This article by Julian Hillebrand and Maximilian H. Nierhoff authors of the book Mastering RStudio for R Development covers the following topics:

• The two main ways to create interactive R Markdown documents
• Creating R Markdown and Shiny documents and presentations
• Using the ggvis package with R Markdown
• Embedding different types of interactive charts in documents
• Deploying interactive R Markdown documents

(For more resources related to this topic, see here.)

Creating interactive documents with R Markdown

In this article, we want to focus on the opportunities to create interactive documents with R Markdown and RStudio. This is, of course, particularly interesting for the readers of a document, since it enables them to interact with the document by changing chart types, parameters, values, or other similar things. In principle, there are two ways to make an R Markdown document interactive. Firstly, you can use the Shiny web application framework of RStudio, or secondly, there is the possibility of incorporating various interactive chart types by using corresponding packages.

Using R Markdown and Shiny

Besides building complete web applications, there is also the possibility of integrating entire Shiny applications into R Markdown documents and presentations. Since we have already learned all the basic functions of R Markdown, and the use and logic of Shiny, we will focus on the following lines of integrating a simple Shiny app into an R Markdown file.

In order for Shiny and R Markdown to work together, the argument, runtime: shiny must be added to the YAML header of the file. Of course, the RStudio IDE offers a quick way to create a new Shiny document presentation. Click on the new file, choose R Markdown, and in the popup window, select Shiny from the left-hand side menu. In the Shiny menu, you can decide whether you want to start with a Shiny Document option or a Shiny Presentation option:

Shiny Document

After choosing the Shiny Document option, a prefilled .Rmd file opens. It is different from the known R Markdown interface in that there is the Run Document button instead of the knit button and icon.

The prefilled .Rmd file produces an R Markdown document with a working and interactive Shiny application. You can change the number of bins in the plot and also adjust the bandwidth. All these changes get rendered in real time, directly in your document.

Shiny Presentation

Also, when you click on Shiny Presentation in the selection menu, a prefilled .Rmd file opens. Because it is a presentation, the output format is changed to ioslides_presentation in the YAML header. The button in the code pane is now called Run Presentation:

Otherwise, Shiny Presentation looks just like the normal R Markdown presentations. The Shiny app gets embedded in a slide and you can again interact with the underlying data of the application:

Dissembling a Shiny R Markdown document

Of course, the questions arises that how is it possible to embed a whole Shiny application onto an R Markdown document without the two usual basic files, ui.R and server.R? In fact, the rmarkdown package creates an invisible server.R file by extracting the R code from the code chunks. Reactive elements get placed into the index.html file of the HTML output, while the whole R Markdown document acts as the ui.R file.

Embedding interactive charts into R Markdown

The next way is to embed interactive chart types into R Markdown documents by using various R packages that enable us to create interactive charts. Some packages are as follows:

• ggvis
• rCharts
• googleVis
• dygraphs

Therefore, we will not introduce them again, but will introduce some more packages that enable us to build interactive charts. They are:

• threejs
• networkD3
• metricsgraphics
• plotly

Please keep in mind that the interactivity logically only works with the HTML output of R Markdown.

Using ggvis for interactive R Markdown documents

Broadly speaking, ggvis is the successor of the well-known graphic package, ggplot2. The interactivity options of ggvis, which are based on the reactive programming model of the Shiny framework, are also useful for creating interactive R Markdown documents.

To create an interactive R markdown document with ggvis, you need to click on the new file, then on R Markdown..., choose Shiny in the left menu of the new window, and finally, click on OK to create the document. As told before, since ggvis uses the reactive model of Shiny, we need to create an R Markdown document with ggvis this way. If you want to include an interactive ggvis plot within a normal R Markdown file, make sure to include the runtime: shiny argument in the YAML header.

As shown, readers of this R Markdown document can easily adjust the bandwidth, and also, the kernel model. The interactive controls are created with input_. In our example, we used the controls, input_slider() and input_select(). For example, some of the other controls are input_checkbox(), input_numeric(), and so on. These controls have different arguments depending on the type of input. For both controls in our example, we used the label argument, which is just a text label shown next to the controls. Other arguments are ID (a unique identifier for the assigned control) and map (a function that remaps the output).

Summary

In this article, we have learned the two main ways to create interactive R Markdown documents. On the one hand, there is the versatile, usable Shiny framework. This includes the inbuilt Shiny documents and presentations options in RStudio, and also the ggvis package, which takes the advantages of the Shiny framework to build its interactivity. On the other hand, we introduced several already known, and also some new, R packages that make it possible to create several different types of interactive charts. Most of them achieve this by binding R to Existing JavaScript libraries.

Resources for Article:

Further resources on this subject:

• Jenkins Continuous Integration [article]
• Aspects of Data Manipulation in R [article]
• Find Friends on Facebook [article]