I have a very simple Rnw file:
\documentclass[10pt,a4paper]{article}
\usepackage[latin1]{inputenc}
\begin{document}
<<mychunk, echo=FALSE, cache=FALSE, fig.keep='all'>>=
plot(rnorm(100),rnorm(100))
lines(c(-1,1),c(-1,1))
#
\end{document}
The R chunk
plot(rnorm(100),rnorm(100))
lines(c(-1,1),c(-1,1))
should just give one figure. Instead, the output tex is
\includegraphics[width=\maxwidth]{figure/mychunk1}
\includegraphics[width=\maxwidth]{figure/mychunk2}
with two separate figures
and
This doesn't happen in all instances of a plot and lines, depending on the arguments, but the code I've given reproduces the problem. It should just have the second figure.
You've set fig.keep="all", and are getting just what would be expected from that setting! As described in the the online documentation, that option "keep[s] all plots (low-level plot changes may produce new plots)".
Try instead fig.keep="high" (the default, so you can also get it by just leaving out the fig.keep argument) or fig.keep="last", depending on what exactly you want.
Related
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 cannot figure out how to arrange two side-by-side plots as explained in the knitr graphics manual page 2 (http://yihui.name/knitr/demo/graphics/). I use the following MWE and the output is below. I would like them to be aligned as shown in the manual for the two cars plots (also on page 2 of the manual). The pdf is generated in RStudio (Knit to PDF).
---
title: "Untitled"
output: pdf_document
---
## R Markdown
```{r,echo=FALSE,out.width='.49\\linewidth', fig.width=3, fig.height=3}
barplot(1:4)
barplot(4:7)
```
To center two plots you can add fig.align='center'to your chunk options. If it produces one plot above the other add also fig.show='hold'. The result should be two centered graphs.
So your final chunk option should look something like:
{r,echo=FALSE, out.width='.49\\linewidth', fig.width=3, fig.height=3,fig.show='hold',fig.align='center'}
An alternative which worked for me: save the plots as files, then put the picture markdown on the same line (from here).
## Show images
 
You can save ggplot plot objects with ggsave.
Base plots are a bit more complicated, see for example here.
I'm putting this answer here because it helped me. Whether it's better for you or not depends on your situation.
I am using knit()and markdownToHTML() to automatically generate reports.
The issue is that I am not outputting plots when using these commands. However, when I use RStudio's Knit HTML button, the plots get generated. When I then use my own knit/markdown function, it suddenly outputs the plot. When I switch to another document and knit that one, the old plot appears.
Example:
```{r figA, result='asis', echo=TRUE, dpi=300, out.width="600px",
fig=TRUE, fig.align='center', fig.path="figure/"}
plot(1:10)
```
Using commands:
knit(rmd, md, quiet=TRUE)
markdownToHTML(md, html, stylesheet=style)
So I guess there are 2 questions, depending on how you want to approach it:
What magic is going on in Rstudio's Knit HTML?
How can I produce/include without depending on RStudio's Knit HTML button?
The only issue I see here is that this doesn't work when you have the chunk options {...} spanning two lines. If it's all on one line, it works fine. Am I missing something?
See how this is not allowed under knitr in the documentation:
Chunk options must be written in one line; no line breaks are allowed inside chunk options;
RStudio must handle linebreaks in a non-standard way.
This is really embarrassing, I really thought I read the documentation carefully:
include: (TRUE; logical) whether to include the chunk output in the
final output document; if include=FALSE, nothing will be written into
the output document, but the code is still evaluated and plot files
are generated if there are any plots in the chunk, so you can manually
insert figures; note this is the only chunk option that is not cached,
i.e., changing it will not invalidate the cache
Simply adding {..., include=TRUE} did the trick. I would say it would be a pretty sensible default though.
I am producing a latex report which produces multiple plots in a dlply call. The dlply call is of course in a single chunk and in order to get labels and captions to change I am using a snippet from Steve Powell below. The approach works but it seems knitr doesnt quite format the output correctly. A simple example that demonstrates:
\documentclass{article}
\begin{document}
<startup,echo=FALSE,results='hide',message=FALSE,tidy=FALSE,warning=FALSE,fig.keep='all',comment=NA>>=
require(knitr)
require(ggplot2)
opts_knit$set(progress = F, verbose = F)
opts_chunk$set(comment=NA,
tidy=FALSE,
warning=FALSE,
message=FALSE,
echo=FALSE,
dpi=600,
fig.width=6.75, fig.height=4, # Default figure widths
dev=c("pdf",'tiff'),
dev.args=list(pdf=list(NULL),tiff=list(compression='lzw')),
error=FALSE)
#
<<plotloop,results='asis'>>=
for(x in seq(1,20)){
x1<-data.frame(x=seq(1,10),y=seq(1,10))
plt<-ggplot(data=x1,aes(x,y))+geom_point()
figLabel=paste('Figure',x,sep='')
capt<-paste('Caption for fig.',x)
cat(knit(text=(paste("<<",figLabel,",fig.pos='ht',fig.cap='",capt,"'>>=\nplt\n#",sep=''))))
}
#
\end{document}
This almost works. The trouble is that knitr places the closing \caption brace outside the \label brace which can be seen in the snippet from the .tex file below:
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}
\color{fgcolor}
\begin{figure}[ht]
\includegraphics[width=\maxwidth]{figure/Figure1} \caption[Caption for fig]{Caption for fig. 1\label{fig:Figure1}}
\end{figure}
\end{knitrout}
latex can handle this if there are only a few figures like this but with larger numbers of plots, it starts to place them incorrectly.
