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.

7 — 2D Data Tracks

9. Glyphs — Part I

Rules can be used to adjust the text of the label. This is done by setting the value parameter in the rule. The rule below sets all labels to X, regardless of their original text. 

<rule>
condition  = 1
value      = X
</rule>

You can combine this with other rules. For example, if the text is sequence, you can set the color of the character based on its identity and then change it to another value. The color rules must have flow=continue to allow the downstream label-changing rule to also be evaluated (recall that without this flow=continue statement, triggered rules terminate the rule chain). 

# first change color
<rule>
condition  = var(value) eq "A"
color      = red
flow       = continue
</rule>

<rule>
condition  = var(value) eq "T"
color      = blue
flow       = continue
</rule>

<rule>
condition  = var(value) eq "C"
color      = green
flow       = continue
</rule>

# change label text, for all data points
<rule>
condition  = 1
value      = X
</rule>

You can turn a text track into a glyph track by changing the font and adjusting the text label to the desired glyph. For example, using the symbol font (fonts/symbols/symbols.ttf, defined under the font name glyph in etc/fonts.conf), you can obtain square glyphs like so 


<plot>
label_font = glyph

<rules>
...
<rule>
condition = 1
value     = m
</rule>
...
</rules>

The symbols font defines the following characters 

 small
 | medium
 | | large
 | | |
 a b c   square
 d e f   rhombus
 g h i   triangle up
 j k l   triangle down
 m n o   circle

upper case - solid
lower case - hollow

By adjusting the padding more tightly, you can pack the square glyphs to touch. By adjusting the color and glyph shape, you can create attractive tracks.