Hi there, been using Roary for 3 years now... awesome tool!
I'm just curious how it is that all the plots it produces aren't single values? For example... the "Number of unique genes" plot should just be a fixed single value of the number of unique genes am i right? So how come it's a collection of whisker plots per genome, that sometimes even has outlier points? How can it have a range of values per genome unless it calculates it for different Nucleotide Identity values or something... It's not as if it also produced a range of gene_presence_absence.csv files.
I'm just curious if anyone knows what these plot ranges are based on
EDIT: i looked all over, but there is no explenation anywhere where the ranges come from. So ended up writing an extensive R script that just calculates it for you based on the gene_abscence_presence.csv file... but would still be interested in knowing the reason for this weird output if anyone knows