Figure position in markdown when converting to PDF with knitr and pandoc

Question

I'm trying to control the position of a plot when converting to PDF using knitr and pandoc. My .Rmd file looks this:

# My report

Some text some text some text some text some text some text some text some text some text


```{r myplot, echo=FALSE, fig.pos="placeHere", results='hide'}

library(ggplot2)

ggplot(mtcars, aes(mpg, drat)) + geom_point()

```

Some text some text some text some text some text some text some text some text some text

\usepackage{graphicx}
\begin{figure}[placeHere]
  \centering
    \includegraphics[width=0.5\textwidth]{placeHere}
\end{figure}

Some text some text some text some text some text some text some text some text some text

I'm converting to PDF using the functions provided here: http://quantifyingmemory.blogspot.co.uk/2013/02/reproducible-research-with-r-knitr.html

How can I place the plot between the second and third blocks of text? The latex code is not working as it currently stands.

EDIT: This is what I'm trying now.

# My report

   ```{r setup, include=FALSE}
# set global chunk options
opts_chunk$set(cache=FALSE)
library(ggplot2)
```

```{r, echo=FALSE, fig.height=3}

ggplot(mtcars, aes(disp, hp)) + geom_point()


```



Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some textSome text Some text Some text 

Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some textSome text Some text Some text 


Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some textSome text Some text Some text 


Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some textSome text Some text Some text 


```{r, echo=FALSE, fig.height=3}



ggplot(mtcars, aes(vs, am)) + geom_point()


```



Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some textSome text Some text Some text 

Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some textSome text Some text Some text 


Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some textSome text Some text Some text 


```{r, echo=FALSE, fig.height=6}



ggplot(mtcars, aes(disp, cyl)) + geom_point()

```


```{r, echo=FALSE, fig.height=6}

ggplot(mtcars, aes(hp, qsec)) + geom_point()


```


Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some textSome text Some text Some text 




```{r, echo=FALSE, fig.height=3}

ggplot(mtcars, aes(hp, wt)) + geom_point()

```



Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some textSome text Some text Some text 



```{r, echo=FALSE, fig.height=5}

ggplot(mtcars, aes(mpg, drat)) + geom_point()

```




Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some textSome text Some text Some text

I may be off base here but I think you're trying to control latex. You want to work with float placement as seen [here](http://en.wikibooks.org/wiki/LaTeX/Floats,_Figures_and_Captions). — Tyler Rinker, May 18 '13 at 17:49
I've taken a look at the wiki page, and have tried to follow code. However still not placing plot where I want it. Post updated with the code I've tried — luciano, May 18 '13 at 18:07
Do you know latex? If so make and Rnw file and use latex coding. If you really want to use Rmd and then convert as you're doing you can't insert a figure in this way (to my knowledge). You'll need to insert an html way (maybe use `![](path/to/image)`. You can use [captions](http://www.w3schools.com/tags/tag_caption.asp) in html as well. Also you may just want to use [html `` ](http://www.w3schools.com/tags/tag_img.asp) tags to place the image. — Tyler Rinker, May 18 '13 at 18:12
I've tried the html approach ![](path/to/image) with my real document and the behaviour of the placement of figures is similar. Therefore, figures are not printing where I've told them to print (quite often they are higher up in document). — luciano, May 18 '13 at 19:10
I don't get it if you want the plot to be moved between the 2nd and third text chunks remove the latex stuff and then move the knitr chunk to after the 2nd sentence. — Tyler Rinker, May 22 '13 at 00:04
Why did you edit your code? Then comments and other things don't make sense to future visitors. append your code instead. I edited your question to reflect this. — Tyler Rinker, May 22 '13 at 15:07
I've post my solution if any of the others doesn't work: https://stackoverflow.com/a/48920525/4249750 — Pablo Casas, Feb 22 '18 at 21:01

paleo13 · Answer 1 · 2016-02-01T06:34:53.723

101

I present an alternative solution. Instead of inserting [H] symbols into a latex document in a post-hoc manner, I suggest redefining the figure environment to ignore any position arguments and use [H].

To do this, create a .tex file in the same directory as the .Rmd file which redefines the figure environment, and update the YAML header in the .Rmd to include the file during compilation.

Here is an example of a .tex file:

\usepackage{float}
\let\origfigure\figure
\let\endorigfigure\endfigure
\renewenvironment{figure}[1][2] {
    \expandafter\origfigure\expandafter[H]
} {
    \endorigfigure
}

Here is example .Rmd which includes it (assuming you called the .tex file 'preamble-latex.tex'):

---
title: "example"
author: "you"
date: "`r format(Sys.time(), '%d %B %Y')`"
output:
  rmarkdown::pdf_document:
    fig_caption: yes        
    includes:  
      in_header: preamble-latex.tex
---

```{r, fig.cap='Markdownvellous!'}
plot(1:10, 1:10)
```

edited Feb 01 '16 at 06:34

answered Nov 19 '15 at 10:30

paleo13

1,349
2
11
9

8

This works nicely, and is much better than the accepted answer IMHO. You could simplify however as the references to vignettes etc are irrelevant here. – bjw Jan 20 '16 at 23:14
2

