Is it possible to produce subfigures (with associated subcaptions) using knitr? Here is a minimal working example:
\documentclass{article}
\begin{document}
<<echo = FALSE, fig.cap = c("Some numbers.", "Some more numbers."), out.width = "0.5\\textwidth", fig.align = "center">>=
plot(1:10)
plot(30:100)
#
\end{document}
This results in two figures labelled Figure 1 and Figure 2 with captions as defined (respectively). But I want them to be labelled "Figure 1a" and "Figure 1b", as you can do with the subcaption LaTeX package.
I know there is a knitr options "fig.env", but this doesn't solve it (at least not using, for example, "fig.env = 'subfigure'"). There is a similar post here regarding Sweave, but the solution is an inelegant hack: http://texblog.org/2011/12/01/sweave-subfig-controlling-figure-size-and-placement/
knitr (>= v1.5) supports subfigures. You can use the chunk option fig.subcap. Here is a minimal example.
\documentclass{article}
\usepackage{subfig}
\begin{document}
<<fig-sub, fig.cap='two plots', fig.subcap=c('one plot', 'the other one'), out.width='.49\\linewidth'>>=
plot(1:10)
plot(rnorm(10), pch=19)
#
\end{document}
Updating the answer from Yihui to reflect the changes in Rmarkdown in the past few years, and also the shift away from Rnw files.
As listed within the knitr chunk options, subfigures require a few additional settings to be set in the chunk header:
fig.subcap is a list of the captions for subfigures
fig.ncol: the number of columns of subfigures
out.width: the output width of the figures. You will normally set this 100% divided by the number of sub columns.
Subfigures also require the LaTeX package subfig. The line \usepackage{subfig} must therefore be included within the YAML, or if you are using an external tex template you can add this to that file.
Here is a basic template:
---
output: pdf_document
header-includes:
- \usepackage{subfig}
---
```{r fig-sub, fig.cap='two plots', fig.subcap=c('one plot', 'the other one'), out.width='.49\\linewidth', fig.asp=1, fig.ncol = 2}
plot(1:10)
plot(rnorm(10), pch=19)
```
Using with ggplot2
If you are plotting subfigures which contains multiple ggplot plots, can messy as they do not line up between the plots. You may want to check out this post here on how to use cowplot to force ggplots to have the same dimensions.
This stackoverflow post will help you make sure that all the plots line up as shown in the image below:
Providing a list to subfigures
Just sharing this as a possible extension of subfigures. Something I like to use them for is feeding them a list of figures. Maybe you have produced a function which you need to run on four different trial groups, or in four separate locations. For example, here is a list of four cities in the UK:
```{r}
locations <- c("Southampton, UK", "London, UK", "Bristol, UK", "Birmingham,
```
This list can then be used within the fig.sub and an lapply to produce a list of subfigures. If you need to run the
```{r fig-sub-2, fig.cap='A collection of maps', fig.subcap= locations, out.width='.49\\linewidth', fig.asp=1, fig.ncol = 2}
library(ggmap)
lapply(locations, function(x)
ggmap(get_map(x))
)
```
This makes the subfigures quite robust. If I need to run my model in an extra couple of cities, all I need to do is add extra values to the location list and the sub figures will be the same length.
You can use Latex's subcaption package.
\documentclass{article}
\usepackage{subcaption}
\begin{document}
\begin{figure}
\centering
\begin{subfigure}[b]{0.3\textwidth}
\centering
<<echo = FALSE, out.width = "0.5\\textwidth", fig.align = "center">>=
plot(1:10)
#
\caption{text for first figure}
\label{fig:gull}
\end{subfigure}%
\begin{subfigure}[b]{0.3\textwidth}
\centering
<<echo = FALSE, out.width = "0.5\\textwidth", fig.align = "center">>=
plot(30:100)
#
\caption{text for second figure}
\label{fig:tiger}
\end{subfigure}
\caption{Figure caption}
\end{figure}
\end{document}
Related
\begin{figure}[h]
\centering
<<echo=FALSE>>=
for(i in 2:38){
print(my_plot_function(i))
}
#
\end{figure}
This is my code, but what is happening is that when I compile my PDF I only get the first two plots that fit on the first page and I do not get the rest of the plots.
I would like to have all of the plots on separate pages.
And how would I go about adding captions to each individual plot in the for loop.
\documentclass{article}
\begin{document}
<<echo = FALSE, fig.cap = c("First, Second, Third"), results = "asis">>=
library(ggplot2)
for (i in 1:3) {
print(qplot(x = 1, y = i))
cat("Arbitrary \\LaTeX code! \\clearpage")
}
#
\end{document}
You can use the chunk option fig.cap to add captions to your plots. Note that this will wrap your figure in a figure environment, turning it into a float.
Use the chunk option results="asis" to be able to print arbitrary text (including LaTeX markup) into your document using cat().
I am producing a rmarkdown document, knitting to PDF and have a figure (figure 1) and a table (table 1) where the table explains the figure in more detail. I have no issue giving either of them a standard caption but I would like to change the table caption to be "Explanation of Figure 1". Is there any way of doing this?
