<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>

CC BY-SA 4.0
2018-09-11T14:22:17.090Z
2018-09-11T14:22:17.090Z
Chris_Rands
<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.sstatic.net/SJ9Nw.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/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>

CC BY-SA 4.0
2018-08-15T10:23:13.107Z
I would be amazed if there were a way to do that.
Devon Ryan
CC BY-SA 4.0
2018-08-15T10:28:47.953Z
@DevonRyan why? i have use cases, but i'm not very familiar with gviz and its implementation
Chris_Rands
CC BY-SA 4.0
2018-08-15T10:31:20.547Z
For track-based plots you would pretty much have to set it up for circular plotting from the very beginning in order for it to work. I'm aware that there are use-cases, but given where gviz was developed and the use-cases there it would be surprising if circular genomes were a consideration during development.
Devon Ryan
<r><bioconductor><gviz>
How to plot circular chromosomes with Gviz?
# How to plot circular chromosomes with Gviz?

(Asked by: username_0 on 2018-08-15)

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.

**Tags:** r, bioconductor, gviz
> **Comments:**
> **username_1**: I would be amazed if there were a way to do that.  
> **username_0**: @DevonRyan why? i have use cases, but i'm not very familiar with gviz and its implementation  
> **username_1**: For track-based plots you would pretty much have to set it up for circular plotting from the very beginning in order for it to work. I'm aware that there are use-cases, but given where gviz was developed and the use-cases there it would be surprising if circular genomes were a consideration during development.  

---

## 1 answers

### Answer by username_0 on 2018-09-11. Score: 1 | Accepted answer

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.


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