Create R markdown chunks WITH different chunk options AND markdown headings in a for loop

Question

I would like to automatically generate R markdown chunks and headings within a for loop in R for a list of data.frames which varies length depending on input. These are then the input for plot generation. This R markdown document will then be knitted to a html_document using the package knitr.

I have attempted the solutions from several similar SO questions which can get me close, but is not what I actually need:

• https://stackoverflow.com/a/44671368/10771401
• https://stackoverflow.com/a/57034752/10771401

The problem is that I have 4 chunks that I'd like to repeat where each chunk has to have different chunk options (fig.width, fig.height) to correctly display the ggplot2 objects in them. So, I can't simply just supply a single set of options in the code chunk itself).

Here is an example of one of my failed attempts (NOTE: the second code block below also contains a comment indicating the chunk options which is required):

# Chunk data demo
data_list <- list(a=data.frame(), b=data.frame(), c=data.frame())
plot_1 <- list()
plot_2 <- list()

for (i in 1:length(data_list)) {
  data_list[[i]] <- data.frame(x = 1:5, y = 1:5)
  plot_1[[i]] <- ggplot(data_list[[i]], aes(x, y)) + geom_point()
  plot_2[[i]] <- ggplot(data_list[[i]], aes(x, y)) + geom_point()
}

#```{r, results='asis'} (Start of R markdown chunk)

# Chunk generation (only 2 chunks are written for brevity)   
for (i in 1:length(data_list)) {
  # Section heading
  cat("\n\n")
  cat("##", names(data_list)[i])

  # Chunk 1 ----
  cat("\n\n")
  cat("### Sub-section 1")
  cat("\n\n")
  cat("**Title 1**")
  cat("\n\n")
  cat('```{r, fig.width=10, fig.height=10}')
  cat("\n\n")
  print(plot_1[[i]])
  cat("\n\n")
  cat('```')
    
  # Chunk 2 ----
  cat("\n\n")
  cat("### Sub-section 2")
  cat("\n\n")
  cat("**Title 2**")
  cat("\n\n")
  cat('```{r, fig.width=10, fig.height=3}') # NOTE: Change in option
  cat("\n\n")
  print(plot_2[[i]])
  cat("\n\n")
  cat('```')
  cat("\n\n")
}
#``` (End of R markdown chunk)

EDIT: Removed the ggsave() calls, as not necessary to illustrate the problem which is apparent in the knitted document.

Answer 1

I see what you are trying to do, and I think the approach you are taking won't work. (But I guess you already knew that!) Here's why:

When you run the asis chunk, you are producing Markdown, not R Markdown. The fig.width and fig.height options need to be handled by knitr when it is processing R Markdown, but that only happens once. The next stage of processing which handles the Markdown is done by Pandoc, and it doesn't know anything about fig.width and fig.height.

So what you need to do is to produce a "child document", then get knitr to include it in your main document. Those are described here: https://bookdown.org/yihui/rmarkdown-cookbook/child-document.html . Basically they are just fragments of R Markdown to include in your main document. Here's a modification of your document that does this:

---
title: "Untitled"
author: "Duncan Murdoch"
date: "2023-02-12"
output: 
  html_document:
    keep_md: true
---

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

## R Markdown

```{r}
library(ggplot2)
# Create the plots
data_list <- list(a=data.frame(), b=data.frame(), c=data.frame())
plot_1 <- list()
plot_2 <- list()

for (i in 1:length(data_list)) {
  data_list[[i]] <- data.frame(x = 1:5, y = 1:5)
  plot_1[[i]] <- ggplot(data_list[[i]], aes(x, y)) + geom_point()
  plot_2[[i]] <- ggplot(data_list[[i]], aes(x, y)) + geom_point()
}
```

```{r echo = FALSE}
# Create a child document
child <- "child.Rmd"
cat("\n", file = child)

# Save typing file = child, append = TRUE every time
# by making a new function to call cat

cat2 <- function(...) cat(..., file = child, append = TRUE)

for (i in 1:length(data_list)) {
  # Section heading
  cat2("\n\n")
  cat2("##", names(data_list)[i])

  # Chunk 1 ----
  cat2("\n\n")
  cat2("### Sub-section 1")
  cat2("\n\n")
  cat2("**Title 1**")
  cat2("\n\n")
  cat2('```{r fig.width=10, fig.height=10}')
  cat2("\n\n")
  cat2("i = ", i, "\n")
  cat2("print(plot_1[[i]])")
  cat2("\n\n")
  cat2('```')
    
  # Chunk 2 ----
  cat2("\n\n")
  cat2("### Sub-section 2")
  cat2("\n\n")
  cat2("**Title 2**")
  cat2("\n\n")
  cat2("```{r fig.width=10, fig.height=3}")
  cat2("\n\n")
  cat2("print(plot_2[[i]])")
  cat2("\n\n")
  cat2('```')
  cat2("\n\n")
}
```

```{r child="child.Rmd"}
```

Answer 2

You can also use the knitr::knit_expand() and pass it to the knitr::knit_child() function.

Edit:

---
output: html_document
---


```{r, echo=FALSE, results='asis'}
library(purrr)
library(ggplot2)
data_list <- list(a=data.frame(x = 1:5, y = 1:5), b=data.frame(x = 1:5, y = 1:10),  c=data.frame(x = 1:5, y = 1:15))


data_plots_1 <- map(data_list, ~ggplot(.x, aes(x, y)) + geom_point())
data_plots_2 <- map(data_list, ~ggplot(.x, aes(x, y)) + geom_point(color = "red"))

fig_width <- c(7,5,5)
fig_height <- c(5,3,3)

data_names <- data_list %>% names()
```



```{r results='asis', echo=FALSE}
structure_text <- purrr::pmap_chr(list(data_names, fig_width, fig_height), \(data_names,  fig_width, fig_height) {
  knitr::knit_expand(text = c(
    "## Title Plot 1 dataset {{data_names}}", 
    "",
    "",
    "```{r, fig.width= {{ fig_width }},  fig.height= {{ fig_height }}, echo =FALSE }",
    "data_plots_1${{data_names}} ",
    "```",
    "",
    "## Title Plot 2 dataset {{data_names}}", 
    "",
    "",
    "```{r, fig.width= {{ fig_width }},  fig.height= {{ fig_height }}, echo =FALSE }",
    "data_plots_2${{data_names}} ",
    "```",
    ""
    ))
})
res <- knitr::knit_child(text = structure_text, quiet = TRUE)
cat(res, sep = '\n')

Old

---
output: html_document
---


```{r, echo=FALSE, results='asis'}
library(purrr)
library(ggplot2)
data_list <- list(a=data.frame(x = 1:5, y = 1:5), b=data.frame(x = 1:5, y = 1:10))
data_names <- data_list %>% names()
fig_width <- c(7,5)
fig_height <- c(5,3)
```



```{r results='asis', echo=FALSE}
structure_text <- purrr::pmap_chr(list(data_names, fig_width, fig_height), \(data_names, fig_width, fig_height) {
  knitr::knit_expand(text = c(
    "## {{ data_names }}", 
    "",
    "",
    "```{r, fig.width= {{ fig_width }},  fig.height= {{ fig_height }}, echo =FALSE }",
    "data_list${{data_names}}  |>",
    "  ggplot(aes(x = x, y = y)) +",
    "  geom_point()",
    "```",
    ""))
})
res <- knitr::knit_child(text = structure_text, quiet = TRUE)
cat(res, sep = '\n')