class CytoscapeClient:
"""This is a wrapper to the py2cytoscape wrapper. The local installation of Py2cytoscape has been modified for it to work"""
def __init__(self, host="localhost", port="1234", version="v1"):
self.cy = CyRestClient(ip=host, port=port, version=version)
def gc(self):
self.cy.gc()
def free_memory(self):
self.cy.gc()
X = self.cy.status()
return max(
X['memoryStatus']['maxMemory'] - X['memoryStatus']['usedMemory'],
X['memoryStatus']['freeMemory'])
def random_id(self, prefix="MY_"):
import random
s = "ABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789"
return prefix + ''.join(
[s[random.randint(0,
len(s) - 1)] for i in range(10)])
def cynet_from_xgmml(self,
s_file,
name=None,
s_layout="force-directed",
l_bundle=True,
t_xy=None,
l_digraph=False):
"""If t_xy is provided, s_layout is ignored
return CyNetwork"""
import os
if not os.path.exists(s_file):
import util
util.warn_msg('Missing file: %s' % s_file)
return None
if not l_digraph:
net = xgmml.Network(s_file, name=name)
else:
import digraph
net = digraph.Digraph(s_file, name=name)
if t_xy is not None:
net.set_XY(t_xy)
s_layout = None
S = net.T_node.header()
#print "---------------->", S
#S=[x for x in S if x not in ('Gene','Name','Symbol')]
#net.T_node.drop(S, axis=1, inplace=True)
##############################
return self.cynet_from_network(net,
name=name,
s_layout=s_layout,
l_bundle=l_bundle)
def cynet_from_network(self,
net,
name=None,
s_layout="force-directed",
l_bundle=True):
"""Input net: xgmml.Network object
return CyNetwork"""
#print "====>>>>>>>>", net.T_node.header()
data = net.to_json()
if name is None:
name = data['data']['name']
#cynet=self.cy.create(suid=net)
cynet = None
for trial in range(
3): # something Cytoscape errors, try up to three times
try:
if cynet is None:
cynet = self.cy.network.create(name=name, data=data)
except:
cynet = None
print("Fail at trail %d" % (trial + 1))
print("JSON data>", data)
if cynet is None:
import sys
util.warn_msg('Error during plot_go_network(): %s' %
sys.exc_info()[0])
print(traceback.format_exc())
id = cynet.get_id()
if s_layout is not None:
#print "apply layout %s" % s_layout
self.cy.layout.apply(name=s_layout, network=cynet)
if l_bundle:
self.cy.edgebundling.apply(cynet)
#print "apply bundle %s" % s_layout
self.cy.layout.fit(cynet)
return cynet
def delete_cynet(self, cynet=None):
"""None means delete all networks"""
if cynet is None:
self.cy.network.delete_all()
else:
self.cy.network.delete(cynet)
def get_network(self, suid):
"""Get xgmml.Network with X,Y coordinates"""
cynet = self.cy.network.create(suid=suid)
net = xgmml.Network.from_json(cynet.to_json())
net.T_node.drop([
x for x in ['graphics_x', 'graphics_y', 'SUID', 'id_original']
if x in net.T_node.header()
],
axis=1,
inplace=True)
t_xy = self.cynet_get_XY(cynet)
if t_xy is not None:
t_xy.drop('Gene', axis=1, inplace=True)
t_xy.rename2({'x': 'graphics_x', 'y': 'graphics_y'})
net.T_node = net.T_node.merge(t_xy,
left_on='id',
right_on='id',
how='left')
return net
def get_cynet(self, cynet):
"""make sure we return a cynet object"""
if type(cynet) in (str, int):
return self.cy.network.create(suid=int(cynet))
return cynet
def cynet_get_XY(self, cynet):
cynet = self.get_cynet(cynet)
data = cynet.get_first_view()
if data is None: return None # view does not exist
nodes = data['elements']['nodes']
X = []
for node in nodes:
# id is an internal id, Gene is our key
X.append({
'id': str(node['data']['id']),
'x': node['position']['x'],
'y': node['position']['y'],
'Gene': node['data']['Gene']
})
t_xy = pd.DataFrame(X)
return t_xy
def cynet_save(self, cynet, s_file="x.png"):
def save_image(s_file, data):
f = open(s_file, 'wb')
f.write(data)
f.close()
cynet = self.get_cynet(cynet)
s_ext = s_file.upper()
if s_ext.endswith('.PNG'):
save_image(s_file, cynet.get_png())
elif s_ext.endswith('.PDF'):
save_image(s_file, cynet.get_pdf())
