plotting gene structure in R

Question

[chictu]

I have a list of amplified genes with genomic intervals and would like to visualise the specific part of gene that is affected. Is there a way to plot a gene and highlight the region of interest? I was thinking a plot with introns and exons of the genes and genomic interval at the bottom with a box highlighting the region of interest but I have no idea how to go about it. Any guidance would be greatly appreciated.

Here is an example of an interval which contains the first few exons of EGFR: chr7:55234427-53437292 (hg19)

Answer 1

[biofalconch]

Maybe give ggtranscript a go

Answer 2

[Matthias Zepper]

ggtranscript seems to be a quite neat new package. The alternative, that is around a bit longer, is Gviz, but you can't straightforwardly combine it with ggplot. To highlight the region of interest, you could either use the Annotation track or the Highlight track.

[chictu]

Thank you for the suggestions! I will give these a try.