I am new to R and Rmd and trying to generate a report using Rmd. This report has several images inserted along with the text. I am able to insert an image by hardcoding the path of the image. I have no problems with that but I need the path as a variable because it varies with the project. Can anyone help me with the syntax for calling a variable within a path to the image?
"Project123" changes based on the project. Is there a way I can declare this variable and call it to define the path?
Help please.
Images can use online R code for dynamic paths and/or alt text. (Early adopters of rmarkdown often tried this method as the default method of including R plots in the reports, using png(filepath...); plot(...); dev.off() followed by what I recommend you use.)
This will allow you to do what you need:
as raw markdown (and not inside a traditional code chunk).
If you aren't familiar with inline code blocks, then know that you can put just about anything in an inline code block. This is handy for including dynamic content in a paragraph of text, for example "the variance of the sample is \r var(sample(99))``". (Often it is just a pre-created variable, if numeric it is often rounded or formated to control the display of significant figures.)
Related
I have been writing a document in bookdown where within the *.Rmd file I call a figure by using the following syntax
\#ref(fig:MyFigureName)
This differs slightly from the notation that you would use in a normal RMarkdown file exporting to latex which would be
\ref{fig:MyFigureName}
The issue I am running into is that when I write something in bookdown the function calling the Figure is not being highlighted properly (see image below).
I have imported my own rsTheme (which is from my understanding, basically a .css file) but I don't see an option to add keywords to highlight.
But I would like for the entire function to be colored differently from the inline text (Photoshop version of desired output shown below)
Does anyone know how I would edit my *rsTheme file in order to accomplish this?
Thanks!
I have a spreadsheet of exam questions that I want to use to generate quizzes and exams using R exams, and I'd like to include graphics in some of the questions.
The template here (http://www.r-exams.org/templates/fruit/) begins by defining the images as long base 64 encoded strings as generated by
base64enc::base64encode("file.png")
This seems fine, but if I have a dozen or so images of which I might only want a question to use one, two, or three images selected at random for programmatically generated exercises, how can I avoid including the encoding for all dozen images with every single exercise?
The best I can think of at the moment is to include LaTeX syntax for graphics inclusion in a spreadsheet of possible question options, and as exercises are generated, use regular expressions to find the file names inside the \includegraphics{} commands that will be included, encode those as base 64 strings, and include them in the exercise file, but I'm wondering if there's a way I can do this without writing my own code to parse LaTeX.
First a few clarifications:
The fruit exercises include the images as Base64 strings because the three icons are quite small (12K per icon) and it is convenient to have all information within the Rnw/Rmd exercise without the need to store graphics files separately. It is just one trick that can be nifty and that we wanted to demonstrate.
For more and larger images one could do the same trick but it is probably less convenient. To illustrate how static images can be included in an exercise, the following template is available: http://www.R-exams.org/templates/Rlogo/ It uses the include_supplement() function to declare a certain file as a supplement for the exercises. If this is a graphic it can then be integrated into the exercises via \includegraphics{...} in Rnw exercises and via  in Rmd exercises.
Each exercise just has to include the supplements it actually uses (and not all files from which these were sampled). And there is no need to do the Base64 encoding manually. This is done by the exams2xyz(...) functions automatically if needed.
Now for the scenario you describe. Say you have an exercise foo.Rmd in which you want to show one of three static images foo-1.png, foo-2.png, foo-3.png and ask questions about it. Then your R code might do something like:
i <- sample(1:3, 1)
img <- paste0("foo-", i, ".png")
include_supplement(img)
which randomly selects one of the three files and declares it to be an attachment. Then within the question text you would include the image via something like:
Caveats:
The code above assumes that the PNG images are located in the same directory as the Rmd exercise itself. If it is in a sub-directory bar/ say, you would need include_supplement(img, dir = "bar") etc.
If this exercise is rendered into HTML then the original file name (foo-1.png or foo-2.png or foo-3.png) would be visible in the HTML source code. This may (or may not) provide a hint for students what the correct answer is. If so, it would be better to include the file with a neutral name, e.g., include_supplement(img, target = "foo.png").
In Rnw exercises the code for including the graphic would be something like: \includegraphics{\Sexpr{img}}.
I want to pass data from Spotfire to R and then display the plot constructed by R.
What is the best way to do this?
I’ve figured out the trick of putting images into Spotfire. It’s not hard if you follow these directions, but it’s done in a way very different from how you guess you would do it in Spotfire, and that’s why it took me awhile to figure out.
