snp.plotter: an R-based SNP/haplotype association and linkage disequilibrium plotting package

Bioinformatics. 2007 Mar 15;23(6):774-6. doi: 10.1093/bioinformatics/btl657. Epub 2007 Jan 18.


snp.plotter is a newly developed R package which produces high-quality plots of results from genetic association studies. The main features of the package include options to display a linkage disequilibrium (LD) plot below the P-value plot using either the r2 or D' LD metric, to set the X-axis to equal spacing or to use the physical map of markers, and to specify plot labels, colors, symbols and LD heatmap color scheme. snp.plotter can plot single SNP and/or haplotype data and simultaneously plot multiple sets of results. R is a free software environment for statistical computing and graphics available for most platforms. The proposed package provides a simple way to convey both association and LD information in a single appealing graphic for genetic association studies.

Availability: Downloadable R package and example datasets are available at and

MeSH terms

  • Algorithms
  • Chromosome Mapping / methods*
  • Computer Graphics*
  • DNA Mutational Analysis / methods*
  • Haplotypes / genetics*
  • Linkage Disequilibrium / genetics*
  • Polymorphism, Single Nucleotide / genetics*
  • Programming Languages
  • Software*
  • User-Computer Interface