The meaning of plotting exons is when you plot genomic coordinates along X-axis (for example chr1 from 1000bp to 2000bp) and draw different gene elements above (for example: exon-intron-exon).

You can easily draw such graphs in R when your input is only gene ID using GenomeGraphs take a look at: 2.1 Plotting a Gene.

Hi you can use genoPlotR to draw exon-intron-exon junctions and make comparissions between genes and genomes. You can add phylogenetic analysis too