How to plot circular genomes with gviz?
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@christopherrands-16908
Last seen 3.2 years ago

I am using Gviz to plot several tracks. I create a GenomeAxisTrack() and then several AnnotationTrack()s that I feed to plotTracks(). This produces a stacked output of tracks with annotated arrows as I want but the displays are linear. In some cases have the complete genomes and I know they are circular (like some bacterial/viral chromosomes), how can I display the plots as circular? 

I tried feeding to AnnotationTrack(); a GRanges() object with a Seqinfo() object specifying the isCircular=TRUE flag, but this didn't change the resulting plot.

Here is minimal code to create a linear plot, I would like a circular one where the first and last arrow join up:

 

library(Gviz)
library(stringr)

track <- AnnotationTrack(start=c(1,5,7), end=c(2,6,10), strand=c('+','+','-'), stacking="dense", fill=c('red','blue', 'black'))
pdf(file=paste("test","pdf", sep="."))
plotTracks(track)
dev.off()

 

 

Thank you!

gviz gviz-package • 664 views
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