Global Imports



In [3]:

    
%pylab inline









    



Populating the interactive namespace from numpy and matplotlib

External Package Imports



In [4]:

    
import os as os
import pickle as pickle
import pandas as pd



In [5]:

    
print 'changing to source dirctory'









    



changing to source dirctory



In [6]:

    
os.chdir('../src')



In [7]:

    
import Data.Firehose as FH

Tweaking Display Parameters

Load default custom.css file from ipython profile



In [8]:

    
from IPython import utils  
from IPython.display import HTML



In [9]:

    
css_file = 'profile_default/static/custom/custom.css'
base = utils.path.get_ipython_dir()
styles = "<style>\n%s\n</style>" % (open(os.path.join(base, css_file),'r').read())
display(HTML(styles))

Pandas display parameters



In [10]:

    
pd.set_option('precision', 3)
pd.set_option('display.width', 300)
plt.rcParams['font.size'] = 12

Tweaking color scheme



In [11]:

    
'''Color schemes for paper taken from http://colorbrewer2.org/'''
colors = plt.rcParams['axes.color_cycle']
colors_st = ['#CA0020', '#F4A582', '#92C5DE', '#0571B0']
colors_th = ['#E66101', '#FDB863', '#B2ABD2', '#5E3C99']

Global Run Variables

Change __OUT_PATH__ to directory on your machine where you want to store the data



In [12]:

    
OUT_PATH = '../Data'
RUN_DATE = '2014_07_15'
VERSION = 'all'
CANCER = 'HNSC'
FIGDIR = '../Figures/'
if not os.path.isdir(FIGDIR):
    os.makedirs(FIGDIR)



In [13]:

    
DESCRIPTION = '''Updating analysis for updated dataset.'''

PARAMETERS = {'min_patients' : 12,
              'pathway_file' : '../ExtraData/c2.cp.v3.0.symbols_edit.csv'
              }



In [18]:

    
#GENE_POS = pd.read_csv('../ExtraData/HGNC_chr_pos.txt')
#GENE_LIST_FILE = '../ExtraData/HGNC_Genes'
#GENES = open(GENE_LIST_FILE, 'rb').read().split('\n')