Visualize Contigs Quality Metrics — plot_contigs

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

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.

A ggplot object displaying contigs quality metrics.