Hello stackoverflow community,
I have trouble with the interaction between text in R plots and the Latex Environment. In R, I programmed a simple distributional plot and added the percentage below a given threshold via the command mtext(expression(paste("x% < 0 < 1-x%")), ...) . Then the graph has been saved as eps.-figure in order to Transfer it to Latex. The latter, however, displays the < and > symbols as inverted exclamation marks (usually, the < are obtained by the command \textless outside the mathmode in Latex).
I further added some font packages in Latex and it becomes possible to type the < signs into the text without drawing on the math mode. In the Graphs from R, however, the inverted exclamation marks remain.
Does anybody knows how to solve this issue? Although I think that it is a general problem between the R text and Latex, please let me know if some code helps to understand the Problem.
Thank you very much for your help and suggestions.
I don't think it is a general issue in the communication between R and LaTeX, although I agree it can be tricky. I wasn't able to reproduce the behavior you described using what I normally do to create graphics for TeX-documents.
Maybe this setup can also solve the problem you describe. Below is an example to print the said expression using Cairo and PDF graphics.
R-script:
library(Cairo)
Cairo(file="pic", type="pdf", dpi=100)
x <- y <- 1:5
plot(x,y)
mtext(expression(paste("x% < 0 < 1-x%")))
dev.off()
TeX-file:
\documentclass[12pt,paper=a4]{article}
\usepackage{graphicx}
\begin{document}
\begin{figure}[tbp]
\includegraphics{pic.pdf}
\end{figure}
\end{document}
The resulting PDF that is compiled using pdflatex appears to show the expression correctly. A quick screenshot:
I just run into the (curious) problem that when submitting a (pdf)LaTeX manuscript to some Elsevier journal the filenames of figures needed to be complete in order to found by their pdf building and checking syste, i.e.:
\includegraphics{picture.pdf}
Is there any easy and convenient way to tell Sweave or knitr to do that?
Edit:
I'm familiar with sweave's include=FALSE option
I also feel quite capable to patch utils:::RweaveLatexRuncode
However, for the moment I'm hoping that there's something more convenient and elegant.
It's also about handing out the .Rnw files as supplementary material or vignettes. From a didactic point of view I don't like these tweaks that make the source code much more complicated for the new users of whom I hope they read it.
(Which is also why I really appreciate the recently introduced print=TRUE in Sweave)
You can modify the plot hook a little bit in knitr to add the file extension:
<<>>=
knit_hooks$set(plot = function(x, options) {
x = paste(x, collapse = '.') # x is file.ext now instead of c(file, ext)
paste0('\\end{kframe}', hook_plot_tex(x, options), '\\begin{kframe}')
})
#
See 033-file-extension.Rnw for a complete example. To understand what is going on behind the scene, see the source code of the default LaTeX hooks in knitr.
A brute force solution is to explicitly create the files yourself in the R snippet. Set the option for graphics etc to false but have the code evaluated so that the file is created, and then have latex call them with the very \includegraphics{} call you show.
I used similar schemes for simple caching: if the target file exists, skip the code creating.
I want to make a report with the graphics I obtain with R. Here I show you both images produced with site_rose(site_ref) and site_time_series(site_ref) I designed.
But after running sweave('Profile.Rnw') and getting Profile.tex I obtain Profile-002.pdf and Profile-003.pdf that these last two documents have 0KB. And so I get a .pdf report without any figure at all. Here I show you the code:
\documentclass[10pt,a4paper]{article}
\usepackage[utf8]{inputenc}
\usepackage[spanish]{babel}
\usepackage{amsmath}
\usepackage{amsfonts}
\usepackage{amssymb}
\title{Anàlisi in situ emplaçament}
\author{Jonel Palou Visa}
\begin{document}
\maketitle
\begin{center}
<<fig=TRUE,echo=TRUE>>=
site_ref <- site_time_series(site_ref,peaks=T,stationary=T)
#
\end{center}
\begin{center}
<<fig=TRUE,echo=TRUE>>=
site_rose(site_ref)
#
\end{center}
\end{document}
I would like to know if there is a problem with the new device I call in order to plot the figures or what is my real problem.
The code for both functions is too large to show here, there isn't any extrange in these functions because to get the figure I only call plot(...)
Without the code of the two functions you created it remains unclear what is going wrong. However, if you use either lattice or ggplot2 not calling print on the object that that came out of ggplot2 or lattice. On the command line these kinds of plots work because print is then called implicitely. So:
print(site_rose(site_ref))
Should produce the correct result. Alternatively, you could start using knitr instead of Sweave. knitr does not have this problem. In general I would recommend using knitr instead of Sweave.
