EvdH0 Update roary_plots from .ix to .loc
Since 0.20.1 .loc is the preferred index lookup method instead of .ix
https://pandas.pydata.org/pandas-docs/version/0.20/whatsnew.html#deprecate-ix
Latest commit a4b2066 Aug 16, 2018

README.md

#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.