plotgardener

plotgardener provides coordinate-based visualization of genomic data in R to create publication-quality multi-panel figures that precisely align tracks to genomic coordinates.

Key Features:

• Coordinate-based plotting system: plotgardener uses a coordinate-based system to control the exact size, position, and arrangement of plots so vertically aligned data correspond to the same genomic regions.
• Edge-to-edge containerized plotting: The package implements edge-to-edge containerized plotting functions that map user-specified containers directly to represented data for consistent alignment within multi-panel figures.
• Integration with ggplot2: plotgardener supports precise placement and sizing of ggplot2 plots within multi-panel layouts.
• Fast, memory-efficient data access: The package provides fast and memory-efficient access to genomic data to support large datasets.
• Support for diverse data and file types: plotgardener accepts a wide variety of genomic data and file types for visualization.
• Bioconductor integration: The package leverages Bioconductor infrastructure and tools for interoperability within the Bioconductor ecosystem.

Scientific Applications:

• Publication-quality multi-panel figures: Creation of publication-ready multi-panel figures that maintain accurate genomic coordinate alignment across panels.
• Genomic track alignment and comparison: Precise alignment of vertically stacked tracks to compare signals or annotations across the same genomic regions.
• Exploratory analysis and figure preparation: Generation of figures for exploratory data analysis and detailed manuscript figure preparation.
• Use in genomics and related fields: Visualization tasks for researchers working with genomic datasets within R and Bioconductor workflows.

Methodology:

plotgardener implements a coordinate-based plotting system and an edge-to-edge containerized visualization approach and provides precise placement and sizing for ggplot2 plots.