Perfect solution. was looking for it for a while – Farid Cheraghi Dec 30 '16 at 07:39
I have been struggling with this too. Thanks so much :-) – splaisan Jan 18 '17 at 20:00
3

I absolutely agree that this answer is more elegant than mine (posted five years ago), and I'd encourage the OP to accept this one instead. – Yihui Xie May 15 '18 at 14:47
I have tried multiple other solutions here. This was the only one that worked. – Nova Aug 21 '18 at 17:42
This answer seems also to work for plain rmarkdown include figures, such as `![Figure](fig.png)`, nice! – Matifou Mar 07 '19 at 23:17
2

If, like me, you encounter the same problem simultaneously for tables - here is a solution: https://stackoverflow.com/questions/44850011/how-to-stop-bookdown-tables-from-floating-to-bottom-of-the-page-in-pdf – puslet88 May 27 '19 at 16:37

Yihui Xie · Accepted Answer · 2018-05-15T14:45:52.420

I'm not aware of such an option for pandoc to set the floating option of figures when converting a Markdown document to LaTeX. If you choose Markdown for its simplicity, you should not expect too much power from it, even with powerful tools like pandoc. Bottom line: Markdown is not LaTeX. It was designed for HTML instead of LaTeX.

Two ways to go:

use the Rnw syntax (R + LaTeX) instead of Rmd (R Markdown) (examples); then you will be able to use the chunk option fig.pos='H' after you \usepackage{float} in the preamble; in this case, you have full power of LaTeX, and pandoc will not be involved

hack at the LaTeX document generated by pandoc, e.g. something like

library(knitr)
knit('foo.Rmd')  # gives foo.md
pandoc('foo.md', format='latex')  # gives foo.tex
x = readLines('foo.tex')
# insert the float package
x = sub('(\\\\begin\\{document\\})', '\\\\usepackage{float}\n\\1', x)
# add the H option for all figures
x = gsub('(\\\\begin\\{figure\\})', '\\1[H]', x)
# write the processed tex file back
writeLines(x, 'foo.tex')
# compile to pdf
tools::texi2pdf('foo.tex')  # gives foo.pdf

If you do not like these solutions, consider requesting a new feature to pandoc on Github, then sit back and wait.

SInce it took me 20 min to find it, I comment here, @yihui and team included a special option in bookdown to do that: https://bookdown.org/yihui/rmarkdown-cookbook/figure-placement.html#fn10 — Julien Colomb, Jul 13 '20 at 09:42

score 18 · Answer 3 · edited Jan 12 '17 at 16:00

I am using KnitR and markdown in RSTUDIO, the solution for my case is adding in the preamble \usepackage{float}:

    ---
title: "Proyect 2"
author: "FV"
date: "2016-12-3"
output:
  pdf_document:
    fig_caption: yes
    fig_crop: no
    fig_height: 2
    fig_width: 3
    highlight: haddock
    keep_tex: yes
    number_sections: yes
    toc: yes
    toc_depth: 2
  html_document:
    fig_caption: yes
    theme: journal
    toc: yes
    toc_depth: 2
header-includes: 
- \usepackage{graphicx}
- \usepackage{float}
---

And then adding this lines of code (fig.pos='H') in the very first lines:

```{r echo=FALSE,warning=FALSE}
 library(knitr)
  opts_chunk$set(fig.path='figure/graphics-', 
                 cache.path='cache/graphics-', 
                 fig.align='center',
                 external=TRUE,
                 echo=TRUE,
                 warning=FALSE,
                 fig.pos='H'
                )
  a4width<- 8.3
  a4height<- 11.7
```

I have just discover that in case it doesn´t work change: fig.pos='H' with fig.pos="H", with double quotation marks — Ferran VilBer, Mar 03 '17 at 13:44
I cannot contradict your experience, but in general it shouldn't matter. In R, there's no difference in interpretation between single and double quotes. https://stackoverflow.com/a/20572492/34935 — dfrankow, Jun 09 '20 at 16:55

score 11 · Answer 4 · answered Aug 31 '16 at 22:07

If what you are looking for is to just control manually where to put your figures, using this webpage: http://www.rci.rutgers.edu/~ag978/litdata/figs/, I found that if you add one backslash "\" somewhere after your plot commands, the plots will not be floating but instead will be printed in their current location.

If you want only some plots to appear, you can modify that option for each.

In your example:

# My report

```{r setup, include=FALSE}
# set global chunk options
knitr::opts_chunk$set(cache=FALSE)

library(ggplot2)
```

Some text Some text Some text Some text Some text Some text Some text Some       text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some textSome text Some text Some text 

```{r, echo=FALSE, fig.height=3}
ggplot(mtcars, aes(disp, hp)) + geom_point()
```
\

Some text Some text Some text Some text Some text Some text Some text Some       text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some textSome text Some text Some text

(etc)

This is the first suggestion that has worked for me! This also works for including images from a file in markdown text *outside* of a chunk. Thanks so much! — emudrak, Feb 06 '19 at 16:16

score 9 · Answer 5 · answered Jul 16 '13 at 17:57

I have a few projects where I convert from .Rmd to .pdf (mostly a beamer slide presentation) and want the graphs to not float (floating figures really don't work with slide presentations).

