Phage Genome Visualization in R

This repository contains R scripts to generate circular and linear genome maps of phage genomes based on annotated GFF3 files. The workflow was developed for visualization of Salmonella phage genomes annotated with Bakta and is suitable for use in comparative genomics or figure preparation for publications.

Features

• Input: GFF3 annotation files without FASTA sequences (*.nofasta.gff3).
• Parsing and normalization of annotation fields.
• Grouping of coding sequences into functional categories:
  • Structural proteins
  • DNA packaging
  • Replication
  • Recombination/Integration
  • Lysis
  • Hypothetical proteins
  • Other
• Visualization:
  • Linear maps using genoPlotR.
  • Circular maps using circlize.
  • Separate rings for positive and negative strands.
  • Color-coded functional categories.
  • Genome position grid with tick marks (2 kb intervals, extended to full genome length).
• Optional GC content/skew track if FASTA sequences are available.

Requirements

• R ≥ 4.1
• Packages: ape, genoPlotR, circlize, (seqinr optional for GC skew)

To install missing packages:

install.packages(c("ape","genoPlotR","circlize","seqinr"), dependencies = TRUE)