I have also tried this with a
fig.cap=paste('testLoop',seq(1,20))
approach and get the same result.
Further clarification: I found this on wikipedia's Latex/Floats... page:
If you want to label a figure so that you can reference it later, you have to add the label after the caption (inside seems to work in LaTeX 2e) but inside the floating environment. If it is declared outside, it will give the section number.
The 'inside seems to work in LaTeX 2e' part caught my attention. It seems it works only because the error is ignored a number of times? I am using
LaTeX2e <2005/12/01>.
I think the bit of code is in hook_plot_tex function line 120 of hooks-latex.R:
fig2 = sprintf('\\caption%s{%s\\label{%s}}\n\\end{%s}\n', scap, cap,
paste(lab, if (mcap) fig.cur, sep = ''), options$fig.env)
This would fix it?
fig2 = sprintf('\\caption%s{%s}\\label{%s}\n\\end{%s}\n', scap, cap,
paste(lab, if (mcap) fig.cur, sep = ''), options$fig.env)
Suggestions? I am not familiar with the github process...
Thanks!
Short answer is it seems to be a LaTeX issue caused by too many \includegraphics commands and no pagebreaks. Function to accomplish multiple figures with captions and labels from within loop (with credit to Steve Powell and Yihui):
plot.knit<-function(chunkLabel,#text for chunk label which is also used for figure file name
capt,#text for caption
plt)#plot object to be placed
{
cat(knit(text=(paste("<<",chunkLabel,",fig.pos='h',fig.cap='",capt,"'>>=\nplt\n#",sep=''))))
}
cat('\\newpage')#some sort of page break must be inserted along the way to keep latex from breaking.
This can be modified to add any of chunk options you would like.
Long Answer:
Here is what I did to get it to work. I downloaded knitr from github, made the suggested alteration above, compiled, and ran example. The altered code did not change the outcome. Further investigation of latex error took me to the LaTeX FAQ where it states:
The error also occurs in a long sequence of float environments, with no intervening text. Unless the environments will fit “here” (and you’ve allowed them to go “here”), there will never be a page break, and so there will never be an opportunity for LaTeX to reconsider placement. (Of course, the floats can’t all fit “here” if the sequence is sufficiently prolonged: once the page fills, LaTeX won’t place any more floats, leading to the error.
Techniques for resolution may involve redefining the floats using the float package’s [H] float qualifier, but you are unlikely to get away without using \clearpage from time to time.
So, I added
cat('\\clearpage')
after the plots are generated in each step of the loop. This resulted in no errors being thrown and the figures in correct locations. Also,
cat('\\newpage')
works and seems to do a better job at placing the figures 2 on a page in my actual document.
The working code:
\documentclass{article}
\begin{document}
<<startup,echo=FALSE,results='hide',message=FALSE,tidy=FALSE,warning=FALSE,fig.keep='all',comment=NA>>=
require(knitr)
require(ggplot2)
opts_knit$set(progress = F, verbose = F)
opts_chunk$set(comment=NA,
tidy=FALSE,
warning=FALSE,
message=FALSE,
echo=FALSE,
dpi=600,
fig.width=6.75, fig.height=4, # Default figure widths
dev=c("pdf",'tiff'),
dev.args=list(pdf=list(NULL),tiff=list(compression='lzw')),
error=FALSE)
#
<<plotloop,results='asis'>>=
for(x in seq(1,20)){
x1<-data.frame(x=seq(1,10),y=seq(1,10))
plt<-ggplot(data=x1,aes(x,y))+geom_point()
figLabel=paste('Figure',x,sep='')
capt<-paste('Caption for fig.',x)
cat(knit(text=(paste("<<",figLabel,",fig.pos='h',fig.cap='",capt,"'>>=\nplt\n#",sep=''))))
cat('\\newpage')
}
#
\end{document}