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.

1 — Configuration and Installation

11. SVG Output

Circos is capable of producing both PNG and SVG images. This section discusses SVG files.

SVG Output

SVG stands for scalable vector graphics and it is a format that defines an image using vector-based primitives (lines, squares, rectangles, etc) rather than pixels. SVG images can be turned into a bitmap (rasterized) at any resolution, which makes them appealing for creating figures for publication. You can edit and rasterize SVG files using applications such as Illustrator or Inkscape.

To turn SVG output on, set the svg flag in the <image> block 

<image>
...
svg = yes
...
</image>

or use the -svg command-line flag 

bin/circos -svg

You can also suppress the creation of the SVG file using 

bin/circos -nosvg

Fonts in SVG files

Text elements in SVG files have the font-family attribute, which specifies the font for the text element.

Make sure that you have all the fonts used by your image installed on your system. Circos uses CMU Modern (see fonts/modern) for all its labels and a custom symbols font (see fonts/symbols). I've had reports from Windows users that Illustrator failed to load the SVG file unless all the fonts used by the figure were installed.

If your text appears smaller than expected, increase the svg_font_scale parameter in etc/housekeeping.conf.