = hs9 spacing = 0.5u ... </tick>