#Roary plots Marco Galardini (email@example.com) has prepared an ipython notebook which can take in a tree (newick) and the gene presence and absence spreadsheet, and generate some nice plots.
The dependancies are:
- python (2 or 3)
python roary_plots.py my_tree.tre gene_presence_absence.csv
The images it produces are:
- A pan genome frequency plot
- A presence and absence matrix against a tree
- A piechart of the pan genome, breaking down the core, soft core, shell and cloud.