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README.md

Data Wrangling and Visualization with Tidyverse

Audience Computational skills required Duration
Biologists Beginner/Intermediate R 3-hour workshop (~3 hours of trainer-led time)

Description

This repository has teaching materials for a 3 hour, hands-on workshop led at a relaxed pace.

Learning Objectives

  • Understanding Tidyverse syntax: Tidyverse syntax is a bit different from base R with pipes, tibbles, and heavy opinions about row names
  • Wrangling data for use with analysis or plotting: Explore the functions available from the dplyr package to turn your data into the format you need it
  • Describe and utilize the ggplot2 grammar of graphics syntax: Create elaborate custom plots by learning the functions and structure for plotting with ggplot2

These materials are developed for a trainer-led workshop, but also amenable to self-guided learning.

Contents

Lessons Estimated Duration
Set up
Data wrangling with Tidyverse 75 min
Data visualization with ggplot2 90 min

Tidyverse practice exercises

Dataset

Download the R project and data for this workshop here. Decompress and move the folder to the location on your computer where you would like to perform the analysis.

Installation Requirements

Download the most recent versions of R and RStudio for your laptop:

Install the required R packages by running the following code in RStudio:

# Install CRAN packages
install.packages("tidyverse")
install.packages("RColorBrewer")

Load the libraries to make sure the packages installed properly:

library(tidyverse)
library(RColorBrewer)

NOTE: The library used for the annotations associated with genes (here we are using org.Hs.eg.db) will change based on organism (e.g. if studying mouse, would need to install and load org.Mm.eg.db). The list of different organism packages are given here.

These materials have been developed by members of the teaching team at the Harvard Chan Bioinformatics Core (HBC). These are open access materials distributed under the terms of the Creative Commons Attribution license (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.