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
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.
<plot> 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 </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> condition = on(hs1) color = blue flow = continue </rule> <rule> condition = var(start) > 50mb && var(end) < 100mb color = green flow = continue </rule> <rule> condition = var(value) =~ /[.]\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.