I would like to add space around figures in RMarkdown. I am knitting to PDF and really don't like how close figures (or also equations) are to the text or to the next figure.
---
output: pdf_document
---
```{r pressure, echo=FALSE}
plot(pressure)
```
```{r pressure2, echo=FALSE}
plot(pressure)
```
There is just too little space between the two plots and this gets more fuzzy when using ggplots.
Right now I use the Latex solution
\vspace{10pt}
but it would be nice if I could make a setting globally for the entire document.
Concerning the spacing before and after plots you can use a simple knitr hook:
```{r, echo = F}
library(knitr)
if(is_latex_output()) {
plot_default <- knit_hooks$get("plot")
knit_hooks$set(plot = function(x, options) {
x <- c(plot_default(x, options), "\\vspace{25pt}")
})
}
```
Here we alter the plot hook in that sense that we just add a spacing of 25pt after each plot output.
Concerning equations you can just add these four length definitions at the beginning of your document:
\setlength{\abovedisplayskip}{25pt}
\setlength{\belowdisplayskip}{25pt}
\setlength{\abovedisplayshortskip}{25pt}
\setlength{\belowdisplayshortskip}{25pt}
The first two alter equations created using the align environment. The latter two those created using $$ ... $$.
Related
From R for Data Science:
To put multiple plots in a single row I set the out.width to 50% for
two plots, 33% for 3 plots, or 25% to 4 plots, and set fig.align =
"default". Depending on what I’m trying to illustrate ( e.g. show data
or show plot variations), I’ll also tweak fig.width, as discussed
below.
How do I put multiple plots on a single row, using the method described above? I could use a package such as patchwork, but the purpose of this post is to understand what's being described above. The R Markdown below doesn't generate what I'd expect, two 'pressure' plots on the same row.
---
title: "Untitled"
author: "April 2018"
date: "4/11/2019"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
Text
```{r pressure1, echo=FALSE, fig.width=6, fig.asp=0.618, out.width="50%", fig.align="default"}
plot(pressure)
plot(pressure)
```
```{r pressure2, echo=FALSE, fig.width=6, fig.asp=0.618, out.width="50%", fig.align="default"}
plot(pressure)
```
I’ve got no idea why your code (or rather, the code from R for Data Science) is not working. But plotting different data makes it work for me:
```{r pressure1, echo=FALSE, fig.width=6, fig.asp=0.618, out.width="50%", fig.align="default"}
plot(cars)
plot(pressure)
```
Alternatively, it seems to be enough to just specify different parameters, e.g.:
plot(pressure)
plot(pressure, main = '')
The fact that inconsequential changes fix the output indicates to me that this is a bug in RMarkdown.
That said, the easiest, most controlled way is to put par(mfrow = c(1, 2)) into the hunk directly before the plotting commands (or a ggplot2 solution such as faceting or {patchwork}).
Tweaking the alignment via the RMarkdown options can be tricky, due to spacing inserted by the conversion to HTML.
You need to specify fig.show = "hold" along with out.width, as you can see here: https://bookdown.org/yihui/rmarkdown-cookbook/figures-side.html
I have a very large phylogenetic tree that I'd quite like to insert into a supplementary material I'm writing using Rmarkdown and knitr. I dislike splitting trees across pages and I doubt anybody would print this out anyway so I thought I'd just have a large page in the middle of the pdf I'm generating.
The question is how do I change page size for one page in an otherwise A4 document? I'm pretty new to knitr and I've found global paper size options but I'm struggling to find ways of setting up what would be the equivalent of sections in Word.
(Update) Hi does anybody else have a suggestion? I tried the pdfpages package but this seems to result in an equally small figure on a page the size of the pdf that is being pasted in i.e. if I make a 20in by 20in pdf figure then paste the page in using \includepdf then I get a 20in by 20in page with a much smaller figure on it (the same as the \eject example above). It seems like knitr or Latex is forcing the graphics to have a specific size regardless of page size. Any ideas? Here's a reproducible example:
---
title: "Test"
output:
pdf_document:
latex_engine: xelatex
header-includes:
- \usepackage{pdfpages}
---
```{r setup, include=FALSE}
require(knitr)
knitr::opts_chunk$set(echo = FALSE,
warning=FALSE,
message=FALSE,
dev = 'pdf',
fig.align='center')
```
```{r mtcars, echo=FALSE}
library(ggplot2)
pdf("myplot.pdf", width=20, height=20)
ggplot(mtcars, aes(mpg, wt)) + geom_point()
dev.off()
```
#Here's some text on a normal page, the following page is bigger but has a tiny figure.
