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.
9 — Recipes
15. Pattern Fills
Ribbons, heatmaps and histograms can be drawn with a pattern fill by setting the pattern parameter.
<link> ... ribbon = yes pattern = checker ... </link>
Patterns
The following patterns are available
- solid
- hline
- hline-sparse
- vline
- vline-sparse
- checker
- checker-sparse
- dot
- dot-sparse
Like fonts, patterns are named in their own block and imported from another configuration file. The file that defines patterns is etc/patterns.conf. The bitmaps for the patterns are found in etc/tiles.
# etc/pattern.conf
vline = tiles/vlines.png
vline-sparse = tiles/vlines-sparse.png
...
The configuration file etc/colors_fonts_patterns.conf takes care of importing all the pattern definitions.
<<include etc/colors_fonts_patterns.conf>>
You can add your own patterns by creating a PNG file and adding it to the pattern block. Use an 8-bit PNG. Transparency is not supported for tiles.
If you do not specify a color for a pattern (see below), the pattern will be used as it appears in the PNG file, without any change in colors.
Colored Patterns
A pattern's colors can be remapped using the color parameter. The predefined patterns are black-on-white, but you can remap a pattern's color by defining a list of old:new colors.
color = white:red,black:orange
To invert a black and white pattern,
color = white:black,black:white
To replace all the colors in a pattern that are not the same as the image's background color, set the color value to a single word. For example, on an image whose background is black
color = red
will color all non-black pixels in the pattern red.
In this tutorial, the links originally are defined with a color.
hs11 27363982 47363982 hs8 1 12346012 color=chr11 hs11 113293528 133293528 hs21 24848956 44848956 color=chr11 hs10 27542441 47542441 hs20 33053889 53053889 color=chr10
A rule is set up so that for 50% of the ribbons, a colored pattern is selected.
For about 25% of the links, only a pattern is selected. Because each link already has a color, the pattern is colored by the existing color (in this case, chromosome color).
Patterns with Transparency
This is not supported by GD. Regardless of whether your PNG file has transparency or not, the tiled pattern will not have transparent components.