How to hold figure position with figure caption in pdf output of knitr?
RKnitrR MarkdownR Problem Overview
I am using knitr (1.9.5 and 1.9.17) and rmarkdown (0.5.3.1), and would like to hold figure position in the pdf output. The generated pdf file is working fine when chunk option fig.pos="H" is used.
However, the figure position is not hold when fig_caption: yes is set in the
yaml header.
How should I fix this problem? Thanks for any suggestions.
EDIT:
After learning the float environment of Latex. I add float package into header.
\usepackage{float}
But the generated tex file always use htbp in the figure environment regard to any fig.pos options are used. After manually changing htbp to H, positions of all figures are hold.
This is my example of rmd file:
---
title: "Untitled"
output:
pdf_document:
fig_caption: yes
includes:
in_header: mystyles.sty
---
# Section 1
Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.
Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.
Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.
Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.
```{r fig1, echo=FALSE, fig.height=8.5, fig.pos="H"}
plot(cars)
```
# Section 2
More test
```{r fig2, echo=FALSE, fig.height=8.5, fig.pos="H"}
plot(cars)
```
# Section 3
```{r fig3, echo=FALSE, fig.height=8.5, fig.pos="H"}
plot(cars)
```
More test
R Solutions
Solution 1 - R
For me adding the float package and then \floatplacement{figure}{H} in YAML solved the issue like :
---
title: "test"
date: "`r Sys.Date()`"
output:
pdf_document :
keep_tex: true
number_sections: true
header-includes:
\usepackage{booktabs}
\usepackage{longtable}
\usepackage{array}
\usepackage{multirow}
\usepackage[table]{xcolor}
\usepackage{wrapfig}
\usepackage{float}
\floatplacement{figure}{H}
---
Solution 2 - R
As Andrew pointed out, this fig.pos doesn't work in chunks, but it does work if it is put in global options:
```{r global_options, include=FALSE}
knitr::opts_chunk$set(fig.pos = 'H')
```
EDIT: the above apparently used to work and needs \usepackage{float} in the preamble:
header-includes:
\usepackage{float}
Solution 3 - R
Update look at this better solution here. (the summary of the problem below is still good, but follow the link to a better solution).
To summarise some testing in RStudio
The knitr chunk argument fig.pos = "H" works as long as fig_caption: yes is not in the yaml header.
Each figure in the generated .tex looks like this
\subsection{my_section}\label{my_section}
\includegraphics{path_to_fig.pdf}
But if fig_caption: yes is in the yaml header then the .tex looks like this
\subsection{my_section}\label{my_section}
\begin{figure}[htbp]
\centering
\includegraphics{path_to_fig.pdf}
\caption{}
\end{figure}
fig.pos = "H" has not been used, "htbp" is there instead.
A workaround for this using RStudio:
put
fig_caption: yes
keep_tex: yes
in the yaml as well as
header-includes: \usepackage{float}
then search and replace [htbp] with [H] in the generated .tex file
then open the .tex file in RStudio and use the "Compile PDF" button.
Example .Rmd
---
title: "Testing fig placement with captions"
author: "Andrew Dolman"
date: "1 September 2015"
output:
pdf_document:
fig_caption: yes
keep_tex: yes
header-includes: \usepackage{float}
---
This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.
When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:
```{r}
summary(cars)
```
You can also embed plots, for example:
```{r, echo=FALSE, fig.pos="H"}
plot(cars)
```
Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.
```{r, echo=FALSE, fig.pos="H"}
plot(cars)
```
Solution 4 - R
Although the answer provided by @Bangyou works, it complicates knitting.
You can also set a global default option for figure placement in latex, including this in your YAML header includes:
\makeatletter\renewcommand*{\fps@figure}{H}\makeatother
As explained here (and here for the \makeat... part).
This way you can just use the knit button in RStudio or rmarkdown::render and be done with it.
Issue is, all figures fill be forced with H and you won't be able to set one to float around.
Solution 5 - R
The option that worked for me:
In the .tex put at the beginning: \usepackage{float}.
At the beginning of the Rmd: knitr::opts_chunk$set(fig.pos = 'H'). The H in upper case).
And in every chunk with an image: fig.cap="lorem blabla" and out.extra='' (parameter value=empty string).
No need to define:
fig_caption: yes and keep_tex: yes in the yaml.
These options make the image to keep their position, either for include_graphics and the plots generated by R code.
I used them in the bookdown enviroment, generating the pdf and the html as expected :)
Solution 6 - R
The code from https://stackoverflow.com/questions/16626462/figure-position-in-markdown-when-converting-to-pdf-with-knitr-and-pandoc/33801326#33801326 helps me, help anyone else find it useful.
---
title: "Example"
author: "Martin"
output: pdf_document
---
```{r}
knitr::knit_hooks$set(plot = function(x, options) {
knitr::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()
```
Solution 7 - R
As Yihui mentioned in his answer (https://stackoverflow.com/questions/16626462/figure-position-in-markdown-when-converting-to-pdf-with-knitr-and-pandoc), we cannot expect too much about formatting from mardown. To workaround this problem, just write some R scripts to replace htbp to H.
Compared with knit from knitr package, I found render from rmarkdown is better to export a tex file. Just remember to add keep_tex: yes in the yaml header of your rmarkdown file.
library(rmarkdown)
render('filepath.Rmd')
x <- readLines('filepath.tex')
pos <- grep('begin\\{figure\\}\\[htbp\\]', x)
x[pos] <- gsub('htbp', 'H', x[pos])
writeLines(x, 'filepath.tex')
tools::texi2pdf('filepath.tex', clean = TRUE) # gives foo.pdf
file.remove('filepath.tex')