Generate volcano plot for Stevenson et al.

Stevenson_volcano_plot.py

#!/usr/bin/env python

import sys
import pandas as pd

import matplotlib as mpl
# Force matplotlib to not use any Xwindows backend.
mpl.use('Agg')
import matplotlib.pyplot as plt

import seaborn as sns


import logging
FORMAT = '%(asctime)s %(message)s'
logging.basicConfig(format=FORMAT)
logger = logging.getLogger(__name__)
logger.setLevel(logging.INFO)

if len(sys.argv) == 2:
    de = pd.read_csv(sys.argv[1], header=0, index_col=False)

    outfn = '.'.join(sys.argv[1].split('.')[:-1]) + '.volcano.eps'

    de['sig'] = de['FDR'] < 0.05

    de=de.sample(frac=1)

    pal = [(0.7,0.7,0.7), (1.0,0.27,0.0)]

    ax = sns.scatterplot(x='logFC', y='logCPM', data=de, hue='sig', palette=pal, size=2, legend=False)

    fig = ax.figure
    fig.savefig(outfn, bbox_inches='tight')

else:
    sys.exit('usage: %s <DE table>' % sys.argv[0])