Hey there, let's work through these two frustrating R Markdown + Python issues you're dealing with:

Issue 1: AttributeError: module 'matplotlib' has no attribute 'pyplot' in R Markdown Python chunks #

You're hitting this error when running matplotlib-related code in an R Markdown Python code chunk. Here's how to fix it:

• First, check which Python environment R Markdown is using: Add an R code chunk at the top of your .Rmd file and run:

  library(reticulate)
  py_config()
  

  This will show you the Python executable path reticulate is relying on. Chances are it's not the same environment where you installed matplotlib.
• Point reticulate to the correct Python environment: If the path doesn't match your matplotlib-enabled environment, set it explicitly with:

  library(reticulate)
  use_python("/absolute/path/to/your/python/environment/python") # Replace with your actual path
  

• Reinstall matplotlib if needed: Open the terminal/command line for your target Python environment, then run:

  pip install --upgrade matplotlib
  

  This ensures matplotlib is fully installed and up-to-date in the environment R Markdown is using.
• Double-check your import line: Make sure you're using the standard import syntax:

  import matplotlib.pyplot as plt
  

Issue 2: Pandas code works in IPython but fails in R Markdown Python chunks #

Your pandas CSV-reading code runs fine in IPython, but throws an AttributeError when you knit the R Markdown document. Here's what to do:

1. Verify Python environment consistency
   • In IPython, run this to get your working Python path:

     import sys
     print(sys.executable)
     

   • Compare this path with the one shown by reticulate::py_config() in R Markdown. If they differ, use reticulate::use_python() (like in Issue 1) to point R Markdown to the IPython environment.
2. Check the CSV file path
   • R Markdown uses the folder containing your .Rmd file as its working directory, which might not match IPython's working directory. To confirm, add this to your Python chunk:

     import os
     print(os.getcwd())
     

   • Either move simplest.csv to R Markdown's working directory, or use an absolute path in pandas.read_csv(), like:

     pandas.read_csv("/full/path/to/your/simplest.csv")
     

3. Ensure pandas is installed in the target environment
   • If the environment is correct but pandas is missing, run this in the environment's terminal:

     pip install pandas
     

内容的提问来源于stack exchange，提问作者Michael Hannon