new_contents: from matplotlib import pyplot as plt
  plt.rcParams['pdf.fonttype'] = 42
  
  import pandas as pd
  import seaborn as sns
  sns.set_style('whitegrid')
  sns.set_palette('Set1')
  
  pcr_plus = set(x.strip() for x in open('pcr-plus.samples'))
  
  df = pd.read_table('simons-indexcov.ped', index_col='sample_id')
  size = 9
  
  pp = df.loc[pcr_plus]
  
  tot = pp['bins.in'] + pp['bins.out']
  
  plt.scatter(pp['bins.lo'] / tot, pp['bins.out'] / tot, alpha=0.55, label='PCR +', s=size, zorder=2)
  
  pf = df.loc[[x for x in df.index if not x in pcr_plus]]
  tot = pf['bins.in'] + pf['bins.out']
  plt.scatter(pf['bins.lo'] / tot, pf['bins.out'] / tot, alpha=0.55, label='PCR free', s=size)
  
  plt.xlabel('Proportion of bins with scaled coverage < 0.15')
  plt.ylabel('Proportion of bins with scaled coverage outside of (0.85, 1.15)')
  plt.xlim(xmin=0.067, xmax=0.0695)
  
  plt.legend()
  plt.savefig('figure4.eps', dpi=1000)
  
subject: add figure 4 script