\newpage
\includepdf[fitpaper=true]{myplot.pdf}
You should be able to use \ejectpage like this:
---
output: pdf_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## R Markdown
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 cars}
summary(cars)
```
## Including Plots
You can also embed plots, for example:
```{r pressure, echo=FALSE}
plot(pressure)
```
Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.
\eject \pdfpagewidth=20in \pdfpageheight=20in
```{r mtcars}
library(ggplot2)
ggplot(mtcars, aes(mpg, wt)) + geom_point()
```
\eject \pdfpagewidth=210mm \pdfpageheight=297mm
Back
(I can only remember the A4 height in mm for some reason)
I have just faced the same struggle when dealing with a large phylogenetic tree.
Based on hrbrmstr's answer, I came up with the snippet below.
The trick is to make knitr generate the figure but not include it in the intermediate .tex right away (hence fig.show="hide"). Then, because figure paths are predictable, you can insert it with some latex after the code chunk.
However, the new page height is not taken into account when positioning page numbers, so they tend to be printed over your image. I have tried to overcome this behavior multiple times, but in the end I simply turned them off with \thispagestyle{empty}.
---
output: pdf_document
---
```{r fig_name, fig.show="hide", fig.height=30, fig.width=7}
plot(1)
```
\clearpage
\thispagestyle{empty}
\pdfpageheight=33in
\begin{figure}[p]
\caption{This is your caption.}\label{fig:fig_name}
{\centering \includegraphics[height=30in, keepaspectratio]{main_files/figure-latex/fig_name-1} }
\end{figure}
\clearpage
\pdfpageheight=11in
I would like to edit a single rmarkdown (Rmd) document with a list of "problems", each followed by its solution. Each solution may contain the results of the R console, but also some explaining (markdown and LaTeX formatted) text. Besides, I would like use knitr in 2 versions: with and without the solutions, changing the source as less as possible, and compiling.
I know that I can use a logical variable in order to conditionally evaluate R code and show plots and R output, but I don't know how to show/hide blocks of (markdown and LaTeX) formatted text, unless I put all that text into R character vectors, which seems hard for keeping things clean and readable.
I found this old question,
Conditionally display a block of text in R Markdown
where the solution was given for simple short text, which was included as an argument of the R print() function.
This other old question,
insert portions of a markdown document inside another markdown document using knitr
was for having a father document and child documents which were conditionally compiled, but I don't want to slice my document into so many pieces.
You could use the asis engine to conditionally include/exclude arbitrary text in knitr, e.g.
```{asis, echo=FALSE}
Some arbitrary text.
1. item
2. item
Change echo=TRUE or FALSE to display/hide this chunk.
```
But I just discovered a bug in this engine and fixed it. Unless you use knitr >= 1.11.6, you can create a simple asis engine by yourself, e.g.
```{r setup, include=FALSE}
library(knitr)
knit_engines$set(asis = function(options) {
if (options$echo && options$eval) paste(options$code, collapse = '\n')
})
```
If you want to include inline R expressions in the text, you will have to knit the text, e.g.
```{r setup, include=FALSE}
library(knitr)
knit_engines$set(asis = function(options) {
if (options$echo && options$eval) knit_child(text = options$code)
})
```
There is a way to hide parts of the document (including text and chunks): to comment them out with html comment marks.
And comment marks can be generated by R in a block according to a variable that can be set at the beginning of the document.
```{r results='asis', echo=FALSE}
if (hide) {cat("<!---")}
```
```{r results='asis', echo=FALSE}
if (hide) {cat("-->")}
```
And just to show a complete working example, in the example below the middle section of the document can be shown or hidden by setting the hide variable to FALSE or TRUE. That might be useful in case there are several sections to hide or show at once - for example, solutions of course problems.
---
title: "Untitled"
date: "15/10/2020"
output:
word_document: default
html_document: default
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
hide <- TRUE #TRUE to comment out part of the document, FALSE to show.
```
## Start
Always shown.
```{r}
hide
```
```{r results='asis', echo=FALSE}
if (hide) {cat("<!---")}
```
## To hide or not to hide
To be hidden or shown according to *hide* variable.
```{r}
"Also to be hidden according to 'hide' variable"
hist(rnorm(10))
```
```{r results='asis', echo=FALSE}
if (hide) {cat("-->")}
```
<!--
Never shown.
-->
## End
Always shown.
Just a caveat: in html output the hidden parts are kept as comments and can be seen just by viewing the source. On the other hand, PDF (LaTex) and Word outputs ignore html comments and the hidden parts aren't included in the knitted documents.
