You may have noticed that this recipe actually plots whole genes, and not the peptide hits we started with. Plotting the genes is the simplest case, but going to the peptides requires only a small change. In Step 5, we create an object, genes_for_prots, which gives the start and end of the genes. The earlier msnid@psms object contains starts and ends of peptides within those genes, indexed from the start of the hit, so by adding one to the other, it is possible to create an object that represents the peptides and not the genes.

For those of you not working with organisms in the UCSC browser, it is still possible to generate a GFF file of the hits to upload into another genome browser—many offer this functionality. Simply stop the recipe at the end of Step 5 and use the rtracklayer::export() function to create a GFF file.