Here’s an overview of how to do it. You create a DocumentProperty which is a binary object, you write some Spotfire code that gives a value to that Document Property, and you display that binary object using a Spotfire Property Control of the “Label” type.
The confusing parts are that you DON’T use the Spotfire “Insert Image” tool at all, and that you DON’T use the filename generated inside the R code in Spotfire at all. Once you get used to the idea that the two most obvious ways you think you would approach the problem in Spotfire are entirely useless and wrong, you can make some progress.
I’ll leave out the spiderplot specifics because the code’s pretty long.
Here’s what you do.
1) Create a document Property in Spotfire of type “Binary”, e.g., “imageThatGoesBackToSpotfire”
2) You write some R code that generates an image and writes it to a file:
# get a temporary directory name on the local machine. You wouldn’t need to do this is you were just
# going to run it on your own, but you need to do it if you intend to let anybody else run it on their own machine.
tempfilebase = tempfile()
# take the tempfilebase and prepend it to a filename.
myFilename<-“someFileName.jpg”
myFullFilename <- paste(tempfilebase,myFilename,sep="")
#open a jpeg
jpeg(filename=myFullFileName)
# generate the image, however you normally would in R
plot(input)
# close the file
dev.off
# open a connection to that file.
myConnection<-file(myFullFileName,open=”rb”)
imageThatGoesBackToSpotfire<- data.frame(r=readBin(myConnection, what="raw", n=(file.info(myFullFileName)$size)))
close(myConnection)
3) Run your R script, above. Select some columns that are the “input” to the plot, and make the R script return outputs to the “imageThatGoesBackToSpotfire” DocumentProperties.
4) Create a text area in Spotfire.
5) Insert a Property Control into the text area of type “label”. (Click on the icon that’s circled in the picture below). This opens a dialog,
You need to register a data function with inputs and outputs, and the specific PNG data needs to be returned as a binary label.
Some details: http://spotfire.tibco.com/tips/2014/02/25/dynamically-displaying-images-in-a-text-area/
I have an idea where I need to be able to dynamically create a PDF-file thats supposed to contain a number of vector-graphical images.. I also need to be able to "absolute" position the vector images within the PDF.. I then later on need to be able to download the generated PDF-file.. is this possible?..has anyone done something like this before?.. as far as I can remember there is a pretty good support for doing this using none vectorized-images (jpg,png etc).. but is it possible to use eps-files and other vector images?
You can use pdflatex to generate the pdf.
(pdf)Latex has really good support for importing svg and eps.
When you use Inkscape you can chose to export to tex/latex and it generates code for you.
Is it possible to include an image in documentation generated by roxygen? I have a number of functions that are essentially wrappers for ggplot() that I'd like to document by showing an example of the output.
As per the change list from the announcement of R 2.14:
Rd markup has a new \figure tag so that figures can be included in
help pages when converted to HTML or LaTeX. There are examples on
the help pages for par() and points().
From: http://cran.r-project.org/doc/manuals/R-exts.html#Figures
To include figures in help pages, use the \figure markup. There are three forms.
The two commonly used simple forms are \figure{filename} and \figure{filename}{alternate text}. This will include a copy of the figure in either HTML or LaTeX output. In text output, the alternate text will be displayed instead. (When the second argument is omitted, the filename will be used.) Both the filename and the alternate text will be parsed verbatim, and should not include special characters that are significant in HTML or LaTeX.
The expert form is \figure{filename}{options: string}. (The word ‘options:’ must be typed exactly as shown and followed by at least one space.) In this form, the string is copied into the HTML img tag as attributes following the src attribute, or into the second argument of the \Figure macro in LaTeX, which by default is used as options to an \includegraphics call. As it is unlikely that any single string would suffice for both display modes, the expert form would normally be wrapped in conditionals. It is up to the author to make sure that legal HTML/LaTeX is used. For example, to include a logo in both HTML (using the simple form) and LaTeX (using the expert form), the following could be used:
\if{html}{\figure{logo.jpg}{Our logo}}
\if{latex}{\figure{logo.jpg}{options: width=0.5in}}
The files containing the figures should be stored in the directory man/figures. Files with extensions .jpg, .pdf, .png and .svg from that directory will be copied to the help/figures directory at install time. (Figures in PDF format will not display in most HTML browsers, but might be the best choice in reference manuals.) Specify the filename relative to man/figures in the \figure directive.