Question: Add a legend to circos plot
0
gravatar for User000
2.2 years ago by
User000270
User000270 wrote:

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.

circos • 1.7k views
ADD COMMENTlink modified 16 months ago by Biostar ♦♦ 20 • written 2.2 years ago by User000270
3
gravatar for bernatgel
2.2 years ago by
bernatgel2.1k
Barcelona, Spain
bernatgel2.1k wrote:

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.

ADD COMMENTlink written 2.2 years ago by bernatgel2.1k

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..

ADD REPLYlink written 2.2 years ago by User000270
3
gravatar for Ibrahim Tanyalcin
2.2 years ago by
Belgium
Ibrahim Tanyalcin980 wrote:

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

Sample Image

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.

ADD COMMENTlink written 2.2 years ago by Ibrahim Tanyalcin980
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