Skip to content

Latest commit

 

History

History
140 lines (90 loc) · 3.13 KB

README.md

File metadata and controls

140 lines (90 loc) · 3.13 KB
Raw

RStudio at TACC

Objectives

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

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)

TACC Visualization Portal

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

Logging in

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

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

Now open RStudio in your browser by clicking the button.

Congratulations!

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

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

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?

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

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

Saving your workspace

You can use the GUI to save and load your workspace

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

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