Is that the whole Sweave file? You won't be able to re-use variables that are defined in your current environment variable when creating a Sweave document. The whole point of Sweave is to reproduce some analysis from end-to-end, so that wouldn't be a good approach to take anyways.
I'd recommend including whatever analysis is necessary to generate the site_ref variable, among others in this Sweave document.
If you insist on taking a shortcut, you could save your current R environment and load it in as the first command in the Sweave document to provide access to those variables.
Use Stangle to extract the R code from your Sweave document, then create a new R session and try running that code. You'll probably get errors about undefined variables, or messages about functions not being defined. You should be able to run the R code contained in your Sweave document in an empty environment and have it work successfully. Then you're ready to render it as a PDF.
I generate a dendrogam using a collection of r commands. It worked just fine and saved the generated dendromgram into a PDF file. To improve efficiency, I wrapped these commands as a function, which does not change anything. However, the pdf is just a blank file without any graphical content. Please let me know what’s wrong with my function defintion. Thanks.
myplot<-function(inputcsv, outputfile){
library(ggdendro)
library(ggplot2)
x<-read.csv(inputcsv,header=TRUE)
d<-as.dist(x,diag=FALSE,upper=FALSE)
hc<-hclust(d,"ave")
dhc<-as.dendrogram(hc)
ddata<-dendro_data(dhc,type="rectangle")
ddata$labels$text <- gsub("\\."," ",ddata$labels$text)
ggplot(segment(ddata))+geom_segment(aes(x=x0,y=y0,xend=x1,yend=y1))
pdf(outputfile, width=30,height=35)
last_plot()
dev.off()
}
R FAQ
Wrap your ggplot call in a print() function.
ggplot and friends return an object, and the plotting only happens when the object is printed. When you do this on the command line the printing happens automatically. When you stick it in a script or function you have to do it yourself.
The debate on whether this is a good idea or a dumb thing that just generates questions like this continues...
The task is to create a file (word, rtf, pdf, html, or whatever) that will capture the output of R (e.g: not the code that created the output), into that format (including text and images).
The way of doing this should involve as little change to the original R script as possible.
If I had cared only for the text or images, then I would use ?sink, or ?pdf. But I don't know how to combine the two into one output in an easy way.
I know there is a way to export R output using r2wd, but it involves too much medaling in the original code for my taste (I imagine the same is true for the sweave solution, although I don't have experience with it to tell)
Here is a sample code for future examples:
START.text.and.image.recording("output.file") # this is the function I am looking for
x <- rnorm(100)
y <- jitter(x)
print(summary(x))
print(head(data.frame(x,y)))
cor(x,y)
plot(x,y)
print(summary(lm(y~x)))
STOP.text.and.image.recording("output.file") # this is the function I am looking for
Update: I was asked way not Sweave, or other options from ReproducibleResearch task view.
The reasons are:
I don't (yet) know LaTeX
Even knowing LaTeX, I want something with simple defaults to simply dump all the outputs together, and in order. "simply" means - as little extra code/file management overhead as possible.
I understand that something like sweave or brew are more scalable, but I am looking to see if there is a more "simple" solution for smaller projects/scripts.
As of 2012 knitr provides a perfect solution to this problem.
For example, create a file with an rmd extension. Wrap your code in a couple of commands as follows:
```{r}
x <- rnorm(100)
y <- jitter(x)
print(summary(x))
print(head(data.frame(x,y)))
cor(x,y)
plot(x,y)
print(summary(lm(y~x)))
```
You can convert it into a self-contained HTML file in several ways. In RStudio you just press a single button Knit HTML.
This is the HTML file produced; to actually view how the HTML displays in a browser, save the file and open it.
Images code, and output are interweaved as you might expect.
Of course, you can and typically would divide up your file into multiple R code chunks. But the point is, you don't have to.
Here are another couple of examples I've created:
Getting started with R Markdown
Case study in using R Markdown
If you know LaTeX, sweave will likely be your best bet. odfWeave is a similar mechanism but for embedding the code in an OpenOffice.org file. For HTML there is the R2html package. But all will likely require you to break the code up a little bit to get the best out of the systems. Alternatively, your sweave/odfweave/html template could source the data generation aspects of the script in a single code chunk, with the output display (print() statements) placed where required. Your graphics could also be called within the script to produce the figures to embed in the document as separate files, which you then include by hand in the template.
