I am knitting an .Rnw file and, unexpectedly, vertical space is lost from the bottom inner margin of my plots and added to the top outer margin.
Here is a minimal working example:
\documentclass{article}
\setlength{\parskip}{1em}
\begin{document}
<<mwe-plot, dev="tikz", dev.args=list(bg="grey95")>>=
par(mar=rep(2,4), oma=rep(0,4))
x <- seq(0, 2*pi, length.out=21)
plot(x, sin(x), type="l")
box("inner")
#
\end{document}
knit() generates mwe-plot-1.pdf, which looks like this:
, but what I expect is this:
.
The issue is apparently due to an interaction between \parskip and tikzDevice, since it is corrected by setting \parskip to zero in the preamble or switching from dev="tikz" to the default dev="pdf". While these are possible solutions, I am looking for a fix that doesn't require doing either.
Note that I tried adding \setlength{\parskip}{0em} immediately before the chunk (after \begin{document}) but this didn't affect the output.
Any hints are appreciated...
Your proximal problem is that the \setlength{\parskip}{1em} statement is being included in the tikz .tex file, which is throwing off the spacing. The solution is to move it from your preamble into the body of your document, i.e.
\documentclass{article}
\begin{document}
\setlength{\parskip}{1em}
...
I figured this out by descending through the layers - first looking at the .tex output created by knit (before the LaTeX -> PDF conversion), then looking at figure/mwe-plot-1.pdf (and realizing, as you suggested, that the problem isn't with stuff that knitr puts in the LaTeX file, but with stuff that tikzDevice puts in the tikz-.tex file), then looking at figure/mwe-plot-1.tex and realizing that it had the \parskip statement embedded. I looked around for a tikzDevice option that would override it, but then realized that it was probably only including stuff from the preamble ...
Related
I am trying to insert a pdf image into an r markdown file. I know it is possible to insert jpg or png images. I was just wondering if it is also possible to insert a pdf image. Thanks very much!
If you are just trying to insert an image that has been exported from, for example, some R analysis into a pdf image, you can also use the standard image options from the knitr engine.
With something like:
```{r, out.width="0.3\\linewidth", include=TRUE, fig.align="center", fig.cap=c("your caption"), echo=FALSE}
knitr::include_graphics("./images/imagename.pdf")
```
Unfortunately you can't specify the initial dimensions of your image output (fig.width and fig.height), which you would need to pre-define in your initial output, but you can specify the ultimate size of the image in your document (out.width). As noted below, however, this is limited to scaling down.
You could also of course leave out the initial directory specification if your files are in the same working directory. Just be aware of operating system differences in specifying the path to the image.
An alternative method is to use Markdown syntax noted by #hermestrismegistus on this post:
{width=65%}
This can also be collected for multiple images side-by side:
{width=33%}{width=33%}{width=33%}
Edit:
After working more extensively with in-text referencing, I have found that using r chunks and the include_graphics option to be most useful. Also because of the flexibility in terms of image alignment (justification).
As an example:
```{r image-ref-for-in-text, echo = FALSE, message=FALSE, fig.align='center', fig.cap='Some cool caption', out.width='0.75\\linewidth', fig.pos='H'}
knitr::include_graphics("./folder/folder/plot_file_name.pdf")
```
The reference can later be used in-text, for example, Figure \#ref(fig:image-ref-for-in-text) illustrates blah blah.
Some important things to note using this format:
You can only expand PDF images via a code chunk up to the out.width and out.height conditions set in the original .pdf file. So I would recommend setting them slightly on the larger side in your original image (just note that any chart text will scale accordingly).
The in-text reference code (in this case image-ref-for-in-text) CANNOT contain any underscores (_) but can contain dashes (-). You will know if you get this wrong by an error message stating ! Package caption Error: \caption outside float.
To stop your plots drifting to the wrong sections of your document, but in a way that unfortunately will generate some white space, the above example includes fig.pos='H'. Where H refers to "hold" position. The same can be achieved for the former Markdown option by placing a full-stop (period .) immediately after the last curly bracket.
Example:
{width=75%}.
Unfortunately, this latter option results in some unsightly full-stops. Another reason I prefer the include_graphics option.
Sorry, I found that there is a similar post before:
Add pdf file in Rmarkdown file
Basically, I can use something like below works well for the html output:
<img src="myFirstAlignment2.pdf" alt="some text" width="4200" height="4200">
And something like below works well for the pdf output:
(1)possible solution
\begin{center} <br>
\includegraphics[width=8in]{myFirstAlignment2.pdf} <br>
\end{center}
(2)possible solution
The myFirstAlignment2.pdf should be replaced with path\myFirstAlignment2.pdf if the pdf file is not in your working directory.
In relation to the comment of the best answer, there is a way to use the second option, and the output not come out tiny.
Use the following syntax below with the height being a large number. Having text in the brackets is necessary for it to work.
