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plotting gene structure in R

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)

visualisation gene-structure
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written by chictu • chictu

2 answers

Maybe give ggtranscript a go

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written by biofalconch biofalconch

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.

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written by Matthias Zepper Matthias Zepper

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

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written by chictu • chictu

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