I have code that aims to generate a graph from an adjacency matrix from a table correlating workers with their manager. The source is a table with two columns (Worker, manager). It still works perfectly from a small mock data set, but fails unexpectedly with the real data: import pandas as pd import networkx as nx # Read input df = pd.read_csv("org.csv") # Create the input adjacency matrix am = pd.DataFrame(0, columns=df["Worker"], index=df["Worker"]) # This way, it is impossible that the dataframe is not square, # or that index and columns don't match # Fill the matrix for ix, row in df.iterrows(): am.at[row["manager"], row["Worker"]] = 1 # At this point, am.shape returns a square dataframe (2825,2825) # Generate the graph G = nx.from_pandas_adjacency(am, create_using=nx.DiGraph) This returns: NetworkXError: Adjacency matrix not square: nx,ny=(2825, 2829) And indeed, the dimensions reported in the error are not the same as in those of the input dataframe am. Does anyone have an idea of what happens in from_pandas_adjacency that could lead to this mismatch? Continue reading...