plot_one_phage: Plot Individual Phage Genome Structure with Annotations

In pctax: Professional Comprehensive Omics Data Analysis

Plot Individual Phage Genome Structure with Annotations

Description

This function creates a circular genome map for a single phage, displaying gene annotations, functional categories, and other genomic features. It automatically extracts topology information and provides flexible parameter customization.

Usage

plot_one_phage(
  one_phage,
  genomad_out_res,
  anno_table = NULL,
  y_var = "strand",
  fill_var = "COG",
  label_var = c("annotation_description"),
  label_wrap = 20,
  palette = "Set3"
)

Arguments

one_phage	Character. Phage sequence identifier (e.g., "k141_10408").
genomad_out_res	List. Output object from pre_genomad function containing virus summary and gene data.
anno_table	Data frame. Optional annotation table with gene information for left join. Must contain a 'gene' column for merging with genomad gene data.
y_var	Character. Variable for y-axis mapping. Default is "strand".
fill_var	Character. Variable for fill color mapping. Default is "COG".
label_var	Character vector. Columns to use for gene description labels.
label_wrap	Integer. Width for wrapping gene description labels. Default is 20.
palette	Character. Color palette for fill categories. Default is "Set3".

Details

The function automatically extracts topology information from the virus summary data and creates a polar coordinate visualization showing:

• Gene arrows indicating direction and position

• Flexible y-axis and fill color mappings

• Genome length and automatically detected topology information

• Gene descriptions with intelligent label placement

Value

A ggplot object displaying the circular phage genome map.

pctax documentation built on Feb. 9, 2026, 9:06 a.m.