#!/bin/env python2
import pypath
if __name__ == "__main__":
pa = pypath.PyPath()
pa.init_network() #exclude=["psite", "signor", "dbptm", "depod", "phelm"])
# remove high-throughput data
pa.remove_htp()
pa.get_directed()
pa.save_network()
else:
ymove = bbox1._points[0][1] - bbox2._points[1][1]
return (xmove, ymove)
# parameters
omnipath = 'All'
prefix = "int"
lab_size = (18, 21)
axis_lab_size = 36
table2file = 'int_curation_stats_stripped.tex'
fisherFile = 'fisher_tests_int'
fontW = 'medium'
console(':: Creating new network object')
net = pypath.PyPath(9606)
# see `default_network.py` for the initialization of this default network
console(':: Loading network')
net.init_network(data_formats.interaction_htp, exclude=['hi3'])
hc = plot.HtpCharacteristics(net,
fname='htp_int_10000.pdf',
title='Interaction resources',
lower=2,
upper=10000)
hc = plot.HtpCharacteristics(net2,
fname='htp_causal_1000.pdf',
title='Causal resources',
lower=1,
# For permission please contact me.
#
# Website: http://www.ebi.ac.uk/~denes
#
import pypath
from pypath import data_formats
from pypath import plot
from collections import Counter
import matplotlib as mpl
import seaborn as sns
import scipy.stats as stats
pw = pypath.PyPath()
pw.init_network(data_formats.pathway)
it = pypath.PyPath()
it.init_network(data_formats.interaction_htp)
def significance(p):
return 'ns' if p > 0.05 \
else '*' if p > 0.01 \
else '**' if p > 0.001 \
else '***' if p > 0.0001 \
else '****'
labels = ['Activitiy flow\npathways', 'Interaction\nnetworks']