Can anyone share their setup for Quarto documents that use both Python and R code blocks?

[ddanieltan]

Description

I am exploring Quarto documents that have both executable Python and R code. As far as I know, this can be achieved be either:

• Option A: setting engine to knitr and using the reticulate package (which will execute python code from R)
• Option B: setting engine to jupyter and using the rpy2 package (which will execute R code form python)

I am curious to know if anyone has a working setup of this that I can reference. Particularly, I am interested to better understand:

1. Package management: Is there a single dependency management tool that can handle both Python and R dependencies + play nice with Option A/B? I am aware of a similar question asked Using (multiple) virtual environments with R and Python #6864 but that thread did not have a conclusive solution

2. Editor Support: Is a Python + R document better supported in RStudio when executing code chunks from Python and R? I primarily use Vscode and execute code chunks in the radian shell. I can't get both Python and R to execute output in that same shell. Often I have to rely on viewing the quarto preview to see output from both Python and R. I am looking for a working setup that I can reference for this?

[cderv]

Not a complete answer, but I'm trying to bring some elements of what I know.

Is there a single dependency management tool that can handle both Python and R dependencies

Regarding R with knitr and reticulate for Python, renv (https://rstudio.github.io/renv/) can handle R and Python dependencies for the same project. More on Python integration at: https://rstudio.github.io/renv/articles/python.html

Is a Python + R document better supported in RStudio when executing code chunks from Python and R?

reticulate (https://rstudio.github.io/reticulate) is what allows to run Python from R. it is well integrated in RStudio IDE (https://rstudio.github.io/reticulate/articles/rstudio_ide.html) and python code cell can be run from the IDE

I primarily use Vscode

Are you using the Quarto extension https://marketplace.visualstudio.com/items?itemName=quarto.quarto ?
I believe it should handle the execution interactively (though there is still the limitation of the Quarto engine used)

Option B: setting engine to jupyter and using the rpy2 package (which will execute R code form python)

I think this option won't allow ```{r} cells, and you'll need to rely on Cell magic
https://rpy2.github.io/doc/latest/html/interactive.html

Never tried though.

[ddanieltan]

That's fantastic, I'll look into renv handling both R and Python dependencies.

[bgall]

The question of whether VS Code (VSC) plays nicely with renv and its management of Python packages in Quarto was outstanding and I can confirm it works. Here's a quick-start gist:

Follow the instructions for setting up R, Python, and Quarto in VSC from the VSC or Quarto sites. Next, install renv from an R terminal in VSC. You can then proceed to renv::init() to set up your renv environment. It will probably ask you then to install several packages that are not found in the environment (e.g. jsonlite) you've set up and you may need to install renv itself into your renv. Restart the terminal, then renv::use_python() to create a Python venv. From there, you can install R packages per usual install.packages() and Python packages with e.g. pip install from the quarto document. If there's any issue, it's almost certainly because the RENV environment variables aren't pointing to your project correctly. You can Sys.getenv() to take a look and assign accordingly.

[jr-leary7]

This is a biology-specific application, but this vignette I wrote uses R & Python code chunks in the same document. Click the Code -> View source button at the top and you can see the YAML header options I used.

[ddanieltan]

Thanks @jr-leary7, very informative! Q:Did you use RStudio as your editor for this vignette?

[jr-leary7]

I used RStudio yes, though I often use VS Code as well.

[JosephBARBIERDARNAL]

For those who land here, in my case, I was looking for this piece of code :

```{r}
#| echo : false
reticulate::use_virtualenv(’ ../../.venv ’)
```

where ../../.venv is the relative path from my quarto document to my python virtual environment.