In [6]:

    

import pandas
filename = "m8/mS/reads_seed0.tsv"

df = pandas.read_table(filename, delimiter = "\t", skiprows=3)


    

In [7]:

    

df.head()


    

    
Out[7]:







  

    

      

      
#sample_index
      
sample_label
      
anatomical_site_index
      
anatomical_site_label
      
character_index
      
character_label
      
ref
      
var
    
  
  

    

      
0
      
0
      
P_0
      
0
      
P
      
0
      
0
      
90
      
99
    
    

      
1
      
0
      
P_0
      
0
      
P
      
1
      
1
      
106
      
115
    
    

      
2
      
0
      
P_0
      
0
      
P
      
2
      
3
      
84
      
106
    
    

      
3
      
0
      
P_0
      
0
      
P
      
3
      
4
      
191
      
0
    
    

      
4
      
0
      
P_0
      
0
      
P
      
4
      
5
      
204
      
0
    
  

In [8]:

    

df['vaf'] = df.apply(lambda x: float(x['var'])/(x['ref']+x['var']), axis=1)
df[df['vaf'] > 0]['sample_label'].unique()


    

    
Out[8]:





array(['P_0', 'P_1', 'M1_0', 'M2_0', 'M3_0', 'M4_0', 'M5_0', 'M6_0',
       'M7_0', 'M8_0'], dtype=object)

In [9]:

    

dfpivot = df.pivot(index = "character_index", columns = "sample_label", values = "vaf")


    

In [10]:

    

%matplotlib inline
from matplotlib import pyplot
import seaborn
seaborn.stripplot(data = df[df['vaf'] > 0], y= 'vaf',x = 'sample_label')
pyplot.gcf().set_size_inches(10,10)


    

In [12]:

    

seaborn.pairplot(dfpivot, vars = [d for d in dfpivot.columns],  diag_kind = 'kde', diag_kws={'bw' : 0.03})
pyplot.savefig("Simul_0.pdf")


    

In [15]:

    

df[df['vaf'] > 0][df['sample_label'] == 'P_0']['vaf'].hist(bins=20)


    

    




/Users/melkebir/anaconda2/lib/python2.7/site-packages/ipykernel/__main__.py:1: UserWarning: Boolean Series key will be reindexed to match DataFrame index.
  if __name__ == '__main__':






    
Out[15]:





<matplotlib.axes._subplots.AxesSubplot at 0x123f06810>






    

In [ ]: