Mercurial > repos > dereeper > roary_plots
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author | dereeper |
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date | Fri, 12 Nov 2021 16:32:26 +0000 |
parents | c47a5f61bc9f |
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#Roary plots Marco Galardini (marco@ebi.ac.uk) 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) - Biopython - numpy - pandas - matplotlib - seaborn Usage: ``` 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.