Mercurial > repos > dereeper > roary_plots
comparison Roary/contrib/roary_plots/README.md @ 0:c47a5f61bc9f draft
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| author | dereeper |
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| date | Fri, 14 May 2021 20:27:06 +0000 |
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| -1:000000000000 | 0:c47a5f61bc9f |
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| 1 #Roary plots | |
| 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. | |
| 3 | |
| 4 The dependancies are: | |
| 5 - python (2 or 3) | |
| 6 - Biopython | |
| 7 - numpy | |
| 8 - pandas | |
| 9 - matplotlib | |
| 10 - seaborn | |
| 11 | |
| 12 Usage: | |
| 13 ``` | |
| 14 python roary_plots.py my_tree.tre gene_presence_absence.csv | |
| 15 ``` | |
| 16 | |
| 17 The images it produces are: | |
| 18 * A pan genome frequency plot | |
| 19 * A presence and absence matrix against a tree | |
| 20 * A piechart of the pan genome, breaking down the core, soft core, shell and cloud. |