You can see an example of how this is done in Alexa-seq using R code. The figure shows LAMA3 with 77 exons. There are two representations of the gene, one that shows the overall structure of exons and their proportional distance and the other has a sort of zoomed in view with exons depicted on log2 scale and introns on log10 scale. In this case some alternative splicing information is marked up. But instead you could indicate mutations. Unfortunately this is not part of an existing R package and is just done with basic R plotting functions in an R script of about 300 lines. But, maybe it will give you some ideas.