RStudio at TACC

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Objectives

• Learn to run RStudio on Maverick through the TACC Visualization Portal
• Import data
• Run R scripts
• Save results
• Visualize results
• Load R modules

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R is a programming environment for statistical and data analysis computations. R is an open source GPL licensed (free to anyone) offspring of S, initially written by Ross Ihaka and Robert Gentleman at Dep. of Statistics of U of Auckland, New Zealand during 1990s. It continues to be in active development; http://www.r-project.org/

Some things that R can do

• Statistics and analysis
• Plotting and graphics
• Data handling and storage
• Scripting (loops, subroutines, etc)

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TACC Visualization Portal

https://vis.tacc.utexas.edu/

Logging in

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• Wait for authentification
• Will automatically switch to displaying Jobs tab
• Select Maverick
• Select a project that has an allocation on Maverick
• Select RStudio

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Wait patiently. Move startup window up with mouse to make sure it did not fail.

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Now open RStudio in your browser by clicking the button.

Congratulations!

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Challenge

• Use VNC. ssh. or git-bash and your basic linux knowledge to find your working directory path on maverick. Copy it.
• Make and save a tab delimited text data file with some random numbers as data.txt

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RStudio Graphical User Interface (GUI)

• Source Editor / Interactive Highlight & Run
• Data Viewer
• Interactive Console
• Workspace / Variable Viewer
• Session History
• File Management
• Plot Viewer
• Package Loader
• Interactive Help

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Open your data

In the interactive console type (using your own work directory):

workdir="/work/01234/jcarson/maverick"
setwd(workdir)

You could also instead use the File Management window on bottom right to set the working directory. Once it is set, read in the file.

x = read.delim(“filename.txt”)

How can you tell it has been read in?

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Importing data from URL

Credit to: http://evomics.org/learning/programming/introduction-to-r/

Upper Left Window

• Tools
• Import Dataset
• From Web URL

Repeat for both datasets

• http://evomicsorg.wpengine.netdna-cdn.com/wp-content/uploads/2013/01/healthy_metadata.txt
• http://evomicsorg.wpengine.netdna-cdn.com/wp-content/uploads/2013/01/sick_metadata.txt

summary(healthy_metadata)
summary(sick_metadata)
boxplot(healthy_metadata$Age, sick_metadata$Age)

Try exporting your plot. Be sure to specify your working directory in the save window

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Saving your workspace

You can use the GUI to save and load your workspace

• Session - save workspace
• Quit RStudio
• Reopen RStudio
• Session - load workspace

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Challenge

• Type demo() to see a list of demos available and try some of them out, e.g. demo(graphics)
• Find a favorite plot and save it as a pdf in your work directory
• Verify that the file is where you wanted to save it