In [2]:

    

%matplotlib inline
import matplotlib as mpl
mpl.use('agg')
import sys;sys.path.insert(1,'/home/arya/workspace/bio/')
import matplotlib as mpl
mpl.use('Agg')
import os
# os.environ["DISPLAY"] = "localhost:11.0"
import numpy as np
import matplotlib.pyplot as plt
import sys,os
path='/'.join(os.getcwd().split('/')[:-4])
sys.path.insert(1,path)
import Utils.Util as utl
import Utils.Plots as pplt
import pandas as pd
pd.options.display.max_rows = 20;
pd.options.display.expand_frame_repr = True
from IPython.display import display
import seaborn as sns
import Scripts.KyrgysHAPH.Util as kutl
import Scripts.KyrgysHAPH.Plot as kplt
import Scripts.HLI.Kyrgyz.IBSScan.IBDScan as ibd
import Scripts.HLI.Kyrgyz.PBS as pbs
from glob import glob
pd.options.display.max_colwidth = 2000;
import matplotlib as mpl
mpl.rcParams['figure.dpi'] = 100
i=pd.Series({'CHROM':22,'start':20000000,'end':20001000})


    

In [116]:

    

i=pd.Series({'CHROM':'M','start':1,'end':17000})
pops=['Healthy','HAPH','CHB']
a=utl.gz.GT('/home/arya/POP/KGZU/chrM.vcf.gz',coding='dominant').T
f=lambda a: pd.Series(a.values.reshape(-1)).value_counts()
p1,p2,p3=kutl.ID(pops[0]).astype(str),kutl.ID(pops[1]).astype(str),kutl.ID(pops[2],maxn=20).astype(str)
p=pd.concat([p1,p2]).astype(int)
a=a.loc[p].T
a=a[a.mean(1)>0].T
X=utl.pcaX(a,5)
x,y=0,1
X.loc[p1.astype(int)].plot.scatter(x=x,y=y,color='b')
X.loc[p2.astype(int)].plot.scatter(x=x,y=y,color='r',ax=plt.gca())


    

    
Out[116]:





<matplotlib.axes._subplots.AxesSubplot at 0x7f7fb0857610>






    

In [111]:

    

POPS=[('Healthy','Sick'),('No-HAPH','HAPH'),('Healthy','HAPH')]
a=pd.concat(map(lambda pops: pd.read_pickle('/home/arya/POP/KGZU/chrM.{}.{}.Fisher.df'.format(pops[0],pops[1])).apply(np.log10).abs(),POPS),1)
a.columns=POPS
pplt.Manhattan(a);


    

In [122]:

    

pops=['Healthy','HAPH','CHB']
a=utl.gz.GT('/home/arya/POP/KGZU+ALL/chrM.vcf.gz',coding='dominant').T
f=lambda a: pd.Series(a.values.reshape(-1)).value_counts()
p1,p2,p3=kutl.ID(pops[0]).astype(str),kutl.ID(pops[1]).astype(str),kutl.ID(pops[2],maxn=20).astype(str)
p=pd.concat([p1,p2,p3])
a=a.loc[p].T
a=a[a.mean(1)>0].T
X=utl.pcaX(a)
X.loc[p1].plot.scatter(x=x,y=y,color='b')
X.loc[p2].plot.scatter(x=x,y=y,color='r',ax=plt.gca())
X.loc[p2].plot.scatter(x=x,y=y,color='r',ax=plt.gca())


    

    
Out[122]:





<matplotlib.axes._subplots.AxesSubplot at 0x7f7fa1f834d0>






    

In [ ]:

    

m=utl.IBD()