Circos > Documentation > Tutorials > Recipes > Labeling Bands
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20 imperatives of information design — BioVis 2012

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8 — Recipes

3. Labeling Karyotype Bands

Use a text track to create labels for the cytogenetic bands. First, if you have defined bands in the karoytype file, use it to generate a data file for this track. This is necessary because the karyotype and text data files have different formats. 

< 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
...

Now use 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. 


<plot>

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

r0 = 1r
r1 = 1r+300p

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

label_size = 12p
label_font = condensed
padding    = 0p
rpadding   = 0p

</plot>

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. 


<rules>
<rule>
importance = 100
condition  = _CHR_ eq "hs1"
color      = blue
flow       = continue
</rule>

<rule>
importance = 90
condition  = _START_ > 50000000 && _END_ < 100000000
color      = green
flow       = continue
</rule>

<rule>
importance = 90
condition  = _LABEL_ =~ /[.]\d\d/
color      = grey
</rule>
</rules>

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.