Course Overview
Course Integrity
This course is compiled automatically on 2022-07-08
The course is tested and available on MacOS, Windows and
Ubuntu Linux for R version 4.2.0 (2022-04-22)
Overview
This course introduces plotting in R.
The course consists of 2 sections, 1 on base R plotting and a second on plotting using ggplot2. Each section is presented as HTML presentations or single page document. Exercises and answer sheets are included after all subsections to practice techniques and provide future reference examples.
Course material and exercises are available to view as rendered HTML at https://rockefelleruniversity.github.io/Plotting_In_R/. All material is available to download under GPL v2 license.
Setting up
System Requirements
Install R
R can be installed from the R-project website.
The R website can be found here http://www.r-project.org/.
The download links and associated installation instructions for multiple platforms can be found below provided by Revolution Analytics. https://cran.revolutionanalytics.com
We recommend installing R 4.2.0 as this is the version used to compile the course. Direct downloads for R 4.2.0 for the main platforms can be found below:
Install RStudio
RStudio can be installed from the RStudio website.
RStudio can be downloaded for all platforms at the link below
https://rstudio.com/products/rstudio/download/
Install required packages
From the course package
install.packages('BiocManager')
BiocManager::install('RockefellerUniversity/Plotting_In_R',subdir='PlottingInR')From CRAN and Bioconductor
install.packages('BiocManager')
BiocManager::install('ggplot2')
BiocManager::install('rmarkdown')
BiocManager::install('viridis')
BiocManager::install('scales')
BiocManager::install('tidyr')
BiocManager::install('lubridate')
BiocManager::install('knitr')
BiocManager::install('testthat')
BiocManager::install('yaml')The Presentations
Plotting in R base
This section focuses on plotting using R base graphics. Session sections:
- Introduction to R plotting
- Plot Types
- Saving plots
Links to presentations:
The html slide presentation can be found at this link Slide
The single page html presentation can be found at this link Single Page
The code use in the presentations can be found at R code
Plotting in with ggplot2
In this session we introduce plotting using ggplot2. Session sections:
- Introduction to Grammar of Graphics
- Plotting using ggplot2
- Custom themes and styles in ggplot2
Links to presentations:
The html slide presentation can be found at this link Slide
The single page html presentation can be found at this link Single Page
The code use in the presentations can be found at R code
Getting help
Course help
For advice, help and comments for the material covered in this course please contact us at the issues page associated to this course.
The link to the help pages can be found here
General Bioinformatics support
If you would like contact us about general bioinformatics advice, support or collaboration, please contact us the Bioinformatics Resource Center at brc@rockefeller.edu.