Lecture slides on iCloud

Overview

In order to document the code and results from a bioinformatics workflow you’ll be introduced to R Markdown and Knitr, and will use these tools to wrap up all your code and outputs (figures, tables, etc) together in a dyanmic document that can be placed in your lab notebook or published as a supplementary file in your manuscript.

Learning objectives

  • Discuss the basic building blocks for assembling a figure
  • Understand the basics of Rmarkdown and dynamic documents
  • Learn how to construct an Rmarkdown doc using ‘essential’ code chunks from the course.
  • make a flexdashboard the incorporates graphics and code

Code

Rmarkdown_template.Rmd - a skeletal template that you can fill out with the code ‘essentials’ that we covered in class.

Rmarkdown_essentials.Rmd - same template as above, but already filled in with essentials

flexdashboard_essentials.Rmd - a different style of Rmarkdown that puts the focus on creating a dashboard of graphics. Particularly powerful when combined with the interactive graphs we produced during the course.


Lecture video

Part 1 – Building blocks for making a good figure

Part 2 - Introduction to markdown

Part 3 - Constructing an Rmarkdown document that compiles to HTML or PDF


Reading

Blog post on Knitr by Karl Broman


Other examples of markdown in action

Supplementary code files from some of our recent papers:

Make your own CV in markdown - uses the Vitae and Scholar packages in R. Here’s mine on github

This course website! - Each page on the course website is just a simple markdown document.

My lab website is just a bunch of markdown files served from github (repo here)