I am having an issue with bookdown, not sure the reason why.
When add images (these are files, so I use knitr::include_graphics) like this:
# This is a minimal example
I want the image "mas.gif". Where is it?
```{r mas, echo=F, fig.cap="image", ref.label="fig:mas"}
knitr::include_graphics("mas.gif")
```
Hmmm...no clue!
The chunk just disappears in the epub, md, tex and pdf files.
What could be wrong? It used to work some while ago...
Just remove , ref.label="fig:mas", like this
# This is a minimal example
I want the image "mas.gif". Where is it?
```{r mas, echo=F, fig.cap="image"}
knitr::include_graphics("mas.gif")
```
Hmmm...no clue!
See the documentation by bookdown package's author:
If we assign a figure caption to a code chunk via the chunk option fig.cap, R plots will be put into figure environments, which will be automatically labeled and numbered, and can also be cross-referenced. The label of a figure environment is generated from the label of the code chunk, e.g., if the chunk label is foo, the figure label will be fig:foo (the prefix fig: is added before foo). To reference a figure, use the syntax \#ref(label), where label is the figure label, e.g., fig:foo.
Related
I think the question is quite self-explanatory but for avoidance of doubt I'll explain with more detail below:
I have an R Markdown document that works well if converted to HTML or uploaded to GitHub. When converting to PDF (using Latex), the results are not so pretty. I find that the biggest problem in a Latex PDF document are line breaks. I can fix the line breaks issue on the PDF document by adding "\ " characters, but that throws my HTML document out of whack too.
Is there a way to manually add line breaks (or "space before/after paragraphs") for the PDF output only?
Thank you!
You can redefine the relevant spacings in the YAML header. \parskip controls the paragraph spacing. Code blocks are shaded using a snugshade environment from the framed package. We can also redefine the shaded environment for code blocks to have some vertical space at the start. Here's a reproducible example. Note: I also added the keep_tex parameter so you can see exactly what the generated tex file looks like, in case this is useful:
title: "test"
author: "A.N. Other"
header-includes:
- \setlength{\parskip}{\baselineskip}
- \renewenvironment{Shaded}{\vspace{\parskip}\begin{snugshade}}{\end{snugshade}}
output:
pdf_document:
keep_tex: true
---
```{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.
Once you output to HTML, you can just print the HTML webpage as PDF. that might be an easy way keep the original format
I can't get R/KnitR to create the LaTeX \label{} statement for a figure. The manual seems to indicate that a \label{} statement will be created by concatenating the string in fig.lp ("fig:" by default) with the label for the R-code chunk. I haven't been able to get this to work, however. No \label{} statement is created for the first figure created by knitting the MWE below. The second figure has it's label added with a workaround that I just discovered, putting the R chunk in a figure environment, and putting the \label tag after or inside the \caption tag.
\documentclass[12pt, english, oneside]{amsart}
\begin{document}
Figure \ref{fig:plot} doesn't have it's label.
<<plot>>=
plot(x=0, y=0)
#
Figure \ref{fig:plot2} has its label.
\begin{figure}
\caption{\label{fig:plot2}}
<<>>=
plot(x=1,y=1)
#
\end{figure}
\end{document}
Okay, I've found a workaround by putting the R chunk in a \begin{figure} . . .\end{figure} environment in LaTeX. I can create the label in that same environment. Still, I'd like to understand how Yihui intends for this to be handled with KnitR.
You need to set fig.cap = '' (or whatever you wish) to ensure that a figure environment is used in the latex document. (you may have noticed that the \begin{figure} ... \end{figure} is missing along with the \label{} component
eg
\documentclass[12pt, english, oneside]{amsart}
\begin{document}
See Figure \ref{fig:plot}.
<<plot, fig.lp="fig:", fig.cap = ''>>=
plot(x=0, y=0)
#
\end{document}
I would agree that the description from the website is less than clear as to this being necessary.
fig.env: ('figure') the LaTeX environment for figures, e.g. set fig.env='marginfigure' to get \begin{marginfigure}
fig.cap: (NULL; character) figure caption to be used in a figure environment in LaTeX (in \caption{}); if NULL or NA, it will be
ignored, otherwise a figure environment will be used for the plots in
the chunk (output in \begin{figure} and \end{figure})
Although the graphics manual is clear, and the reasoning makes sense
Figure Caption
If the chunk option fig.cap is not NULL or NA, the
plots will be put in a figure environment when the output format is
LATEX, and this option is used to write a caption in this environment
using \caption{}. The other two related options are fig.scap and
fig.lp which set the short caption and a prefix string for the figure
label. The default short caption is extracted from the caption by
truncating it at the first period or colon or semi-colon. The label is
a combination of fig.lp and the chunk label. Because figure is a float
environment, it can float away from the chunk output to other places
such as the top or bottom of a page when the TEX document is compiled.
If you were wishing to replicate a R session output, you wouldn't want the figures to float away from the line of code which defines how they were created.
I created a custom function which sets mfrow to nxn and creates n^2 scatter plots, with multiple data sets on each plot, based on an input list of data frames. The signature of my plotting function looks like this:
plot.return.list<-function(df.list,num.plot,title)
Where df.list is my list of data frames, num.plot is the total number of plots to generate (used to set mfrow) and title is the overall plot title (the function generates titles for each individual sub-graph).
