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.
Related
When I knit a document containing multiple plots obtained through purrr:map function, I get text slides in between each plot slide containing unwanted list index information (see image slides 2, 4, and 6). I'd like to remove these and just have plots.
I've tried results = "hide" and results = FALSE in the header.
These just return one plot instead of many, AND the text is still
there.
I've tried adding invisible() around my code as recommended
here. I don't see a difference.
How can I remove these and just have three slides with the three plots with no text?
---
title: "Reprex"
output: powerpoint_presentation
---
```{r include=FALSE}
library(tidyverse)
```
```{r echo=FALSE, results = FALSE}
ys <- c("mpg","cyl","disp")
ys %>% map(function(y)
invisible(ggplot(mtcars, aes(hp)) + geom_point(aes_string(y=y))))
```
Try this:
To suppress the console output use purrr::walk instead of map. See e.g. https://chrisbeeley.net/?p=1198
To get each plot printed on a separate slide use results='asis' and add two newlines via cat('\n\n') after each plot.
---
title: "Reprex"
output: powerpoint_presentation
---
```{r include=FALSE}
library(tidyverse)
```
```{r echo=FALSE, results='asis'}
ys <- c("mpg","cyl","disp")
walk(ys, function(y) {
p <- ggplot(mtcars, aes(hp)) + geom_point(aes_string(y=y))
print(p)
cat('\n\n')
})
```
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)')
```
Say, I have the following RNotebook chunk that plots a figure:
```{r}
plot(cars)
```
Now, I want to plot it as a 10x10 figure. I could use this:
```{r fig.height = 10, fig.width = 10}
plot(cars)
```
and that works fine. But say I want to redefine global figure sizes and default to those. I tried using this:
```{r}
knitr::opts_chunk$set(fig.height = 10, fig.width = 10)
plot(cars)
knitr::opts_chunk$get()$fig.width
knitr::opts_chunk$get()$fig.height
```
but this doesn't resize the figure correctly and yet the default figure sizes have been changed when I check them. Can someone explain where I'm going wrong?
A little playing around and, with an html_document output type, it works if you put the opts_chunk call in the chunk ahead of where you want it to be used.
---
title: "R Notebook"
output:
html_document
---
```{r, setup}
knitr::opts_chunk$set(fig.width = 5)
```
```{r}
knitr::opts_chunk$set(fig.width = 8)
```
```{r}
plot(cars)
```
```{r}
knitr::opts_chunk$set(fig.width = 12)
```
```{r}
plot(cars)
```
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.
I am using RStudio and knitr to knit .Rmd to .docx
I would like to include inline code in figure captions e.g. something like the following in the chunk options:
fig.cap = "Graph of nrow(data) data points"
However, knitr does not evaluate this code, instead just printing the unevaluated command.
Is there a way to get knitr to evaluate r code in figure/table captions?
knitr evaluates chunk options as R code. Therefore, to include a variable value in a figure caption, just compose the required string using paste or sprintf:
fig.cap = paste("Graph of", nrow(data), "data points")
Note that this might be problematic if data is created inside this chunk (and not in a previous chunk) because by default chunk options are evaluated before the chunk itself is evaluated.
To solve this issue, use the package option eval.after to have the option fig.cap be evaluated after the chunk itself has been evaluated:
library(knitr)
opts_knit$set(eval.after = "fig.cap")
Here a complete example:
---
title: "SO"
output:
word_document:
fig_caption: yes
---
```{r fig.cap = paste("Graph of", nrow(iris), "data points.")}
plot(iris)
```
```{r setup}
library(knitr)
opts_knit$set(eval.after = "fig.cap")
```
```{r fig.cap = paste("Graph of", nrow(data2), "data points.")}
data2 <- data.frame(1:10)
plot(data2)
```
The first figure caption works even without eval.after because the iris dataset is always available (as long as datasets has been attached). Generating the second figure caption would fail without eval.after because data2 does not exist before the last chunk has been evaluated.