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Introduction

What is snp.plotter?

snp.plotter is an R package that creates publishable-quality plots of p-values using single SNP and/or haplotype data. Main features of the package include options to display a linkage disequilibrium (LD) plot and the ability to plot multiple sets of results simultaneously. Plots can be created using global and/or individual haplotype p-values along with single SNP p-values. Images are created as either Portable Document Format or Encapsulated (EPS) files.

What do snp.plotter images look like?

Here is a sample image as both a PDF and a EPS image. PDF images can be viewed using the free Adobe Reader software. EPS (or PDF) images can be viewed using front-end software for Ghostscript, a Postscript and PDF interpreter: Ghostview and GV for Unix/X11 systems and GSView for Windows.

Who are the intended users of snp.plotter?

Researchers conducting gene association studies who need to create images showing results in the form of p-values of their work along with a linkage disequilibrium plot to show the underlying structure of the study population. Because snp.plotter is a visualization tool, the type of study design used either family-based, case-control, or a combination is irrelevant.

What are the main features of snp.plotter?

• Publishable-quality graphics in resolution-independent formats
• Free and open source
• Visualization of global or individual haplotype p-values
• Visualization of results either physically spaced or evenly spaced
• Ability to plot multiple sets of results
• Optional web interface
• Customizable parameters
  • Labels
  • Symbols
  • Colors/color schemes
  • LD metric
  • P-value threshold