Question: ggbio plotIdeogram(..., zoom.region) broken ?
0
3.4 years ago by
kevin.rue230
University of Oxford
kevin.rue230 wrote:

Hi all,

I am just  trying to plot data with ggbio with an ideogram to highlight the region plotted underneath.

I have basically followed the vignette, and I cannot see any change with/without the zoom.region= argument. I have tried the which= argument as well, without better luck. I am pretty sure that in a past release of ggbio, I made a colored rectangle appear on the Ideogram to highlight the region plotted in the other tracks.

Here is code to replicate the issue:

library(biovizBase)
data(hg19IdeogramCyto, package = "biovizBase")
biovizBase::isIdeogram(hg19IdeogramCyto) ## return TRUE
plotIdeogram(hg19IdeogramCyto, "chr1")
plotIdeogram(hg19IdeogramCyto, "chr1", xlabel = TRUE)
plotIdeogram(hg19IdeogramCyto, "chr1",  zoom.region = c(1e7, 1.5e7))


With the last line not showing anything more on the ideogram as far as I can see.

Thanks!

Kevin

> library(BiocInstaller)
Bioconductor version 3.3 (BiocInstaller 1.22.2), ?biocLite for help
> biocValid()
[1] TRUE
biovizbase ggbio • 422 views