General R plotting functions
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readme.md

readme.md

R Plotting Functions

Overview

  • A collection of R functions. New plotting functions will be added along with examples as I finish them
  • Partially to help scientists and others who want to avoid proprietary software like Excel and GraphPad's Prism. This allows analysis software/code to be portable across labs and countries.
    • Also encourages storage of data portable, plain text file formats (e.g. .csv) rather than binary formats (e.g. .xls).

Features

  • Commented R plotting functions (see \functions).
  • Example scripts for each function (see \examples).
  • Example output plots (using given functions) to compare against.
  • Tested in R 2.15.2.

Installation

Git

Go to your personal LaTeX projects directory (or wherever) and clone the repository using the command below:

git clone https://github.com/gaara42/R_plot_functions

Manual

  • Download the files using the GitHub .zip download option
  • Unzip the files and rename the folder to whatever name you want, references are relative only below the root folder.

Dependencies

  • Download R).
    • Make sure to have all packages updated.
    • Several packages need to be added to get function to work

Instructions

###Overview

  • Tested in R 2.15.2, can check old version if people find compatibility issues.
  • \functions contains plotting functions, with naming convention view.PLOT_TYPE.R.
  • \examples are example plotting functions, with naming convention analysis.PLOT_TYPE.EXAMPLE_NAME.R.
  • \plots are example plots, with naming convention plot.PLOT_TYPE.EXAMPLE_NAME.jpg.
    • JPEGs are used in the repository since they are widely supported, use postscript() function to get vector output, which is higher quality, especially if combining R with LaTeX.

###PCA Function

  • Use to analyze datasets with many dimensions for a few conditions. For example, looking at microarray (gene expression) data for patients with or without cervical cancer.
  • \functions\view.pca.R
    • The main function pcaplot accepts both data.frame and string reference to a file.
    • If given a file path, it will attempt to parse into a data.frame.
      • Make sure file has headers and row names. If not, set rownames and headers to FALSE when calling pcaplots
  • \examples\analysis.pca.USA.R is an example implementation usng the USArrests data.frame that is auto-loaded in 2.15.2
    • Note, USArrests is the correct input format for this function.

Changelog

What's New

  • Cleaned up PCA function and added description of inputs (2013.01.10)
  • Added to GitHub (2013.01.10)

In Development

  • Clean-up code and comments, add additional R features.
  • Codes for: box, bar, scatter, line, density and other types of common plots.
  • More examples!

##License

Biafra Ahanonu bahanonu@gmail.com

This program is free software: you can redistribute it and/or modify it under the terms of the GNU. Attribution is appreciated, but not required, if parts of the software are used elsewhere.