Knitr: Include Figures in Report *And* Output Figures to Separate Files

knitr: include figures in report *and* output figures to separate files

Use the option self_contained: no if you are using html_document, or keep_tex: yes if you use pdf_document, so that rmarkdown will not remove the figure files after rendering the output document.

Setting knitr to output separate images

self_contained is an option for html_document, not a top-level YAML setting. The document below works using just that. PNG is the default figure type, so you don't need to specify that.

---
title: "Untitled"
output: 
  html_document:
    self_contained: no
---

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

## Including Plots

You can also embed plots, for example:

```{r pressure, echo=FALSE}
plot(pressure)
```

In RMarkdown, is there a global option that can be set for all figures and tables to be placed in their own page?

I am doing this by using \pagebreak before and after the coding chunk.

It is possible to program what you do using a knitr hook.

For instance, the following knitr hook defines a new pagebreak chunk option:

knitr::knit_hooks$set(chunk = function(x, options) {
  if(identical(options$pagebreak, TRUE)) {
    paste("\\pagebreak", x, "\\pagebreak", sep = "\n")  
  } else {
    x
  }
})

When this new pagebreak chunk option is TRUE, it does exactly what you describe: \pagebreak is inserted before and after the chunk output.

Therefore, you can use this new chunk option in a code chunk like that:

```{r pressure, pagebreak=TRUE}
plot(pressure)
```

or set this option for all the chunks in your document with:

knitr::opts_chunk$set(pagebreak = TRUE)

Here is a minimal Rmd file which uses this hook:

---
output: pdf_document
---

```{r setup, include=FALSE}
knitr::knit_hooks$set(chunk = function(x, options) {
  if(identical(options$pagebreak, TRUE)) {
    paste("\\pagebreak", x, "\\pagebreak", sep = "\n")  
  } else {
    x
  }
})

knitr::opts_chunk$set(pagebreak=TRUE)
```

Some text.

```{r pressure}
plot(pressure)
```

More text.

How to add multiple figures across multiple pages in a chunk using knitr and RMarkdown?

I have solved my problem.

In the generated tex file, there aren't new lines after each figure. This tex code us generated using rmd file above:

\includegraphics{test_files/figure-latex/plot_phenotype-1.pdf}
\includegraphics{test_files/figure-latex/plot_phenotype-2.pdf}
\includegraphics{test_files/figure-latex/plot_phenotype-3.pdf}
\includegraphics{test_files/figure-latex/plot_phenotype-4.pdf}

The solution is to add a new line after each cycle to print a figure.

cat('\r\n\r\n')

Not sure why I need two "\r\n" here. The generated tex file looks like:

\includegraphics{test_files/figure-latex/plot_phenotype-1.pdf}

\includegraphics{test_files/figure-latex/plot_phenotype-2.pdf}

\includegraphics{test_files/figure-latex/plot_phenotype-3.pdf}

\includegraphics{test_files/figure-latex/plot_phenotype-4.pdf}

This is the full example of my Rmd file

---
title: "Knitr test"
output:
  pdf_document:
    keep_tex: yes
date: "6 April 2015"
---

## Section A

Row B

```{r plot_phenotype, echo = FALSE, fig.height=8, fig.width=6.5}
library(ggplot2)
library(grid)
for (i in seq(1, 4))
{
    grid.newpage()
    p <- ggplot(cars, aes(speed, dist)) + geom_point()

    print(p)
    cat('\r\n\r\n')
}

```

How to place table of contents on separate page using Knitr for PDF without using separate files?

You could add \\clearpage at the end of your abstract. Therefore, it would become:

abstract: "Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Maecenas porttitor congue massa. Fusce posuere, magna sed pulvinar ultricies, purus lectus malesuada libero, sit amet commodo magna eros quis urna. Nunc viverra imperdiet enim. Fusce est. Vivamus a tellus. Pellentesque habitant morbi tristique senectus et netus et malesuada fames ac turpis egestas.\\clearpage"

You need to add one aditional slash (\) to escape the LaTeX command \clearpage.

-output

---

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