This may be impossibly simple but not finding anything that lays out in direct enough fashion. So I have a lengthy string of code and upon using ggsave (look below) produces the desired chart in My Documents folder. What would I put after this in order to have the Figure 2.png to show up on the second slide? At the moment, when I knit it says, "## Saving 7.5 x 4.5 in image".
ggsave("Figure 2.png",Figure6UnEmploymentChart)
Related
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.)
When writing .rmd or .Rnw reports in RStudio, the outline view shows both code chunks and regular sections. While code chunks appear italic, regular sections do not. However, writing large reports with many similar named chunks will lead to a really bulky outline view with many similar labels.
Is there currently a way to turn one of them off? Either regular sections or the code chunks.
As per my comment: global options -> Rmarkdown -> show in document outline change to show sections only
I love knitr & rmarkdown, but I often find myself in situations where I have a lengthy report that takes some nontrivial amount of time to run. After it's generated, I notice my inevitable typos in text. However, re-knitting everything to just fix a couple typos (just in text, not code) takes a long time and seems avoidable. I was about to start taking a hack at developing my own solution to this, but I'm thinking it's the kind of thing that could already have a mature solution which would likely be more robust than the one I'd build.
I'm wondering if there is solution out there within knitr or third party that would allow me to edit just the text of my reports without rerunning code, generating plots and outputs etc. I know, I can simply edit the generated html text, but then those changes must be replicated in the R/Rmd code that generated it, or they get out of sync. I'm envisioning a function like this:
argument 1: the R/Rmd script with text edits (no code changes)... perhaps a warning is generated when code chunks change
argument 2: the html output file from the last time the R script in argument was knitted without the text edits.
return: the html report (argument 2) updated with the comments in the R/Rmd script (argument 1).
I use the cache option sometimes for large datasets. I toggle eval and echo on and off when developing if I'm just working on the text of my report. However, I'm looking for a function that would take care of all this for me, so one doesn't have to mess with the code and chunk options to make small edits to text.
Here's an interim solution that lets you retain the speed of making changes directly to the rendered text, but you have to do a little work after you're done making changes.
Assuming the following files:
input.knitr is the original Knitr file with text and code integrated.
output.html is the resulting HTML code that has been rendered by Knitr.
Consider making direct text edits to output.html and then running something like Meld visual merge tool:
meld output.html input.knitr
Then manually select the edits in output.html that are new and should be fixed in the original source input.knitr. Tools such as Meld do a pretty good job of aligning the texts so that the chunks and knitted output will appear as large "changes" that, in practice, you would ignore. You would focus on the small changes in the non-chunk sections.
I am doing a forest plot and want to save it to a PDF file.
My forest plot is oversize (8in*20in). It can fit in a one page PDF like this:
dev.print(pdf, file="C:\\Work\\plot.pdf", width=8, height=20);
But then it is too long: When I print this PDF on a A4 paper, it has to be shrinked to fit the paper.
So I want to save it to a two-page PDF file (from R). Ps: it is not a question about how to set the printer.
How to do this?
So, you are able to generate an 8in x 20in == 203.2mm x 508mm == 576pt x 1440pt sized PDF showing a plot.
It is not entirely clear to me from your question what exactly you want:
Generate the PDF plot so that it is divided into two different pages from the beginning?
Take the PDF as is and during the print job setup find these settings which would print it onto two different pages by posterizing the original page?
Post-process the PDF that you created to posterize it and create a 2-page output PDF (which you can then print)?
Assuming '1.': generate PDF plot distributed over 2 pages
Sorry, I cannot help here...
Assuming '2.': print setup to print 1 PDF page on 2 sheets of paper
If you print a PDF from Adobe Acrobat or from Adobe Reader, then you'll find a setting in the print dialog named "Poster". Here you can select to print one PDF page across multiple pieces of paper. (It also lets you select if you want some overlap from piece to piece, and if you want to add cut marks and the like to the printouts).
Assuming '3.': post-process 1 PDF page to stretch over 2 A4 pages
MuPDF is a lightweight PDF (and other document formats) viewer, made by the same company that also maintains Ghostscript. MuPDF ships with an additional command line utility, mutool.
Its subcommand poster can divide PDF pages into smaller tiles and 'posterize' them. So this command will achieve what you want:
mutool poster -x 1 -y 2 input.pdf output.pdf
The output.pdf will be divided into 1 part (i.e. not divided) in x-, and into 2 equal parts in y-direction. (You could divide it into any other number of segments if you wanted). So output.pdf will have two pages, each sized 8in x 10in. A4 paper is sized 8.26in x 11.69in when measured in Inches.
When printing these, you'll still need to enable the Print to fit Page Size checkbox in the print dialog if you want to make best use of the A4 page size.
Ghostscript is a command line tool that can (amongst many other functions) be used to process PDF files (PDF in, modified PDF out). It can be (ab)used to cut PDF pages into halfs.
Here are a few previous StackOverflow answers which describe how to do it. You'll need to adapt some parameters to your specific size(s), but the principles should be clear from those examples (even though some of these split pages into left and right halves, not top/bottom as you may require):
Linux-based tool to chop PDFs into multiple pages (SuperUser)
Freeware to split a pdf's pages down the middle? (SuperUser)
Convert PDF 2 sides per page to 1 side per page (SuperUser)
How can I split a PDF's pages down the middle? (SuperUser)
Cropping a PDF using Ghostscript 9.01 (StackOverflow)
PDF - Remove White Margins (StackOverflow)
Split one PDF page into two (StackOverflow)
The method described there is more tedious and not as straight-forward as with the mutool poster method.
Maybe not the answer you are looking for but you could print it in another vectorial format (e.g. svg) and then export it as pdf on two pages with a (vectorial) image editor.
Edit: If ploting in pdf works well despite the big size of the graph there are also tools to split pdf pages. You can find some directions here:
https://superuser.com/questions/437148/how-to-split-a-pdf-onto-multiple-pages-on-command-line
Windows equivalent of pdfposter could be Rasterbator or PosteRazor, for example.
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/