plot_contigs_quality: Visualize Contigs Quality Metrics

In pctax: Professional Comprehensive Omics Data Analysis

Visualize Contigs Quality Metrics

Description

This function creates a scatter plot to visualize the quality metrics of contigs from geNomad and CheckV analysis results.

Usage

plot_contigs_quality(
  genomad_out_res,
  show_valid = FALSE,
  point_size = 1.4,
  point_alpha = 0.6,
  base_size = 15
)

Arguments

genomad_out_res	List. Output object from pre_genomad function containing virus summary data.
show_valid	Logical. Whether to display only valid (high-quality) viral sequences. Default is FALSE (show all sequences).
point_size	Numeric. Size of the points in the plot. Default is 1.4.
point_alpha	Numeric. Transparency of the points (0-1). Default is 0.6.
base_size	Numeric. Base font size for the plot. Default is 15.

Value

A ggplot object displaying contigs quality metrics.

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