text: user104: 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 I have the complete genomes and I know they are circular (like some bacterial and 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 one where the first and last arrow join up in a circle:
  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'))
  png(file=paste("test","png", sep="."))
  plotTracks(track)
  dev.off()
  
  
  Note, I am not interested in alternative software recommendations, I would like to solve this with gviz if it is possible. Also asked this here.
  
  user104: The primary author of Gviz confirmed to me via email that this is not possible:
  
  Gviz will only give you the traditional linear tracks. There are a
    bunch of solutions available for visualizing circular genomes, most of
    which are more interactive in nature and not implemented in the rather
    static R graphics context. GGplot2 has some support for circular axes,
    too. If you want to stay within the R environment I’d start there.
    Ggbio is another option providing a somewhat higher-level interface.
  
  
original_text: 104: <p>I am using Gviz to plot several tracks. I create a <code>GenomeAxisTrack()</code> and then several <code>AnnotationTrack()</code>s that I feed to <code>plotTracks()</code>. This produces a stacked output of tracks with annotated arrows as I want but the displays are linear. In some cases I have the complete genomes and I know they are circular (like some bacterial and viral chromosomes), how can I display the plots as circular?</p>
  
  <p>I tried feeding to <code>AnnotationTrack()</code>; a <code>GRanges()</code> object with a <code>Seqinfo()</code> object specifying the <code>isCircular=TRUE</code> flag, but this didn't change the resulting plot.</p>
  
  <p>Here is minimal code to create a linear plot, I would like one where the first and last arrow join up in a circle:</p>
  
  <pre><code>library(Gviz)
  library(stringr)
  
  track &lt;- AnnotationTrack(start=c(1,5,7), end=c(2,6,10), strand=c('+','+','-'), stacking="dense", fill=c('red','blue', 'black'))
  png(file=paste("test","png", sep="."))
  plotTracks(track)
  dev.off()
  </code></pre>
  
  <p><a href="https://i.stack.imgur.com/SJ9Nw.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/SJ9Nw.png" alt="enter image description here"></a></p>
  
  <p>Note, I am not interested in alternative software recommendations, I would like to solve this with gviz if it is possible. Also asked this <a href="https://support.bioconductor.org/p/112040/" rel="nofollow noreferrer">here</a>.</p>
   104: <p>The primary author of Gviz confirmed to me via email that this is not possible:</p>
  
  <blockquote>
    <p>Gviz will only give you the traditional linear tracks. There are a
    bunch of solutions available for visualizing circular genomes, most of
    which are more interactive in nature and not implemented in the rather
    static R graphics context. GGplot2 has some support for circular axes,
    too. If you want to stay within the R environment I’d start there.
    Ggbio is another option providing a somewhat higher-level interface.</p>
  </blockquote>
  