This creats plots fine when I run the function from the console. However, I'm trying to get this figure into a markdown document using RStudio, like so:
```{r, fig.height=6,fig.width=6}
plot.return.list(f.1.list,4,bquote(atop("Numerical Approximations vs Exact Soltuions for "
,dot(x)==-1*x*(t))))
```
Since I haven't set the echo option in my {r} statement, this prints both the plotting code as well as the plot itself. However, if my first line instead reads:
{r, fig.height=6,fig.width=6,echo=FALSE}
Then both the code AND the plot disappear from the final document.
How do I make the plot appear WITHOUT the code? According to the example RStudio gives, setting echo=FALSE should make the plot appear without the code, but that isn't the behavior I'm observing.
EDIT: I seem to have tracked my problem down to kable. Whether or not I'm making a custom plot-helper function, any call to kable kills my plot. This can be reproduced in a markdown:
---
title: "repro"
author: "Frank Moore-Clingenpeel"
date: "October 9, 2016"
output: pdf_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
library(knitr)
options(default=TRUE)
repro.df<-data.frame((0.1*1:10)%*%t(1:10))
```
```{r, echo=FALSE}
kable(repro.df)
```
```{r, fig.height=6,fig.width=6,echo=FALSE}
plot(repro.df[,1],repro.df[,2])
```
In this code, the plot won't plot because I have echo set to false; removing the flag makes the plot visible
Also note that in my repro code, kable produces a table with a bunch of garbage in the last line--I don't know why, but this isn't true for my full original code, and I don't think it's related to my problem.
Thanks for the reproducible example. From this I can see that the problem is you don't have a newline between your table chunk and your plot chunk.
If you were to knit this and examine the MD file produced by knit (or set html_document as your output format and have keep_md: true to look at it), you would see that the table code and plot code are not separated by any newline. Pandoc needs this to delimit the end of the table. Without it, it thinks your  is part of the table and hence puts it as a "junk line" in the table rather than an image on its own.
Just add a newline between the two chunks and you will be fine. (Tables need to be surrounded with blank lines).
(I know you are compiling to LaTeX so it may confuse you why I am talking about markdown. In case it does, when you do Rmd -> PDF, Rmarkdown uses knit to go from RMD to MD, and then pandoc to go from MD to tex. This is why you still need to make sure your markdown looks OK).
I'm producing a solutions manual for a book, using .Rmd files with the following YAML header:
---
title: "DDAR: Solutions and Hints for Exercises"
date: "`r Sys.Date()`"
output:
word_document:
reference_docx: solutions-setup.docx
---
where I control the general layout of the document with the reference_docx to get an output Word document.
There will be many figures, and I'd like to set some global graphics parameters to give relatively tight bounding boxes and reasonable font sizes
in the figures without having to tweak each one from what I see in a PDF document.
I tried the following, but the par() setting doesn't seem to have any effect:
{r setup, echo=FALSE}
options(digits=4)
par(mar=c(5,4,1,1)+.1)
Instead I get images like the following in my document with larger bounding boxes than I would like and with much larger font sizes than I would like.
I know how to control all this in .Rnw files produced with LaTeX, but I
can't find how to do it in .Rmd -> Word. Is there a chunk hook I could
use? I don't think that there is an out.width chunk option that re-scales
a figure as in LaTeX.
#scoa's answer shows how to use a hook to set some graphical parameters at the beginning of each chunk. This is necessary because "by default, knitr opens a new graphics device to record plots and close it after evaluating the code, so par() settings will be discarded", i.e. graphical parameters for later chunks cannot be set in an early setup-chunk but need to be set for each chunk separately.
If this behavior is not wanted, the package option global.par = TRUE can be used:
opts_knit$set(global.par = TRUE)
Finding the correct values for the margins is sometimes quite painful. In these cases, hook_pdfcrop can help. In all chunks where the option crop = TRUE, white margins will be removed. To apply this to all chunks, use
library(knitr)
knit_hooks$set(crop = hook_pdfcrop)
opts_chunk$set(crop = TRUE)
This works for docx output as well because "when the plot format is not PDF (e.g. PNG), the program convert in ImageMagick is used to trim the white margins" (from ?hook_pdfcrop).
Note that under some circumstances, cropping plots has the side effect of sometimes apparently different "zoom" factors of plots: This happens in cases where we start with identical sized elements on two plots but larger white margins around one of the plots. If then both are resized to a fixed output width after cropping, elements on the plot with larger margins look larger. However, this is not relevant for docx output because out.width/out.height cannot be used in that case.
The knitr documentation for hooks actually uses small margins as an example of what you can do with hooks. Here is a solution (adapted from this documentation).
---
output: word_document
---
```{r setup, echo=FALSE}
library(knitr)
knit_hooks$set(small.mar = function(before, options, envir) {
if (before) par(mar=c(5,4,1,1)+.1) # smaller margin on top and right
})
opts_chunk$set(small.mar=TRUE)
```
```{r}
plot(iris$Sepal.Length)
```
Using opts_chunk$set(small.mar=TRUE) is a way to avoid passing it to every chunk in the document.
The margin appears fixed (screenshot from the docx output in libreoffice with default reference-docx).
Is there a way to specify the placement of captions for figures generated by R using KnitR? I'm hoping that there's something functionally equivalent to xtable()'s caption.placement option.
A minimal working example is provided below.
\documentclass[12pt, english, oneside]{amsart}
\begin{document}
The caption for Figure \ref{fig:plot} is placed below the figure. Could we place it above, instead?
<<plot, echo=FALSE, fig.cap="Default caption placement is below the figure.">>=
plot(x=0, y=0)
#
\end{document}
This would likely be best to deal with in the latex style for all figures, but you can customize figures with hooks. The fig.env chunk option controls the environment the block is inserted into. You could always make your own version of figure with your own formatting.