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AMR for Python

Source: vignettes/AMR_for_Python.Rmd
AMR_for_Python.Rmd

Introduction

The AMR package for R is an incredible tool for antimicrobial resistance (AMR) data analysis, providing extensive functionality for working with microbial and antimicrobial properties. But what if you’re working in Python and still want to benefit from the robust features of AMR?

The best way is to access R directly from Python with the help of rpy2, a simple yet powerful Python package. You can easily call functions from the AMR package to process your own data in your own Python environment. This post will guide you through setting up rpy2 and show you how to use R functions from AMR in Python to supercharge your antimicrobial resistance analysis.

What is rpy2?

rpy2 is a Python library that allows Python users to run R code within their Python scripts. Essentially, it acts as a bridge between the two languages, allowing you to tap into the rich ecosystem of R libraries (like AMR) while maintaining the flexibility of Python.

Key Features of rpy2:

  • Seamlessly call R functions from Python.
  • Convert R data structures into Python data structures like pandas DataFrames.
  • Leverage the full power of R libraries without leaving your Python environment.

Setting Up rpy2

Before diving into the examples, you’ll need to install both R and rpy2. Here’s a step-by-step guide on setting things up.

Step 1: Install R

Ensure that R is installed on your system. R has minimal dependencies and is very simple to install:

  • Linux
    • Ubuntu / Debian:
      sudo apt install r-base
    • Fedora:
      sudo dnf install R
    • CentOS/RHEL:
      sudo yum install R
    • Arch Linux:
      sudo pacman -S r
  • macOS (with Homebrew):
    brew install r
  • Other Systems:
    Visit the CRAN download page.

Step 2: Install the AMR package in R

On Linux and macOS, open Terminal and run:

Rscript -e 'install.packages("AMR")'

For other systems, open your R console and install the AMR package by running:

On any system, you can also install the latest development version of the AMR package by setting repos to our beta channel:

install.packages("AMR", repos = "https://msberends.r-universe.dev")

Step 3: Install rpy2 in Python

To install rpy2, simply run the following command in your terminal:

pip install rpy2

Step 4: Test rpy2 Installation

To ensure everything is set up correctly, you can test your installation by running the following Python script, which essentially runs R in the background:

import rpy2.robjects as ro

# Test a simple R function from Python
ro.r('1 + 1')

If this returns 2, you’re good to go!

Working with AMR in Python

Now that we have rpy2 set up, let’s walk through some practical examples of using the AMR package within Python.

Example 1: Converting Taxonomic Data

Let’s start by converting taxonomic user input to valid taxonomy using the AMR package, from within Python:

import pandas as pd
import rpy2.robjects as ro
from rpy2.robjects.packages import importr
from rpy2.robjects import pandas2ri

# Load the AMR package from R
amr = importr('AMR')

# Example user dataset in Python
data = pd.DataFrame({
    'microorganism': ['E. coli', 'S. aureus', 'P. aeruginosa', 'K. pneumoniae']
})

# Apply mo_name() from the AMR package to the 'microorganism' column
ro.globalenv['r_data'] = data
ro.r('r_data$mo_name <- mo_name(r_data$microorganism)')

# Retrieve and print the modified R DataFrame in Python
result = ro.r('r_data')
result = pandas2ri.rpy2py(result)
print(result)

In this example, a Python dataset with microorganism names like E. coli and S. aureus is passed to the R function mo_name(). The result is an updated DataFrame that includes the standardised microorganism names based on the mo_name() function from the AMR package.

Example 2: Generating an Antibiogram

One of the core functions of the AMR package is generating an antibiogram, a table that summarises the antimicrobial susceptibility of bacterial isolates. Here’s how you can generate an antibiogram from Python:

# Run an antibiogram in R from Python
ro.r('result <- antibiogram(example_isolates, antibiotics = c(aminoglycosides(), carbapenems()))')

# Retrieve the result in Python
result = ro.r('as.data.frame(result)')
print(result)

In this example, we generate an antibiogram by selecting aminoglycosides and carbapenems, two classes of antibiotics, and then convert the resulting R data frame into a Python-readable format.

Example 3: Filtering Data Based on Gram-Negative Bacteria

Let’s say you want to filter the dataset for Gram-negative bacteria and display their resistance to certain antibiotics:

# Filter for Gram-negative bacteria with intrinsic resistance to cefotaxime
ro.r('result <- example_isolates[which(mo_is_gram_negative() & mo_is_intrinsic_resistant(ab = "cefotax")), c("bacteria", aminoglycosides(), carbapenems())]')

# Retrieve the filtered result in Python
result = ro.r('as.data.frame(result)')
print(result)

This example uses the AMR functions mo_is_gram_negative() and mo_is_intrinsic_resistant() to filter the dataset and returns a subset of bacteria with resistance data.

Example 4: Customising the Antibiogram

You can easily customise the antibiogram by passing different antibiotics or microorganism transformations, as shown below:

# Customise the antibiogram with different settings
ro.r('result <- antibiogram(example_isolates, antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"), mo_transform = "gramstain")')

# Retrieve and print the result
result = ro.r('as.data.frame(result)')
print(result)

Here, we use piperacillin/tazobactam (TZP) in combination with tobramycin (TOB) and gentamicin (GEN) to see how they perform against various Gram-negative bacteria.

Conclusion

Using rpy2, you can easily integrate the power of R’s AMR package into your Python workflows. Whether you are generating antibiograms, analyzing resistance data, or performing complex filtering, rpy2 gives you the flexibility to run R code without leaving the Python environment. This makes it a perfect solution for teams working across both R and Python.