The code chunks are listed below, please let me know if I need to provide more information:
YAML:
- \usepackage{caption} #and several others
output:
bookdown::pdf_document2:
keep_tex: no
latex_engine: xelatex
Code Chunks:
Figure 1:
```{r figure-1, fig.cap="Figure"}
ggplot()
```
Table 1:
```{r table, fig.cap="Explanation of Figure \#ref(fig:figure-1)"}
knitr
kableExtra::kable(caption = "Explanation of Figure \#ref(fig:figure-1)")
```
The main error message with one backslash is "Error: '#' is an unrecognized escape in character string" and suggests I forgot to quote character options, which is not true.
With two backslashes the document knits but produces the caption "Explanation of Figure reffig:table"
3 backslashes: the same error as with 1.
4 backslashes: the error is "pandoc-citeproc: reference ref not found. ! Package caption Error: \caption outside float."
Appreciate any suggestions!
Just a workaround, but may helps.
The \\#ref(fig:xxx) option works well when knitting to a html_document2.
To me pdf - creation worked fine when using pandoc in the terminal.
E.g.:
---
title: "Cross ref"
output:
bookdown::html_document2:
collapsed: no
theme: readable
toc: yes
link-citations: yes
---
```{r firstplot, fig.cap = "A plot with points." }
library(ggplot2)
plot_A = ggplot(data = data.frame(x = c(1:10),
y = seq(3, 8, length.out = 10)),
aes(x = x, y =y))+
geom_point()
plot_A
```
Now a second plot with a reference to Fig.: \#ref(fig:firstplot).
```{r secondplot, fig.cap = "This is the same as Fig.: \\#ref(fig:firstplot)
but now with a red line." }
library(ggplot2)
plot_A + geom_line(alpha = .75,col = "red")
```
after knitting just move to the folder containing the html and using pandoc
pandoc mini_ex-crossref.html -o mini_ex.pdf
I tried many different approaches text references, chunk captions, caption argument in the kable function and I´m sure there is a clever solution somewhere, so here is just a workaround with pure Latex.
Add a latex chunk with a label before the chunk with the figure:
```{=latex}
\begin{figure}
\caption{Figure 1}
\label{Fig-1}
```
```{r figure-1, echo = FALSE}
ggplot(mtcars) +
geom_point(aes(cyl, gear))
```
```{=latex}
\end{figure}
```
Now you can refer to Fig-1 in your latex-caption for the table with normal latex code \ref{Fig-1}:
```{=latex}
\begin{table}
\caption{Explanation of Figure \ref{Fig-1}}
```
```{r table}
kableExtra::kable(x = mtcars)
```
```{=latex}
\end{table}
```
Notes:
* In my opinion this is just a workaround.
* It´s not possible to use the chunk option fig.cap = "" and the latex code in parallel
J_F referenced Yihui Xie's excellent explanation of using text references in RMarkdown (https://bookdown.org/yihui/bookdown/markdown-extensions-by-bookdown.html#text-references), which you can use for figure and table captions that require more complicated things than plain text (e.g., formatting, cross-references, etc.). This may be a more flexible solution overall than remembering to escape the backslash in Robert's answer, and does not require a workaround with LaTeX.
As Yihui explains, all you need to do is define a text reference on a single line in markdown and reference that in the chunk option "fig.cap" or the "caption" parameter in knitr::kable(). Just be careful to make sure that each text reference is one paragraph that does not end in a white space.
Here's a basic example.
---
title: "Cross-referencing figures and tables within captions."
output: bookdown::pdf_document2
editor_options:
chunk_output_type: console
---
```{r load-packages}
library(knitr)
library(flextable)
```
(ref:first-fig-caption) Here's a complicated figure caption for the first figure, which can include complicated text styling like $m^2$ and references to other elements in the document, like Table \#ref(tab:mtcars) or Fig. \#ref(fig:cars).
```{r pressure, fig.cap = '(ref:first-fig-caption)'}
plot(pressure)
```
(ref:second-fig-caption) Here's a second complicated figure caption, also referencing Table \#ref(tab:mtcars).
```{r cars, fig.cap = '(ref:second-fig-caption)'}
plot(cars)
```
(ref:caption-table1) A caption for the first table. Check out this cross reference to Fig. \#ref(fig:pressure).
```{r mtcars}
mtcars |>
head() |>
kable(caption = '(ref:caption-table1)')
```
I am creating a series of plots using ggplot2. Each of these are programmatically named and I want use the names to give each their own figure caption. I want to pull the names from the list and pass them to fig.cap dynamically.
