Changing chunk background color in RMarkdown

We can use the class.source option in the code chunk header to provide custom CSS to R Markdown. This is explained in the following post:

Add a CSS class to single code chunks in RMarkdown

Putting together an example, I might set a class called "badCode" then have a bit of CSS to change the background as you might like. Here's my .Rmd:

---
output: html_document
---

```{css}
.badCode {
background-color: red;
}
```

```{r mtcars}
summary(mtcars)
```

```{r cars, class.source="badCode"}
summary(cars)
```

Remember markdown supports HTML outside of code blocks.

I would surround the code chunks with a div with a custom class that styled them how I wanted. This example styles the code in blue, the output in light blue

<style>
div.blue pre { background-color:lightblue; }
div.blue pre.r { background-color:blue; }
</style>

<div class = "blue">
```{r bluecars}
summary(cars)
```
</div>

```{r normal}
summary(cars)
```

This solution is a bit hack-y, but it works. The gist of it is to make two code chunks, swapping the {r} designator with a unique class name. Then add css code to style each chunk.

---
output: html_document
---

<style>
pre.bluecars {
    background-color: #aabbff !important;
}
pre.redcars {
    background-color: #ffbbbb !important;
}
</style>

## chunk-specific bg colors

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

- blue

```{bluecars}
summary(cars)
```

```{r, echo=FALSE}
summary(cars)
```

- normal

```{r}
summary(cars)
```

- red

```{redcars}
summary(cars)
```

```{r, echo=FALSE}
summary(cars)
```

I found the following way to color (code) chunks in Rmarkdown documents that I knit to PDF:

Use a pandoc highlighting scheme as a basis

pandoc --print-highlight-style pygments > my.theme

Then edit my.theme by using a regex to set all

"text-color": null

Then, you can change this property to any color you like (this one here is lightgrey)

"background-color": "#f8f8f8"

In the YAML of your .Rmd document under "pdf_document", put the following

pandoc_args: --highlight-style=my.theme

For my use case this is all I need.