Course Description

This course provides an introduction to the R programming language through the tidyverse. A variety of plots will be taught using RNA-seq data from a published paper.

Course Objectives

After this course you should be able to:

• Import data and plot graphs with ggplot2
• Create a documented and reproducible piece of R code

Topics Covered

Week 1

• Creating bar plots, density plots, box pots, violin plots

Week 2

• Creating volcano plots

Week 3

• Creating stripcharts using faceting

Week 4

• Practice

Course Materials

Week 1

• Introduction
• First plots

Week 2

• Volcano plots

Week 3

• Stripcharts

Week 4

• TCGA challenge
• Interactive volcano plot challenge
• FACS challenge
• REDCap challenge

Course Cheatsheet

• Cheatsheet

Course Presenter

Maria Doyle, Research Computing Facility

Course Helpers

Liz Christie, Bowtell Lab
Miriam Yeung, Dawson Labs
Roxane Legaie, Pathology Department
David Ma, Pathology Department
Anna Trigos, Goode Lab

Acknowledgements

This course has been created and run by the Peter Mac Data Science Training team. Some of the material is based on the resources below and others as attributed.

Useful Resources

The ggplot2 cheatsheet
base R cheatsheet
Data Manipulation and Visualisation by University of Cambridge
An Introduction to ggplot by Babraham Bioinformatics
An intro to R and tidyverse by Monash Bioinformatics Platform