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1 #Roary plots
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2 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.
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3
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4 The dependancies are:
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5 - python (2 or 3)
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6 - Biopython
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7 - numpy
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8 - pandas
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9 - matplotlib
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10 - seaborn
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11
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12 Usage:
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13 ```
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14 python roary_plots.py my_tree.tre gene_presence_absence.csv
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15 ```
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16
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17 The images it produces are:
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18 * A pan genome frequency plot
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19 * A presence and absence matrix against a tree
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20 * A piechart of the pan genome, breaking down the core, soft core, shell and cloud.
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