gc_plot: Plot Scaled Gene Clusters with Arrows

In gclink: Gene-Cluster Discovery, Annotation and Visualization

Plot Scaled Gene Clusters with Arrows

Description

Generates a compact, publication-ready arrow plot of gene clusters previously processed with gc_scale. Each cluster is displayed on its own horizontal track, with gene directionality, labels, and user-defined colour schemes.

Usage

gc_plot(
  data = GC_meta,
  color_theme = c("#3BAA51", "#6495ED", "#DD2421", "#EF9320", "#F8EB00", "#FF0683",
    "#956548", "grey")
)

Arguments

data	A data frame produced by gc_scale, must include the columns Pstart, Pend, Pgenome, gene_group, Pdirection, and gene_label.
color_theme	Character vector of colours, in the same order as the factor levels of gene_group. Defaults to an 8-colour palette; supply fewer or more colours as needed.

Value

A ggplot object that can be further customised or printed. The plot uses gggenes::geom_gene_arrow() and gggenes::geom_gene_label() with the following elements:

• One facet per Pgenome (cluster).

• Genes coloured by gene_group.

• Arrow direction encoded by Pdirection.

• Optional gene labels inside arrows.

gclink documentation built on Sept. 9, 2025, 5:39 p.m.