Therefore, when the hidden parts are supposed to be somehow confidential (e.g. exam solutions) PDF or Word output should be used instead of html.
For those looking for a solution when knitting to pdf through LaTex, the answer from #Pere won't work for you (because LaTex doesn't understand the <!--- --> pair as indicating a comment).
Below is one possible workaround:
---
output:
pdf_document
---
\newcommand{\ignore}[1]{}
```{r echo=FALSE}
include <- TRUE
```
```{r results='asis', echo=FALSE}
if(!include){cat("\\ignore{")}
```
Included bla bla
```{r results='asis', echo=FALSE}
if(!include){cat("}")}
```
```{r echo=FALSE}
include <- FALSE
```
```{r results='asis', echo=FALSE}
if(!include){cat("\\ignore{")}
```
NOT Included bla bla
```{r results='asis', echo=FALSE}
if(!include){cat("}")}
```
I want to have my graph output display on the next slide while the code chunk stays on the first. I am using the default ioslides in Rstudio. I would think that it would be some attribute of the code chunk but I can't figure out what it is.
---
output: ioslides_presentation
---
## Slide with Plot
```{r, echo=TRUE}
plot(cars)
```
Any one have any idea on how to do this in Rstudio?
I want to use this for educational purposes. First showing the code and than revealing the graph. Now I am stuck with doing double code chunks with echo=FALSE and TRUE and eval=FALSE and TRUE.
It's easier to run the code twice, once not evaluating the code, the second time not showing the code.
---
title: "Plot Separation"
output: ioslides_presentation
---
## Plot 1
```{r, eval = FALSE}
plot(1:10)
```
## Plot 2
```{r, echo = FALSE}
plot(1:10)
```
It also avoids the error when smaller is true.
To move a plot to the next slide, you need to add a horizontal rule ---- before it (see documentation). You can modify the default plot hook to do it:
```{r setup, include=FALSE}
library(knitr)
local({
hook_plot = knit_hooks$get('plot')
knit_hooks$set(plot = function(x, options) {
paste0('\n\n----\n\n', hook_plot(x, options))
})
})
```
If you want all your plots to appear on the next slide Yihui's answer is the way to go. But if you want some plots to appear on the same slide you may be better off doing it manually, similar to what you are already doing (and what Dario suggested). Except that I would strongly recommend the use of chunk references. That way you avoid the need to duplicate the code.
---
title: "Plot Separation"
output: ioslides_presentation
---
## Plot code
```{r cars_plot, echo = TRUE, eval = FALSE}
plot(cars)
```
## Plot display
```{r cars_plot, echo = FALSE, eval = TRUE}
```
```
I agree this would be desirable, but I'm finding ioslides to be buggy. Ioslides project started eith google, but was let go a while ago.
You may have better luck with beamer/home slides. But does require a LaTeX distribution to be installed.
I am using knitr and pandoc to write reports into word (we need to be able to circulate for comments using track changes etc).
It is working very well so far, but I have found that the plots are all coming out with captions at the bottom, and I don't want captions. While I could just delete them in the word doc, if I can stop them showing in the code it would be better.
So for the following code in markdown:
Test test test
```{r}
summary(cars)
```
You can also embed plots, for example:
```{r fig.width=7, fig.height=6}
plot(cars)
```
I then run the following code in R:
library("knitr")
# Stackoverflow table test 1.html
knit2html("captiontest.rmd")
FILE <- "captiontest"
system(paste0("pandoc -o ", FILE, ".docx ", FILE, ".md"))
And the graph, in the word document, has the caption "plot of chunk unnamed-chunk-2"
I know I can change this caption, e.g. {r fig.width=7, fig.height=6, fig.cap='hello'}, but I thought that fig.cap=NULL would make it hidden. Instead it seems to make the whole plot disappear.
Are plots required to have a caption - do I just have to go through each word doc and delete them manually? Or is there a way to hide them?
Kind of a dirty trick, but:
You can set fig.cap="" on the chunk in question:
Test test test
```{r}
summary(cars)
```
You can also embed plots, for example:
```{r fig.width=7, fig.height=6, fig.cap=""}
plot(cars)
```
Or, you can set fig.cap="" for all chunks at once in an initializing chunk at the beginning of your Rmd document:
Test test test
```{r options-chunk}
opts_chunk$set(fig.cap="")
```
```{r}
summary(cars)
```
You can also embed plots, for example:
```{r fig.width=7, fig.height=6}
plot(cars)
```