Host_parasite_Interaction_matrix2graph.py

import pandas as pd
import networkx as nx
import matplotlib.pyplot as plt

# read the file
df1 = pd.read_excel (r'C:\Users\saySa\OneDrive\Desktop\Dataset\A_HP_041.xls',index_col=[0])

# Delete the first column that has data on the total number of samples
del df1['Num. of hosts sampled']

# Convert to a list
df2 = df1.stack().reset_index()

# Get indexes for which column 0 has value 0
indexNames = df2[ df2[0] == 0 ].index

# Delete these row indexes from dataFrame
df2.drop(indexNames , inplace=True)

#create a graph with labels
G=nx.from_pandas_edgelist(df=df2, source='level_0', target='level_1', create_using=nx.Graph())
nx.draw(G,with_labels =True)

# Host-parasite interaction
# Analysis

print(nx.info(G), "\n")
print("Network Density: ",nx.density(G))
print("Network Transitivity: ",nx.transitivity(G))
print("Network Assortativity: ",nx.assortativity.degree_pearson_correlation_coefficient(G))
print("Average Shortest Path Length: ",nx.average_shortest_path_length(G))