BioTrain - Bioinformatics and Statistical Training

Quarto is an environment which allows you to create documents containing R code, R output and formatted text. It allows you to write professional looking reports of your R analysis and compile these into HTML or PDF documents. These are the ideal way to share your analysis with others.

Here we go through how to create, edit and publish Quarto documents from within R studio to make your life easier when writing and communicating your R work.

Pre-Course Requirements & Suggestions

This course assumes that you have knowledge or skills equivalent to those taught in the following courses.

Introduction to R

Please ask us if you're unsure if you have the necessary knowledge or skills for this course.

Whilst not required, it may be useful to attend the following courses to supplement the knowledge you'll get from this one.

Creating Complex Figures with GGPlot

Creating a Quarto Document

We create our first quarto document in R. We look at the basic structure of the document in both the code and visual editor and explain the workflow for writing and compiling the document.

Using Markdown

The formatted text sections of a quarto document use the markdown formatting language. We give an introduction to the basic syntax of markdown and use this to create some text sections in our document.

R Code Blocks

In contrast to conventional R scripts, in a quarto document you break up your R code into small sections called code blocks. We cover the best practices for dividing your code into blocks, and the very small number of changes you'd make in the code itself to make it work correctly in a quarto document.

Document themes and appearance

The default appearance of a quarto document is very good and many people won't change this. We will look at the options you have to change the structure of the document, adding a table of contents for easier naviation for example. We will also look at how you can customise the appearance of your document to make something more personalised.

Notebook Automation

Although most quarto documents are created and compiled manually it is possible to automate this so you can generate automated documents from new datasets for example. We show some options for automation within quarto.

Documenting R Analyses with Quarto