This repository contains the complete R code and data to reproduce all figures from the protocol paper of ggalign package.

This repository includes eight protocol directories (protocol1 through protocol8), each containing the corresponding R script that generates all figures for that protocol. The scripts cover:

• Protocol 1: Data-free composition
• Protocol 2: Quad layouts for heatmap visualization
• Protocol 3: Circular layouts for radial data display
• Protocol 4: Stack layouts and nested composition
• Protocol 5: Multi-omics expression heatmaps
• Protocol 6: Somatic mutation oncoplot
• Protocol 7: Circos plots for genomic data
• Protocol 8: Cross-connections between genes and pathways

• R (≥ 4.2.0)
• ggalign (≥ 1.2.0.9000)

For questions about the code or protocols, please open an issue on this repository or contact the corresponding authors.