snp.plotter

snp.plotter produces high-quality visualizations of genetic association study results by integrating SNP and haplotype p-value plots with linkage disequilibrium displays.

Key Features:

• High-Quality Plotting: Generates publication-quality graphics for SNP and haplotype association results.
• Linkage Disequilibrium (LD) Visualization: Displays LD plots beneath P-value plots with a choice of r² or D' metrics.
• Axes and Label Customization: Allows X-axis scaling by equal spacing or physical map of markers and customization of plot labels, colors, and symbols.
• LD Heatmap Color Schemes: Supports custom color schemes for LD heatmaps to represent linkage patterns visually.
• Simultaneous Multi-Set Plotting: Plots multiple result sets concurrently for comparative analyses.
• SNP and Haplotype P-value Display: Presents single-SNP p-values alongside individual and global haplotype p-values.
• Integration with R: Implements plotting and analysis functionality within the R statistical environment.

Scientific Applications:

• Genetic Association Visualization: Visualizes associations between genetic variants (SNPs) and traits or diseases using P-value plots.
• Linkage and Association Interpretation: Integrates P-value and LD information to aid interpretation of association strength and genetic linkage patterns.
• Candidate Region Identification: Aids identification of candidate genomic regions for follow-up by combining association and LD patterns.
• Comparative Result Analysis: Enables comparison of multiple association result sets within a single visualization.

Methodology:

Plots single-SNP and/or haplotype data, displaying single-SNP p-values and individual/global haplotype p-values and rendering LD plots beneath P-value plots using r² or D' with options for equal marker spacing or physical-map-based spacing.