Is there a way to do this? Here is a MCVE, and you can switch between the list and the individual plots to see the figures disappear or show up:
---
output: pdf_document
---
```{r, include = FALSE}
library(ggplot2)
library(knitr)
opts_chunk$set(echo=FALSE)
```
```{r}
## Plot 1
listOfPlots <- list(
# Plot 1
ggplot(data = diamonds) +
geom_point(aes(carat, price)),
## Plot 2
ggplot(data = diamonds) +
geom_point(aes(carat, depth))
)
names(listOfPlots) <- c("This is caption 1", "This is caption 2")
```
```{r, fig.cap = c("This is caption 1", "This is caption 2"), echo=TRUE}
listOfPlots
# listOfPlots$`This is caption 1`
# listOfPlots$`This is caption 2`
```
Notes:
Yihui and others have said (https://groups.google.com/forum/#!topic/knitr/MJVLiVyGCro), that to have multiple figures in a chunk and give them a figure caption, you need to have echo=TRUE because inline figures and pandoc stuff.
I don't want to show code and the number of figures may be variable so I don't want to hard code things. Interestingly, using a list of ggplots also does not work even if echo=TRUE. I have to individually call each ggplot.
There needs to be spaces between plots in R Markdown if they are to be given their own caption. As stated by Yihui on your link, the trick here is to add some line breaks between the two images.
```{r, fig.cap=c("Caption 1", "Caption 2")}
listOfPlots[[1]]
cat('\n\n')
listOfPlots[[2]]
```
Note, the double square brackets are used to only return the plot itself.
Using a Loop
Assuming you are looking for a more generalizable method which could work for a list of any length, we can automate the creation of the line breaks between the plots using a loop. Note that results="asis" is required in the chunk header:
```{r, fig.cap=c("Caption 1", "Caption 2"), echo=FALSE, results="asis"}
for(plots in listOfPlots){
print(plots)
cat('\n\n')
}
```
As a final tip, you may wish to use the name of the list directly within the caption. The syntax {r, fig.cap = names(listOfPlots)} would be able to achieve this.
I label my figures like this.
---
title: "xxx"
output:
pdf_document:
fig_caption: true
---
And then in each chunk
```{r, fig.cap="some caption"}
qplot(1:5)
```
This works quite nicely. However in chunks where I plot multiple figures within a loop I can't specify a caption. This produces no caption at all:
```{r, fig.cap="another caption"}
qplot(1:5)
qplot(6:10)
```
How can I specify a figure that counts from the same number as the first chunk for each plot?
You can use a fig.cap argument of length 2 (or the size of your loop):
```{r, fig.cap=c("another caption", "and yet an other")}
qplot(1:5)
qplot(6:10)
```
Found an easy way to dynamically produce plots and add them to the pdf with individual captions, using knitr::fig_chunk as described here. This is also a workaround for OPs comment that message=false (or echo=False or results='asis' for that matter) supresses the fig.cap argument.
```{r my-plots, dev='png', fig.show='hide', echo=FALSE}
# generate plots first
qplot(1:5)
qplot(6:10)
```
```{r, echo=FALSE, results='asis'}
# then put them in the document with the captions
cat(paste0("![some caption](", fig_chunk(label = "my-plots", ext = "png", number = 1), ")\n\n"))
cat(paste0("![another caption](", fig_chunk(label = "my-plots", ext = "png", number = 2), ")\n\n"))
```
Hopefully this helps someone who stumbles upon this question in the future.
When typesetting an R Markdown document to PDF, if a function draws multiple plots, those plots often appear side-by-side, with only the first plot fully within the margins of the page.
Minimal R Markdown example:
---
title: "Example re plotting problem"
author: "Daniel E. Weeks"
date: "May 3, 2016"
output: pdf_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## Multiple plots within a loop
```{r}
plots <- function() {
plot(rnorm(100))
hist(rnorm(100))
}
for (i in 1:3) {
plots()
}
```
Here is a screenshot of page 2 of the generated PDF
which shows the problem. I have searched online, but haven't yet found a solution to this problem.
Thank you.
The plot hook solution proposed by user2554330 is simple and works well. So this code draws all the plots within the margins of the resulting PDF:
---
title: "Example re plotting problem"
author: "Daniel E. Weeks"
date: "May 3, 2016"
output: pdf_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## Multiple plots within a loop
```{r}
plots <- function() {
plot(rnorm(100))
hist(rnorm(100))
}
```
## Call plotting function
```{r}
my_plot_hook <- function(x, options)
paste("\n", knitr::hook_plot_tex(x, options), "\n")
knitr::knit_hooks$set(plot = my_plot_hook)
for (i in 1:3) {
plots()
}
```
The problem is that the generated .tex file has no spaces between the \includegraphics{} calls. LaTeX gives warnings about overfull hboxes, because the graphics aren't big enough to sit alone on a line, and are too big when it puts two on each line.
You can tell LaTeX (TeX really) to output the bad lines without putting two figures on each line by adding
\pretolerance=10000
in the text before the code chunk. You'll probably want to set it back to its default value
\pretolerance=100
after the code chunk, or LaTeX won't try hyphenation afterwards, and text can look really ugly.
Another way to fix this would be to force each figure to be in its own paragraph. You can do this by adding this code
my_plot_hook <- function(x, options)
paste("\n", knitr::hook_plot_tex(x, options), "\n")
knitr::knit_hooks$set(plot = my_plot_hook)
into a code chunk before you do your plotting. This puts a blank line
before and after each figure.