Course Overview
Course Integrity
This course is compiled automatically on 2024-11-22
The course is tested and available on MacOS, Windows and
Ubuntu Linux for R version 4.4.0 (2024-04-24)
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/. This website has all the latest information about R updates, conferences and installation
You can use this direct links to the install for each major OS:
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 R packages
R Packages can be installed from the course package or from CRAN/Bioconductor. These commands should be written into the R console. Once R and RStudio is installed, you can copy and paste these install commands into lower left pane of RStudio which should be labelled “Console”. If you run into any errors, do this one line at a time.
From the course package
install.packages('BiocManager')
install.packages('remotes')
BiocManager::install('RockefellerUniversity/Plotting_In_R',subdir='PlottingInR')From CRAN and Bioconductor
install.packages('BiocManager')
BiocManager::install('ggplot2')
BiocManager::install('paletteer')
BiocManager::install('RColorBrewer')
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.