For example (and this isn't a full .Rnw file for running through sweave) in a sweave file you'd put something like this high up in the template which sources the main part of the R script that will do the analysis and generate the R objects:
<<run_script, eval=TRUE, echo=FALSE, results=hide>>=
source("my_script.R")
#
Then you will need to insert code chunks where you want printed output:
<<disp_output, eval=TRUE, echo=FALSE, results=verbatim>>=
## The results=verbatim is redundant as it is the default, as is eval=TRUE
print(summary(x)) ## etc
#
Then you will need chunks to insert the figures.
Separating your analysis code from the output (printed and/or figures) is probably good practice as well, especially if the analysis code is expensive in compute terms. You can run it once - or even cache it - whilst updating the output/display code as you need to.
Example Sweave File
Using csgillespie's example sweave file I would set things up like this. First the my_script.R file containing the core analysis code:
x <- rnorm(100)
y <- jitter(x)
corXY <- cor(x,y)
mod.lm <- lm(y~x)
Then the Sweave file
\documentclass[12pt]{article}
\usepackage{Sweave}
\begin{document}
An introduction
<<run_analysis, eval=TRUE,echo=FALSE, results=hide>>=
source("my_script.R")
#
% Later
Here are the results of the analysis
<<show_printed_output, echo=FALSE>>=
summary(x))
head(data.frame(x,y))
#
The correlation between \texttt{x} and \texttt{y} is:
<<print_cor, echo=FALSE>>=
corXY
#
Now a plot
\begin{figure}[h]
\centering
<<echo=FALSE, eval=TRUE, fig=TRUE, width=6, height=4>>=
plot(x,y)
#
\caption{\textit{A nice plot.}}
\end{figure}
\end{document}
What you seem to be wanting doesn't exist; a simple way of combining R code and output into a document file. That is if you don't consider sweave and its ilk simple. You might need to rethink what you want to do or how you arrange your analysis and graphics and output code, but you are likely best served looking at one of the suggested options (sweave, odfweave, brew, R2html).
HTH
I would encourage you to use Sweave, but a rudimentary functionality that is not pretty can be achieved with sink().
A regular txt file:
sink(file = "test.txt", type = "output")
summary(cars)
sink()
or add some HTML tags:
sink(file = "tal_test.html", type = "output")
cat("<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.01//EN\"", "\n")
cat("\"http://www.w3.org/TR/html4/strict.dtd\">", "\n")
cat("<HTML>", "\n")
cat("<HEAD>", "\n")
cat("<TITLE>My first HTML document</TITLE>", "\n")
cat("</HEAD>", "\n")
cat("<BODY>", "\n")
summary(cars)
cat("</BODY>", "\n")
cat("</HTML>", "\n")
sink()
I wrote a script called Roux about a year ago which does this. I wanted to be able to create HTML transcripts from running an R script, including any images, without having to change the script.
You call Roux from the command line, like this:
roux example.R
and roux will:
run the script in R (requiring the Roux package first automatically)
syntax highlight the .Rout output using Pygments
insert images in the correct location
the Roux R package is a very small R package which modifies plot() and some other functions to automatically write to a random filename rather than the default interactive graphics device.
I have used this a lot, and it works really well for me, although I'm sure if more people use it with new packages then minor issues will arise, most likely that you'll have a different function which generates a graph and Roux won't know that it should open a PNG device for you.
Since speaking with Tal about this I have updated and improved the code, and it's now up here:
http://bitbucket.org/ananelson/roux/src
so if you run into any issues, please report them to the issue tracker there on Bitbucket.
I have added support for LaTeX transcripts so you can easily create PDFs which have the transcript of your R script including images. (You can see an example if you look in the example-output directory, find the "raw" link to download it.)
You do need to have Python and the Pygments python library intalled. If you have an older version of Python and run into any issues, please let me know.
I wrote about Roux on my blog but didn't publicize it that much because my efforts have been focused on a new project called Dexy which is intended as a replacement for Sweave. If you want more flexibility and control or are interested in literate documentation then you might want to check out Dexy too.
You mentioned sweave in your question but not really why it isn't suitable. Your question seems perfect for Sweave. In fact, your example code could have came from the second Sweave example.
