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 tutorial shows you how to use rules with the text track. All tracks allow for rules and using rules works the same way for each track. The previous tutorial used rules to color text.
We'll draw some sequence on the image and color the base pairs. We'll use a monospaced font using
label_font = mono
There are two data files used in this example,
data/6/sequence.txt (20,000 entries)
# sequence.txt ... hs1 2 2 C hs1 3 3 A hs1 4 4 A ...
data/6/sequence.long.txt (100,000 entries).
# sequence.long.txt ... hs1 1 1 A hs1 1 1 C hs1 1 1 A hs1 1 1 G hs1 2 2 T hs1 2 2 A hs1 2 2 C hs1 2 2 T ...
The ideogram in the image is
hs1:0-20kb, but it's a good idea to start with a smaller interval to see how things work, e.g.
hs1:0-1. A track with 100,000 bases can take a very long time to draw—the code that determines the character layout has not been optimized.
A good way to include rules is using the <<include ... >> directive to read them from another file. This keeps the configuration file tidy and allows you to reuse the same rules for other tracks.
<plots> # default values for all <plot> blocks type = text color = black label_font = mono label_size = 32 # radial padding rpadding = 0.2r <plot> file = data/6/sequence.txt r1 = 0.9r r0 = 0.3r label_size = 16 # angular padding padding = -0.25r <rules> <<include rule.textcolor.conf>> </rules> </plot> </plots>
rule.textcolor.conf file is
<rule> condition = var(value) eq "A" color = red </rule> <rule>
condition = var(value) eq "T" color = blue </rule> <rule> condition = var(value) eq "C" color = green </rule>
The text label is referenced using
var(value) and the conditions check whether the text is
C. The default track coloring assumes the label is
G, so we don't have to check for this condition.
With rules, you can adjust any attribute of the text
characters. For example, you can adjust the size of the letters in the
label by setting
label_size. This is done in the tracks immediately
inside and outside the circle.
<rule> # If the text is not A, then hide it. When this rule triggers, # other rules are not evaluated. condition = var(value) ne "A" show = no </rule> # This rule is applied to any text that didn't pass the previous # rule (i.e. only A). The label is set to a random value between # 12 and 48. The rand() function returns a uniformly sampled # random value in the interval [0,1). <rule> condition = 1 label_size = eval(12+32*rand()) </rule>