karyoploteR

karyoploteR generates non-circular linear chromosomal karyoplots and overlays genomic annotations and experimental datasets for visualization and analysis.

Key Features:

• Customizable Linear Genomes: Produces non-circular linear chromosomal plots for entire genomes from any species with configurable appearance.
• Integration with R base graphics: Uses R base graphics principles for plot construction and customization.
• Modular Design: Provides a main function that creates empty karyoplots to which multiple supplementary functions can add content.
• Layered Annotation and Data Addition: Supports adding genomic annotations, experimental datasets, and custom graphical elements as successive layers.
• Support for User-Defined Functions: Allows incorporation of custom plotting functions in addition to predefined plotting functions.
• Control over Data Positioning and Representation: Enables explicit control of how and where data and annotations are placed within the plot.

Scientific Applications:

• Genomic data visualization: Visualizes complex genomic annotations and experimental datasets along linear chromosomes to support data exploration and interpretation.
• Comparative genomics: Displays chromosomal features across genomes to facilitate visual comparison between species or assemblies.
• Genome-wide association studies (GWAS): Presents loci and associated signals along chromosomes to assist the interpretation of GWAS results.

Methodology:

Implements plotting with R base graphics via a modular API that creates empty karyoplots which are incrementally enriched with data layers, annotations, and user-defined plotting functions.