GTEX Gene Expression Analysis

In [74]:

    

%matplotlib inline


    

In [77]:

    

import pandas as pd
import numpy as np
import os as os
import matplotlib.pyplot as plt 
import seaborn as sns


    

In [2]:

    

GTEX = '/cellar/users/agross/Data/DiffExp/GTEX/'


    

In [61]:

    

GTEX_WEB = 'http://gtexportal.org/static/datasets/gtex_analysis_v4/'
files = [('annotations/GTEx_Data_V4_Annotations_SampleAttributesDS.txt', 
          'SampleAttributes.txt'),
         ('annotations/GTEx_Data_V4_Annotations_SubjectPhenotypes_DS.txt', 
          'SubjectPhenotypes.txt'),
         ('rna_seq_data/GTEx_Analysis_V4_RNA-seq_RNA-SeQCv1.1.8_gene_rpkm.gct.gz',
          'rna_gene_rpkm.gct.gz')]


    

In [64]:

    

def download_files():
    for f in files:
        source = GTEX_WEB + f[0]
        target = GTEX + f[1]
        !curl $source -o $target
    f = GTEX + files[2][1]
    !gunzip $f
d = os.listdir(GTEX)
if (files[0][1] in d) & (files[1][1] in d) & (files[2][1][:-3] in d):
    print 'Using downloaded files...'
else:
    print 'Downloading GTEX files'
    download_files()


    

    




Using downloaded files...

In [54]:

    

meta = pd.read_table(GTEX + 'SampleAttributes.txt',
                     index_col=0)
gtex_pat = pd.read_table(GTEX + 'SubjectPhenotypes.txt',
                     index_col=0)
gtex = pd.read_table(GTEX + 'rna_gene_rpkm.gct', skiprows=2, index_col=[0,1])
gtex.index = gtex.index.get_level_values(1)


    

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tissue_type = meta['SMTSD']


    

In [84]:

    

def plot_tissues_across_gene(gene, log=True):
    fig, ax = plt.subplots(figsize=(10,15))
    if log:
        v = np.log2(gtex.ix[gene]).dropna().clip_lower(-4)
    else:
        v = gtex.ix[gene].dropna()
    sns.violinplot(v, groupby=tissue_type, 
                   cut=.1, inner = 'points', ax=ax, vert=False)


    

In [88]:

    

#Do not import
plot_tissues_across_gene('GABRD', log=True)