Circos > Documentation > Tutorials > Recipes > Labeling Bands

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9 — Recipes

3. Labeling Karyotype Bands

This tutorial show syou how to add a narrow band of text labels to your figure. We'll label the cytogenetic bands on the ideograms for the example.

First, we'll extract the position and names of the bands from the human karyotype file that is included with Circos (data/karyotype/karyotype.human.txt).

> cat data/karyotype.human.txt | grep band | awk '{print $2,$5,$6,$3}'
hs1 0 2300000 p36.33
hs1 2300000 5300000 p36.32
hs1 5300000 7100000 p36.31

This data file to populate a text track. In this example, I've placed the band labels immediately outside the ideogram circle, which required that I shift the ticks outward.


type  = text
color = red
file  = data/8/text.bands.txt

r0 = 1r
r1 = 1r+300p

label_size = 12
label_font = condensed

show_links     = yes
link_dims      = 0p,2p,6p,2p,5p
link_thickness = 2p
link_color     = black

label_snuggle        = yes
max_snuggle_distance = 1r
snuggle_tolerance    = 0.25r
snuggle_sampling     = 2
snuggle_refine       = yes


adjusting text color

One way to adjust the color of the text is to use rules. For example, the three rules below adjust the color of the text based on chromosome, position and text label, respectively.

condition  = on(hs1)
color      = blue
flow       = continue

condition  = var(start) > 50mb && var(end) < 100mb
color      = green
flow       = continue

condition  = var(value) =~ /[.]\d\d/
color      = grey


You can also adjust the color of the label (or any other format parameter) by including the corresponding variable/value pairs directly in the data file.

hs10 111800000 114900000 q25.2 color=orange
hs10 114900000 119100000 q25.3 color=orange
hs10 119100000 121700000 q26.11 color=purple
hs10 121700000 123100000 q26.12 color=purple
hs10 123100000 127400000 q26.13 label_size=24p
hs10 127400000 130500000 q26.2 label_size=18p
hs10 130500000 135374737 q26.3 label_size=14p

Remember that rules will override these settings, unless overwrite=no is set in a rule.