Create RMarkdown chuncks in a loop

Question

I would like to be able to create RMarkdown chuncks in a loop. I have tried doing this through a for loop, without much success. I imagine this could probably be possible through lapply, as one would do for creating UIs in a shiny app. However, I haven't had any success so far.

Reprex:

---
title: "Untitled"
output:
  html_document:
    theme: united
    highlight: tango
    toc: true
    toc_float:
      collapsed: false
      smooth_scroll: false
---

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

```{r}
library(dplyr)
library(ggplot2)

df <- datasets::iris %>% 
  dplyr::as_tibble()
```

## setosa

```{r}
df %>% 
  dplyr::filter(Species == "setosa") %>% 
  ggplot2::ggplot(ggplot2::aes(Sepal.Length, Petal.Length)) + 
  ggplot2::geom_point()
```

## versicolor

```{r}
df %>% 
  dplyr::filter(Species == "versicolor") %>% 
  ggplot2::ggplot(ggplot2::aes(Sepal.Length, Petal.Length)) + 
  ggplot2::geom_point()
```

## virginica

```{r}
df %>% 
  dplyr::filter(Species == "virginica") %>% 
  ggplot2::ggplot(ggplot2::aes(Sepal.Length, Petal.Length)) + 
  ggplot2::geom_point()
```

My goal is to create the headings (setosa, versicolor, and virginica) and the chuncks with a loop.

For example:

for(i in c("setosa", "versicolor", "virginica")) {

  ## i

  df %>% 
    dplyr::filter(Species == i) %>% 
    ggplot2::ggplot(ggplot2::aes(Sepal.Length, Petal.Length)) + 
    ggplot2::geom_point()
}

Any ideas on how accomplish this?

Do you need the repeated code to show up in the output? Or do you just need to have the heading for each group, and then the resulting plot under that? — Marius, Jul 15 '19 at 06:55
Maybe [this](https://stackoverflow.com/questions/19080917/dynamic-number-of-calls-to-a-chunk-with-knitr) is what you need. — Stéphane Laurent, Jul 15 '19 at 07:03

score 7 · Accepted Answer · answered Jul 15 '19 at 07:06

If you want to create headings + outputs within a loop, you can do:

```{r species_loop, results='asis'}
for(i in c("setosa", "versicolor", "virginica")) {

  cat(paste0("\n\n## ", i, "\n"))

  p <- df %>% 
    dplyr::filter(Species == i) %>% 
    ggplot2::ggplot(ggplot2::aes(Sepal.Length, Petal.Length)) + 
    ggplot2::geom_point()
  print(p)
}
```

So:

Using results='asis' to allow output that you cat() to be interpreted as Markdown syntax
cat()ing the required markdown syntax to produce the headers (surrounded by some newlines to make sure it's interpreted properly)
Explicitly print()ing the plot within the loop.

jay.sf · Answer 2 · 2019-07-15T07:28:04.460

A function based on cat would replicate your chunks for every iris species. For the one-time chunks use single cats.

FUN <- function(x) cat("\n##", x, "
```{r}
df %>%
  dplyr::filter(Species == ",x, ") %>%
  ggplot2::ggplot(ggplot2::aes(Sepal.Length, Petal.Length)) +
  ggplot2::geom_point()
```\n")

To produce the shown .Rmd file, you could use sink. (For sake of brevity I'll omit the header here.)

sink(file="iris.Rmd")  ## start `sink`

cat("```{r}
library(dplyr)
library(ggplot2)
df <- datasets::iris %>% 
  dplyr::as_tibble()
```")

invisible(sapply(c("'setosa'", "'versicolor'", "'virginica'"), FUN))

sink()  ## end `sink`

You'll find your .Rmd file in your working directory (getwd()).

Create RMarkdown chuncks in a loop

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