Automation of the PathLinker App paper Lovastatin Analysis

In [20]:

    

# necessary libraries and dependencies
import sys
from py2cytoscape.data.cyrest_client import CyRestClient
from py2cytoscape.data.style import StyleUtil

import networkx as nx
import pandas as pd
import json
import requests

print("python version: " + sys.version)
# The py2cytoscape module doesn't have a version. I installed it 2018-04-13
#print("py2cytoscape version: " + py2cytoscape.__version__)
print("networkx version: " + nx.__version__)
print("pandas version: " + pd.__version__)
print("requests version: " + requests.__version__)


    

    




python version: 2.7.12 (default, Dec  4 2017, 14:50:18) 
[GCC 5.4.0 20160609]
networkx version: 2.1
pandas version: 0.22.0
requests version: 2.18.4

In [34]:

    

# !!!!!!!!!!!!!!!!! Step 0: Start Cytoscape 3.6 with cyREST App !!!!!!!!!!!!!!!!!!!!!!!!!!
# Cytoscape must be running to use the automation features

# Step 1: create an instance of cyRest client
cy = CyRestClient()

# Reset the session
#cy.session.delete()


    

In [35]:

    

# Step 2: Import/Create the network that PathLinker will run on
network_file = 'background-interactome-pathlinker-2015.txt'

# create a new network by importing the data from a sample using pandas
df = pd.read_csv(network_file, header=None, sep='\t', lineterminator='\n',
                 names=["source", 'target', 'weight', 'evidence'])

# and create the networkx Graph from the pandas dataframe
# this is a directed network, so I'm using the networkx DiGraph instead of the default undirected Graph
G = nx.from_pandas_edgelist(df, "source", "target", edge_attr=['weight'], create_using=nx.DiGraph())
    
# create the CyNetwork object from the networkx in CytoScape
cy_network = cy.network.create_from_networkx(G, name = 'background-interactome-pathlinker-2015', collection = 'F1000 PathLinker Lovastatin Use Case')

# obtain the CyNetwork object SUID
cy_network_suid = cy_network.get_id()


    

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# TODO the force-directed layout isn't working for some reason. All nodes are still left in the same position. 
# commenting out for now
# # give the network some style and a layout
# my_style = cy.style.create('defaut')

# # copied from here: https://github.com/cytoscape/cytoscape-automation/blob/master/for-scripters/Python/basic-fundamentals.ipynb
# basic_settings = {    
#     'NODE_FILL_COLOR': '#6AACB8',
#     'NODE_SIZE': 55,
#     'NODE_BORDER_WIDTH': 0,
#     'NODE_LABEL_COLOR': '#555555',
    
#     'EDGE_WIDTH': 2,
#     'EDGE_TRANSPARENCY': 100,
#     'EDGE_STROKE_UNSELECTED_PAINT': '#333333',
    
#     'NETWORK_BACKGROUND_PAINT': '#FFFFEA'
# }

# my_style.update_defaults(basic_settings)

# # Create some mappings
# my_style.create_passthrough_mapping(column='name', vp='NODE_LABEL', col_type='String')

# cy.layout.apply(name="force-directed", network=cy_network)
# cy.style.apply(my_style, cy_network)


    

In [37]:

    

# TODO create a better view
# for some reason, the force-directed layout isn't working.
# for now, just delete the default uninformative layout
headers = {'Content-Type': 'application/json', 'Accept': 'application/json'}
# delete the created view
url = "http://localhost:1234/v1/networks/%s/views" % (cy_network_suid)
requests.request("DELETE", url, headers=headers)

# # create a new one
# url = "http://localhost:1234/v1/networks/%s/views" % (cy_network_suid)
# requests.request("POST", url, headers=headers)

# # apply the default style
# url = "http://localhost:1234/v1/apply/styles/default/%s" % (cy_network_suid)
# requests.request("GET", url, headers=headers)

# url = "http://localhost:1234/v1/apply/fit//%s" % (cy_network_suid)
# requests.request("GET", url, headers=headers)

# # apply the force directed layout
# url = "http://localhost:1234/v1/apply/layouts/force-directed/%s" % (cy_network_suid)
# requests.request("GET", url, headers=headers)


    

    
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<Response [201]>

In [39]:

    

# Step 3: Construct input data to pass to PathLinker API function

# construct PathLinker input data parameters for API request
params = {}

# the node names for the sources and targets are space separated 
# and must match the "name" column in the Node Table in Cytoscape
params["sources"] = "P35968 P00533 Q02763"
params["targets"] = "Q15797 Q14872 Q16236 P14859 P36956"

