Org R Sandbox

2020-05-25

This post presents the workflow of interacting with R in org mode. I am mainly seeking three functions in this workflow: automatic output; persistent R session across multiple source blocks; ability to present both codes and outputs.

Preparation #

• org-babel for executing and tangling source blocks
• ESS for interacting directly with R in emacs through the inferior R process

Instruction #

• set up proper sub-tree/buffer header arguments, for this blog post I used sub-tree header arguments: :header-args:R: :session *R* :exports both :eval no-export
• run org-bable-execute-src-block (or on sub-tree/buffer level) to produce outputs in the text area

Example #

Plot output #

• For the following code block, I used the source block header arguments #+begin_src R :results output graphics file :file test.svg :output-dir ~/itflows/static
• Note on the header arguments:
  • use :results graphics file when producing base R plot. use :results output graphics file for ggplot (see https://orgmode.org/worg/org-contrib/babel/languages/ob-doc-R.html).
  • remember to specify :output-dir as the static folder in your hugo directory, or else the org-link to the output plot after code evaluation will be directed to the same directory as the .org file by default

setwd('~/itflows/static') # output plot stored in the static directory of your hugo blog
library(dplyr)
library(ggplot2)
print(ggplot(iris, aes(x =  Sepal.Width, y = Sepal.Length)) +
      geom_point() +
      theme_bw()
      )
                                        # If the source code block uses grid-based R graphics, e.g., the lattice and ggplot2 packages, then care must be taken either to print() the graphics object, specify :results output, or run the code in a :session", use print() to produce proper .svg output

square <- function(x) # test session persistency
  {
    x * x
  }

plot(matrix(rnorm(100), ncol=2), type="h")

Plain text output #

• source block header arguments: #+begin_src R :results output

square(1:10)

 [1]   1   4   9  16  25  36  49  64  81 100