Plot Individual Phage Genome Structure with Annotations

Source: R/other_software.R

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.

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".

Value

A ggplot object displaying the circular phage genome map.

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