Example Sweave file
If you know Latex then Sweave isn't that difficult. Here's your example file as a Sweave file:
\documentclass[12pt,BCOR3mm,DIV16]{scrreprt}
\usepackage{Sweave}
\begin{document}
An introduction
<<eval=TRUE,echo=TRUE>>=
x <- rnorm(100)
y <- jitter(x)
print(summary(x))
print(head(data.frame(x,y)))
cor(x,y)
#
Now a plot
\setkeys{Gin}{width=0.5\textwidth}
\begin{figure}[h]
\centering
<<echo=FALSE, eval=TRUE, fig=TRUE, width=6, height=4>>=
plot(x,y)
#
\caption{\textit{A nice plot.}}
\end{figure}
\end{document}
Under linux, just save the file as tmp.Rnw. Then
R CMD Sweave tmp.Rnw
pdflatex tmp.tex
There is also LyX, which has an Sweave interface. The R / LyX / Sweave interface code is on CRAN at http://cran.fhcrc.org/contrib/extra/lyx/. LyX itself is in most of the Linux distros. All of this magic can be made to work on Windows, but it's definitely non-trivial. On Windows, I'd recommend Inference for R from Blue Reference for literate R progamming.
Well, I just remind that I was using Asciidoc for short reporting or editing webpage. Now there's an R plugin (ascii on CRAN), which allows to embed R code into an asciidoc document. The syntax is quite similar to Markdown or Textile, so you'll learn it very fast.
Output are (X)HTML, Docbook, LaTeX, and of course PDF through one of the last two backends.
Unfortunately, I don't think you can wrap all your code into a single statement. However, it supports a large number of R objects, see below.
> methods(ascii)
[1] ascii.anova* ascii.aov* ascii.aovlist* ascii.cast_df*
[5] ascii.character* ascii.coxph* ascii.CrossTable* ascii.data.frame*
[9] ascii.default* ascii.density* ascii.describe* ascii.describe.single*
[13] ascii.factor* ascii.freqtable* ascii.ftable* ascii.glm*
[17] ascii.htest* ascii.integer* ascii.list* ascii.lm*
[21] ascii.matrix* ascii.meanscomp* ascii.numeric* ascii.packageDescription*
[25] ascii.prcomp* ascii.sessionInfo* ascii.simple.list* ascii.smooth.spline*
[29] ascii.summary.aov* ascii.summary.aovlist* ascii.summary.glm* ascii.summary.lm*
[33] ascii.summary.prcomp* ascii.summary.survfit* ascii.summary.table* ascii.survdiff*
[37] ascii.survfit* ascii.table* ascii.ts* ascii.zoo*
Non-visible functions are asterisked
This is in light of romunov's answer, but still. You can just write your own print that wraps the output in some HTML formatting and embeds the output to a HTML file. The same can be done with pictures with Data URI scheme, for instance by using img function from base64 R package.
You can use the R2HTML package to output a session to html and there are some similar functions in the TeachingDemos package (see txtStart) for output to enhanced text and word (via R2wd). Non-graphics commands will be included in the file automatically and the current plot can be inserted by a single command.
Through the wonders of twitter, someone reached out and sent me a link to this page, regarding a package called "roux". It was created a year ago, and I have never heard about it (apparently neither have most of you).
This package seems to do exactly what I was looking for in my question, although the installation seems non trivial.
I hope to play with this solution and also to see if other R members might go into this project to better enhance R.
good suggestion by #znmeb to try Lyx - a more word-like front end for LaTeX, and as the documentation points out, there is a good article of its use with Sweave on page 2 of this edition of R news
This is how I did it in Ubuntu 10.04 follwoing the guidelines in the lyx sweave repository:
sudo apt-get install lyx
cd ~./lyx
wget http://cran.fhcrc.org/contrib/extra/lyx/preferences
cd layouts
wget http://cran.fhcrc.org/contrib/extra/lyx/literate*
wget http://cran.fhcrc.org/contrib/extra/lyx/literate-article.layout
wget http://cran.fhcrc.org/contrib/extra/lyx/literate-book.layout
wget http://cran.fhcrc.org/contrib/extra/lyx/literate-report.layout
wget http://cran.fhcrc.org/contrib/extra/lyx/literate-scrap.inc
cd ~/texmf/tex
wget http://www.biostat.jhsph.edu/~rpeng/ENAR2009/Sweave.sty
start Lyx
Preferences -> Reconfigure
restart Lyx
File -> new
Document -> Settings -> Document Class -> article (Sweave noweb)
useful links:
lyx sweave repository
R news article about Lyx and Sweave