{width=100% height=400}
None of the answers outlined worked well for me in terms of sizing the pdf, so adding another answer using the code chunk options for out.height and out.width to control the size:
```{r out.height = "460px", out.width='800px', echo=F}
knitr::include_graphics("./images/imagename.pdf")
```
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}
Sounds like it should be a common problem, but I didn't find an obvious trick.
Consider the knitr Rnw file below,
\documentclass[twocolumn, 12pt]{article}
\usepackage{graphicx}
\begin{document}
%\SweaveOpts{dev=pdf, fig.align=center}
\begin{figure*}
<<aaa, fig.width=8, fig.height=5, fig.show=hold>>=
plot(1,1)
#
\end{figure*}
\end{document}
I would like this wide figure to span two columns, using a {figure*} LaTeX environment. Is there a hook for that?
EDIT: wrapping the chunk in figure* gives the following output.
Two facts:
knitr makes everything accessible for you, so LaTeX tricks are often unnecessary;
there is a chunk hook with which you can wrap your chunk results;
A simple-minded solutions is:
knit_hooks$set(chunk = function(x, options) {
sprintf('\\begin{figure*}\n%s\n\\end{figure*}', x)
})
I leave the rest of work to you to take care of more details in options (e.g. when options$fig.keep == 'none', you should not wrap the output in figure*). You may want to see how the default chunk hook for LaTeX is defined in knitr to know better how the chunk hook works.
However, in this case, I tend to write the LaTeX code by myself in the document instead of automatically creating it. After you have got figure*, you may start to think about \caption{} and \label{} (not hard, but I still want to see them in LaTeX).
Not sure about how knitr but for Sweave (and basic latex) there is in fact a trick: have the R code produce a pdf file, and then use standard \includegraphics to pull it in.
So with this:
\documentclass[twocolumn, 12pt]{article}
\usepackage{graphicx}
\begin{document}
%\SweaveOpts{dev=pdf}
<<aaa,fig=FALSE,print=FALSE,echo=FALSE>>=
pdf("mychart.pdf", width=6, height=3)
set.seed(42)
plot(cumsum(rnorm(100)), type='l', main="yet another random walk")
invisible(dev.off())
#
\begin{figure*}
\includegraphics{mychart.pdf}
\end{figure*}
\end{document}
I got the document below (which I then converted from pdf to png):
I also had a similar problem while preparing a figure that should span two columns in a IEEE two-column conference paper.
Setting the chunk hook caused some strange error in my setup.
Even this simple hook: knit_hooks$set(chunk = function(x, options) x)
But after looking into knitr::opts_chunk$get(), I realized that simply setting fig.env="figure*" solves the problem in an elegant way.
Here is how my chunk looks like in an Rnw file:
<<fig1, fig.width=18, fig.height=6, fig.env="figure*">>=
#
I would like to make an R code chunk (in Sweave) printed inside a framed box in the resulting pdf.
Is there an easy solution for doing that?
The short answer is that yes, there is an easy way. Just add the following lines, or something like them to the preamble of your Sweave document:
\DefineVerbatimEnvironment{Sinput}{Verbatim} {xleftmargin=2em,
frame=single}
\DefineVerbatimEnvironment{Soutput}{Verbatim}{xleftmargin=2em,
frame=single}
This works because the appearance of code (and output) chunks is controlled by the definition of the Sinput and Soutput environments. These are both Verbatim environments as provided by the LaTeX package fancyvrb. (Click here for a 73 page pdf describing the numerous options that fancyvrb provides).
A quick look in the file Sweave.sty reveals the default definition of those two environments:
\DefineVerbatimEnvironment{Sinput}{Verbatim}{fontshape=sl}
\DefineVerbatimEnvironment{Soutput}{Verbatim}{}
\DefineVerbatimEnvironment{Scode}{Verbatim}{fontshape=sl}
To change those definitions, just add \DefineVerbatimEnvironment statements of your own devising either: (a) at the end of the Sweave.sty file; or (b) at the start of your *.Snw document.
Finally, here's an example to show what this looks like in practice:
\documentclass[a4paper]{article}
\usepackage{Sweave}
\DefineVerbatimEnvironment{Sinput}{Verbatim} {xleftmargin=2em,
frame=single}
\DefineVerbatimEnvironment{Soutput}{Verbatim}{xleftmargin=2em,
frame=single}
\title{Sweave with boxes}
\begin{document}
\maketitle
<<echo=FALSE>>=
options(width=60)
#
Here is an example of a code chunk followed by an output chunk,
both enclosed in boxes.
<<>>=
print(rnorm(99))
#
\end{document}
knitr, a successor of Sweave, by default outputs all echoed R code in boxes, and also formats it to the margins. Other nice features include syntax coloring and PGF integration.
Sweave code of average complexity needs only minor if any adaptions to run with knitr.