R Studio Cloud

During the workshop, we will be using the statistical computing software called R to perform calculations and produce data visualisations.

Fortunately, we have a cloud-based version of R available to us at the following website: R Studio Cloud.

Please follow the steps below to:

  1. Create Account

  2. Create Project

  3. R Markdown

  4. Install Packages

Create Account

Navigate to the R Studio Cloud website and click on the GET STARTED FOR FREE button.

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Select a free acount. This will provide us with enough resources for the workshop (1 GB RAM, 1 CPU and 25 hours per month). In reality this is a tiny resource allocation - many computational operations in genomics require exponentially more resources which are performed on high performance compute (HPC) clusters or more recently, on the cloud.

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Enter a valid email address and fill out the rest of the information (password, name). R Studio Cloud will send you an email with a link to verify your email address. Click on the link to verify your email address - you should now be able to log into R Studio Cloud.

Select R Studio Cloud from the options listed below:

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Create Project

Once your account has been created, you need to create a project for the workshop. This is to let R Studio Cloud know what type of environment you want to work in, and allows them to track your resource usage.

Select New Project > New R Studio Project.

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R Studio Interface

When you open your project, you will be presented with a window containing four panels:

  1. Code editor: You can type and execute code in this window. The benefit of this window is your code is saved in a ‘notebook’ allowing you to save your work.

  2. R console: You can also execute code here, but the code is not saved. The console also outputs error messages and is useful for debugging errors.

  3. Workspace and History: Any data object you create is saved in this panel. You can click on any of the objects to view them in a separate tab in the Code editor window.

  4. Plots and Files: This panel is primarily used to view any files present in your folder and check what packages you have loaded in your current session.

Note

The Plots and Files panel will not display many files as the folder is on the cloud - not your computer/laptop!

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R Markdown

During the workshop we want to be able to create PDF or HTML documents containing our code and code outputs. To do this, we will be using the R Markdown document type.

In your project workspace, select File > New File > R Markdown…

You will be prompted to install packages, select yes.

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You can now make R Markdown documents, which we will return to later in the workshop.

Install Packages

In your project workspace, you have some very basic packages that come pre-installed. We will need to install more packages for the workshop.

Installing packages to your workspace is analogous to installing apps on your phone via the App Store / Google Play except we are installing packages from Bioconductor - a home for open source bioinformatics software.

In the console, please insert the following lines of code to install the required packages:

install.packages("ggplot2")
install.packages("pheatmap")
install.packages("ggpubr")
install.packages("rcolorbrewer")
install.packages("cluster")
install.packages("gplots")
install.packages("caret")
install.packages("e1071")