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.
- 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
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.
“Warning - videos below are from 2020 lectures and will soon be updated for 2021.”
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
Other examples of markdown in action
Supplementary code files from some of our recent papers:
This course website! - Each page on the course website is just a simple markdown document.