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.
Related
I need to implement a figure caption in a plot that is generated by the vtree package in R markdown. I learned that this is a htmlwidget and figure captions should now be possible for htmlwidgets used in R markdown with install.packages('webshot') and webshot::install_phantomjs() (reference: https://bookdown.org/yihui/bookdown/html-widgets.html#ref-R-DT.
But days after I am not really any step further. I did not find any example (show case) for this issue (fig.cap for htmlwidgets in R markdown in the net) so my hope is that someone out there can give me some help!
In my iris dataset example, in Fig. 1 the caption is not working in contrast to Fig. 2.
my iris set example RMD file:
YAML
---
title: "test"
author: "TJ"
date: "14 12 2020"
output: html_document
---
code chunk 1: load libraries and data
knitr::opts_chunk$set(echo = TRUE)
library(vtree)
library(webshot)
library(tidyverse)
attach(iris)
df <- iris %>%
select(Species) %>%
cbind(sapply(levels(.$Species), `==`, .$Species))
code chunk 2: Figure 1
{r fig1, echo=FALSE, fig.cap="Vtree plot"}
vtree(iris, "Species")
code chunk 3: Figure 2
{r fig2, echo=FALSE, fig.cap="Scatter plot iris dataset"}
plot(Sepal.Length, Sepal.Width, main="Scatterplot Example",
xlab="Sepal Length ", ylab="Sepal Width ", pch=19)
There is a workaround using the Magick package.You save the image as .png using grVizToPNG (make sure you comment this line out before you render your document or put it in a separate chunk with ´{r eval = FALSE}, otherwise you will get an error during rendering:
```{r eval=FALSE, echo = FALSE}
myimage <- vtree(iris, "Species")
saveMyimage <- grVizToPNG(myimage, width=800)
```
Here you use the Magickpackage:
```{r magick, echo= FALSE}
MyimagePNG <- image_read("myimage.png")
image_annotate(MyimagePNG, "Vtree plot", size = 35, gravity = "southwest")
```
I am new to Rmarkdown and shiny and forgive me for some naive questions. I have build a code in two parts first where I do all the processing and second where I call the Rmarkdown to knit it.
The first code example.R is as follows and works fine independently (with only glitch of plots being trimmed from sides):
# Create a label for the knitr code chunk name
## #knitr ExternalCodeChunk020
library(Seurat)
library(tidyverse)
library(sleepwalk)
library(gridExtra)
library(plotly)
library(DT)
# Set up some sample data
data(mtcars)
# Display the xvars
# Note that I don't really want to display the xvars, but this line is included
# to demonstrate that text output won't show up in the RMarkdown in this example.
a <- ggplotly(ggplot(mtcars, aes(cyl,mpg)) + geom_boxplot())
b <- ggplotly(ggplot(mtcars, aes(wt,mpg)) + geom_point())
subplot(a, b, nrows=1)
DT::datatable(mtcars, class = "cell-border stripe", rownames = FALSE, filter ="top",
editable =TRUE, extension = "Buttons", options = list(dom="Bfrtip",
buttons =c("copy", "csv", "excel", "pdf","print")))
ggplotly(ggplot(mtcars,aes(x=mpg)) + geom_histogram(binwidth=5))
# Display the date and time
# Similar to xvars above, this line is intended to demonstrate that text output
# won't be displayed in this RMarkdown example.
Sys.Date()
The second part of the code (mrkdwn.Rmd) is where I try to knit and generate Rmarkdown report:
---
title: "Code Chunks"
author: "Author"
date: "November 13, 2020"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
knitr::read_chunk("example.R")
```
This first code chunk prints the externally located code,
but it does not execute the code. The next code chunk
executes the externally located code, but it does not print code
itself. Text output is suppressed, and figures are plotted,
but only after all of the code is executed.
```{r DisplayCodeChunk, eval = FALSE, echo = FALSE}
<<ExternalCodeChunk020>>
```
```{r RunCodeChunk, echo = FALSE, eval = TRUE, results = 'hide'}
<<ExternalCodeChunk020>>
```
the output doesn't contain plots. I am not sure what is going wrong, could anyone of you help me in fixing this.