The approach that I use is to add an escaped space after the line in the .md file. This means that the graph is inside of a paragraph rather than being a paragraph of its own, this means that pandoc will not wrap it in a figure environment (it also means that I cannot use a caption with it) and therefore places it at exactly that position.

I use a Makefile to do all the conversions for me, so after running R and knitr it will automatically run a Perl script (though it could be done using R or other tools) that finds where the plots are inserted and adds the escaped space at the end of the line.

This answer fixed the problem for me. For anyone who doesn't know what an escaped space is, you use a backslash like so: `![SourceTree commit message](images/sourcetree-commit-message.png)\ ` — pwaring, Mar 06 '17 at 19:58

Martin Schmelzer · Answer 6 · 2018-03-23T13:10:11.920

Using a knitr hook

I somehow stumbled over this question and want to add another approach. Here I make use of the awesome flexibility supplied by knitr hooks. I simply change the plot hook to use the knitr function hook_plot_tex(). Afterwards I can just use the chunk option fig.pos as we are used to in Rnw documents in order to position figure environments (fig.cap must be set in order to invoke the figure environment).

This works in the examples provided by the OP. I guess they also work in (somehow) more complicated examples. Why this can be done that easily and is not the default for Rmd documents, I am not sure. Maybe Yihui can clarify that.

Here is the code:

---
title: "Example"
author: "Martin"
output: pdf_document
---

```{r}
knitr::knit_hooks$set(plot = function(x, options)  {
  hook_plot_tex(x, options)
})
```


```{r myplot, echo=FALSE, results='hide', fig.cap='Test', fig.pos='h'}
library(ggplot2)
ggplot(mtcars, aes(mpg, drat)) + geom_point()
```

Without fig.pos='h', the plot will usually jump to the second page.

If pandoc throws an error, make sure to add fig.pos = 'h'. – cibr Mar 12 '19 at 21:28 — cibr, Mar 12 '19 at 21:28

score 0 · Answer 7 · answered May 22 '13 at 00:15

0

Is this what you're after:

```{r setup, include=FALSE}
# set global chunk options
opts_chunk$set(cache=FALSE)
library(ggplot2)
```

# My report

Some text some text some text some text some text some text some text some text some text

Some text some text some text some text some text some text some text some text some text

```{r myplot, echo=FALSE}

ggplot(mtcars, aes(mpg, drat)) + geom_point()

```

Some text some text some text some text some text some text some text some text some text

answered May 22 '13 at 00:15

Tyler Rinker

108,132
65
322
519

That seems to work if keeping the figure height the same in each plot. But doesnt work if varying figure heights. I've edited post to more closely reflect what my actual document looks like. If you try my code, you will see plots dont appear in same order in PDF as they do in .Rmd file. – luciano May 22 '13 at 07:25
have you looked at [knitr's documentation](http://yihui.name/knitr/options)? `out.height='380px'` Please spend some time with the documentation. Yihui has spent a great deal of time making terrific documentation and minimal examples. – Tyler Rinker May 22 '13 at 11:54
Having spent more time with this, I realise the problem occurs when the .md file (which is outputted by knitr) is converted to a .pdf file (by Pandoc). Adding a backslash to the html code in the .md file controls the figure placement, like this: ` ![plot of chunk unnamed-chunk-1](figure/unnamed-chunk-1.png)\ ` However, this introduces a new problem: the figure caption is lost. The problem continues...! – luciano May 26 '13 at 07:30

score 0 · Answer 8 · edited Nov 06 '17 at 19:01

The solution is not too straightforward, maybe someone else will be able to streamline it.

The basic steps. (Windows 7)

You can add the argument fig.pos="H" to the knitr options, either globally or for each individual chunk. NOTE the capital H. This instructs latex to place figure floats exactly where they are called in the Rmd file.
BUT, this requires the package to be used by latex, this you can specify in the template that pandoc uses to construct pdf files. You do this by adding the line \usepackage{float}
BUT, you first need to find the current template file to modify. I could not find this anywhere but you can get pandoc to print the contents of the template to the console with this command: pandoc -D latex
Cut and paste this template code into an empty text file.
Add the line: \usepackage{float}
Save under the filename "default.latex" in a directory such as C:\Users\YOURNAME\pandoc\templates
Add the option --data-dir=C:/Users/YOURNAME/pandoc/templates" to your call to pandoc OR Pandoc.convert("my file.md", format="pdf", options=c("--data-dir=C:/Users/YOURNAME/pandoc/templates")) if using pander in R.

I hope this works for you.

This person is attempting to make an html2pdf document from an Rmd file not an Rnw file. — Tyler Rinker, May 22 '13 at 11:56
You're right sorry. It doesn't work. I don't know why I thought it did. — Andrew, May 23 '13 at 08:30

Figure position in markdown when converting to PDF with knitr and pandoc

8 Answers8

Using a knitr hook

Linked

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