Python code • Giotto

To use Python code we prefer to create a python wrapper/functions around the python code, which can then be sourced by reticulate. As an example we show the basic principles of how we implemented the Leiden clustering algorithm in Giotto.

1 Write python wrapper

Write python wrapper (below) and store as python_leiden.py in /inst/python:

import igraph as ig 
import leidenalg as la 
import pandas as pd
import networkx as nx

def python_leiden(df, partition_type, initial_membership=None, weights=None, n_iterations=2, seed=None, resolution_parameter = 1):
    
    # create networkx object
    Gx = nx.from_pandas_edgelist(df = df, source = 'from', target =  'to', edge_attr = 'weight')  

    # get weight attribute
    myweights = nx.get_edge_attributes(Gx, 'weight')

    ....

    return(leiden_dfr)

2 Source python code with reticulate

py_leiden_filepath = system.file("python", "python_leiden.py", package = 'Giotto')
reticulate::source_python(file = py_leiden_filepath)

3 Use the python code as R code

The function name is the same as that defined in the python script. See doLeidenCLuster() for more detailed information.

pyth_leid_result = python_leiden(
    df = network_edge_dt,
    partition_type = partition_type, 
    initial_membership = init_membership, 
    weights = 'weight', 
    n_iterations = n_iterations,
    seed = seed_number, 
    resolution_parameter = resolution
)

4 Add the python function name

Add the python function name to the globalVariables() call under globals.R so that it does not get flagged by devtools::check()