OmicsCircos: How to control space between segments?
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@free2roamfred-14302
Last seen 8.2 years ago

The circos function in the OmicsCircos package draws chromosomal segments with some space between them. How to control the width of this space?

For instance, if I wanted to represent a single circular chromosome (e.g. a bacterial chromosome), how would I use the circos function to plot this, since the current function plots the single chromosome with a space at the end such that the circle appears disjointed?

Here's the code I've used to plot the single chromosome:

circos(R=400, cir=angles, type="chr", print.chr.lab=F, W=4, scale=F)

 


 

omicscircos • 1.1k views
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@free2roamfred-14302
Last seen 8.2 years ago

Upon the suggestion from the authors of the package:

Changing the angle.end parameter to 362 instead of the default 360 does the trick!

angles <- segAnglePo(seg.dat=seg, seg=seg$chrom, angle.start = 0, angle.end = 362)

This can be used to control the spacing between the segments. Needs some trial and error though!

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