# the number of shortest path to compute, must be greater than 0
# Default: 50
params["k"] = 50

# Edge weight type, must be one of the three: [UNWEIGHTED, ADDITIVE, PROBABILITIES]
params["edgeWeightType"] = "PROBABILITIES" 

# Edge penalty. Not needed for UNWEIGHTED 
# Must be 0 or greater for ADDITIVE, and 1 or greater for PROBABILITIES 
params["edgePenalty"] = 1

# The column name in the Edge Table in Cytoscape containing edge weight property, 
# column type must be numerical type 
params["edgeWeightColumnName"] = "weight"

# The option to ignore directionality of edges when computing paths
# Default: False
params["treatNetworkAsUndirected"] = False

# Allow source/target nodes to appear as intermediate nodes in computed paths
# Default: False
params["allowSourcesTargetsInPaths"] = False

# Include more than k paths if the path length/score is equal to kth path length/score
# Default: False
params["includeTiedPaths"] = False

# Option to disable the generation of the subnetwork/view, path rank column, and result panel
# and only return the path result in JSON format
# Default: False
params["skipSubnetworkGeneration"] = False


    

In [ ]:

    

# perform REST API call
headers = {'Content-Type': 'application/json', 'Accept': 'application/json'}

# construct REST API request url
url = "http://localhost:1234/pathlinker/v1/" + str(cy_network_suid) + "/run"
# to just run on the network currently in view on cytoscape, use the following:
#url = "http://localhost:1234/pathlinker/v1/currentView/run"

# store request output
result_json = requests.request("POST", 
                          url,
                          data = json.dumps(params),
                          params = None,
                          headers = headers)
#print(json.loads(result_json.content))


    

In [43]:

    

# Step 4: Store result, parse, and print
results = json.loads(result_json.content)

print("Output:\n")

# access the suid, references, and path rank column name
subnetwork_suid = results["subnetworkSUID"]
subnetwork_view_suid = results["subnetworkViewSUID"]
# The path rank column shows for each edge, the rank of the first path in which it appears
path_rank_column_name = results["pathRankColumnName"]
    
print("subnetwork SUID:       %s" % (subnetwork_suid))
print("subnetwork view SUID:  %s" % (subnetwork_view_suid))
print("Path rank column name: %s" % (path_rank_column_name))
print("")

# access the paths generated by PathLinker
paths = results["paths"]

# print the first 10 paths out of 50 paths
for path in paths[:3]:
    print("path rank:  %d" % (path['rank']))
    print("path score: %s" % (str(path['score'])))
    print("path:       %s" % ("|".join(path['nodeList'])))
    
# access network and network view references
subnetwork = cy.network.create(suid=subnetwork_suid)
#subnetwork_view = subnetwork.get_first_view()


    

    




Output:

subnetwork SUID:       675728
subnetwork view SUID:  675743
Path rank column name: path rank 1

path rank:  1
path score: 0.5625
path:       P00533|P0CG47|Q16236
path rank:  2
path score: 0.5625
path:       P00533|P10275|P14859
path rank:  3
path score: 0.5625
path:       P00533|P10275|Q15797

In [45]:

    

# write the paths to a file
paths_file = "lovastatin-analysis-results/pathlinker-50-paths.txt"
print("Writing paths to %s" % (paths_file))
with open(paths_file, 'w') as out:
    out.write("path rank\tpath score\tpath\n")
    for path in paths:
        out.write('%d\t%s\t%s\n' % (path['rank'], str(path['score']), "|".join(path['nodeList'])))


    

    




Writing paths to lovastatin-analysis-results/pathlinker-50-paths.txt

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# TODO map the nodes to gene names
# cy.idmapper.map_column(subnetwork, )


    

In [46]:

    

# png
subnetwork_image_png = subnetwork.get_png()
subnetwork_image_file = 'lovastatin-analysis-results/pathlinker-50-paths.png'
print("Writing PNG to %s" % (subnetwork_image_file))
with open(subnetwork_image_file, 'wb') as f:
    f.write(subnetwork_image_png)

from IPython.display import Image
Image(subnetwork_image_png)

# # pdf
# subnetwork_image_pdf = subnetwork.get_pdf()
# subnetwork_image_file = subnetwork_image_file.replace('.png', '.pdf')
# print("Writing PDF to %s" % (subnetwork_image_file))
# with open(subnetwork_image_file, 'wb') as f:
#     f.write(subnetwork_image_pdf)
# # display the pdf in frame
# from IPython.display import IFrame
# IFrame('use_case_images/subnetwork_image.pdf', width=600, height=300)

# # svg
# subnetwork_image_svg = subnetwork.get_svg()

# from IPython.display import SVG
# SVG(subnetwork_image_svg)


    

    




Writing PNG to lovastatin-analysis-results/pathlinker-50-paths.png






    
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