Mercurial > repos > dereeper > roary_plots
annotate Roary/contrib/roary_plots/README.md @ 0:c47a5f61bc9f draft
Uploaded
author | dereeper |
---|---|
date | Fri, 14 May 2021 20:27:06 +0000 |
parents | |
children |
rev | line source |
---|---|
0 | 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. |