Add a legend to circos plot

Question

[User000]

Hello,

I would like to add A,B,C tracks labelling to a circos plot. Would you suggest how to do it? I already left a space between the chromosomes.

Answer 1

[bernatgel]

As far a I know, there is no functionality in Circos to add labels to tracks. We usually use an external program (Inskscape or similar) to add the labels when preparing the figure to publish.

Another option would be to use a text track with the track names, and try to position them as if they were features in the genome.

Or, if your data does not need the circular layout, you could change completely and use karyoploteR instead, which supports track labels.

[User000]

thanks a lot, yes i have seen inkscape before, seems to be confusing. Would you mind to explain shortly how to use it? I might try GIMP as well if it works..

Answer 2

[Ibrahim Tanyalcin]

Hey,

If you are not going to add a lot of labels an svg editor will be fine. You open the .svg output of circos and open that with inkscape. You can add over your text labels and save it as png/pdf.

One other option I remember I did for my self a long time ago is to combine 2 symmetric but reverse oriented connectograms to mimic a label. marker. Then add a text track right below/above it. Here is a link to an example for what I mean, look at the yellow "repeat" regions:

Example for NFKB1

Here is an image of the part I am mentioning

And here is the connector file to give you an idea:

connector.txt:

NFKB1 556500000 541000000 property=repeat
NFKB1 556500000 572000000 property=repeat
NFKB1 596500000 580000000 property=repeat
NFKB1 596500000 613000000 property=repeat
NFKB1 629500000 613000000 property=repeat
NFKB1 629500000 646000000 property=repeat
NFKB1 665500000 649000000 property=repeat
NFKB1 665500000 682000000 property=repeat
NFKB1 700000000 683000000 property=repeat
NFKB1 700000000 717000000 property=repeat
NFKB1 733500000 717000000 property=repeat
NFKB1 733500000 750000000 property=repeat

You can find rest of the tracks Here

Hope that gives you an idea.