Just a self-reminder.
If you are using a for loop to output multiple plots, ggplot doesn't work.
Continuely add content (row or column) to a data frame and then export it to file.
Run R script with argument.
Use Python (BioPython and gffutils) to extract sequences for gene features.
In practice this is used to replace all IDs in a GFF file with your desired IDs, e.g. g10 to Smp_300010 but also g10.t1 to Smp_300010.1 (without 't').