Use of \renewcommand and \protect to get custom figure caption prefixes and references in Tufte-handout PDF using knitr

th.Rmd

---
output:
  rmarkdown::tufte_handout:
    default
header-includes:
  \usepackage{caption}
  \captionsetup[figure]{labelfont=bf}
  \renewcommand{\thefigure}{S\arabic{figure}}
---

``` {r setup}
library(ggplot2)
data("mtcars")
knitr::opts_chunk$set(
  out.width = 3.150,
  out.height = 3.150
  )
```

```{r myPlot, fig.cap = "\\protect\\label{fig:myPlot}My plot"}
g <- ggplot(mtcars, aes(x = cyl, y = mpg)) + geom_point()
print(g + theme_minimal(base_size = 8, base_family = "Helvetica"))
```

Some text about \ref{fig:myPlot}.

```{r anotherPlot, fig.cap = "Another plot. Compare this to \\ref{fig:myPlot}"}
g <- ggplot(mtcars, aes(x = disp, y = mpg)) + geom_point()
print(g + theme_minimal(base_size = 8, base_family = "Helvetica"))
```