I know that an easy fix is to put both parts of the code together inside the Rmarkdown like this:
---
title: "test3"
output: html_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}
library(Seurat)
library(tidyverse)
library(sleepwalk)
library(gridExtra)
library(plotly)
library(DT)
# Set up some sample data
data(mtcars)
# Display the xvars
# Note that I don't really want to display the xvars, but this line is included
# to demonstrate that text output won't show up in the RMarkdown in this example.
a <- ggplotly(ggplot(mtcars, aes(cyl,mpg)) + geom_boxplot())
b <- ggplotly(ggplot(mtcars, aes(wt,mpg)) + geom_point())
subplot(a, b, nrows=1)
DT::datatable(mtcars, class = "cell-border stripe", rownames = FALSE, filter ="top",
editable =TRUE, extension = "Buttons", options = list(dom="Bfrtip",
buttons =c("copy", "csv", "excel", "pdf","print")))
ggplotly(ggplot(mtcars,aes(x=mpg)) + geom_histogram(binwidth=5))
# Display the date and time
# Similar to xvars above, this line is intended to demonstrate that text output
# won't be displayed in this RMarkdown example.
Sys.Date()
```
## Including Plots
You can also embed plots, for example:
```{r pressure, echo=FALSE}
plot(pressure)
```
Since I need to process large datasets and generate graphs/plots and table I would prefer to keep them separately, so that my Rmarkdown doesn't crash. May be this is wrong and there could be a better approach, please suggest.
Many thanks for your time and help.
I am transitioning to Bookdown from Markdown. Although it seems as though this should be straightforward I am getting an unexpected knit failure once I have added the 3rd (usually) code chunk in a chapter (not index.rmd) file. I have tried using code from the example code by Allaire and Xie with the same result. The problem does not occur if all the markdown code is in one file i.e. no chapters. Here is the sample code from the index and 1st chapter files. Sorry about the formatting; I'm not sure how to format markdown code in stackoverflow so the 3 back tics consistently show.
---
classoption: openany # Removes blank pages (Arrgh!!)
site: "bookdown::bookdown_site"
output:
bookdown::tufte_book2:
latex_engine: xelatex
---
```{r setup, include=FALSE}
library(ggplot2)
# invalidate cache when the tufte version changes
knitr::opts_chunk$set(tidy = FALSE, cache.extra = packageVersion("tufte"))
```
And this is the first chapter code:
# Figures
## Margin Figures
Images and graphics play an integral role in Tufte's work. To place figures in the margin you can use the **knitr** chunk option `fig.margin = TRUE`. For example:
```{r fig-margin, fig.margin = TRUE, fig.cap = "MPG vs horsepower, colored by transmission.", fig.width=3.5, fig.height=3.5, cache=TRUE, message=FALSE}
library(ggplot2)
mtcars2 <- mtcars
mtcars2$am <- factor(
mtcars$am, labels = c('automatic', 'manual')
)
ggplot(mtcars2, aes(hp, mpg, color = am)) +
geom_point() + geom_smooth() +
theme(legend.position = 'bottom')
```
In fact, you can include anything in the margin using the **knitr** engine named `marginfigure`. Unlike R code chunks ```` ```{r} ````, you write a chunk starting with ```` ```{marginfigure} ```` instead, then put the content in the chunk. See an example on the right about the first fundamental theorem of calculus.
```{marginfigure}
We know from _the first fundamental theorem of calculus_ that for $x$ in $[a, b]$:
$$\frac{d}{dx}\left( \int_{a}^{x} f(u)\,du\right)=f(x).$$
```
It fails here
knitr::kable(
mtcars[1:6, 1:6], caption = 'A subset of mtcars.'
)
Deleting the code after "It fails here" makes it knit properly for me.
Dropbox link with scripts, log, and pdf's.
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 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.