Question: How to plot circular genomes with gviz?
1
11 months ago by
Christopher.Rands10 wrote:

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 • 357 views
modified 11 months ago • written 11 months ago by Christopher.Rands10

Apparently this simply isn't possible with Gviz, see here https://bioinformatics.stackexchange.com/questions/4890/how-to-plot-circular-chromosomes-with-gviz/