plot_checkm2_res: Visualize CheckM2 Genome Quality Assessment Results

Description

This function creates a scatter plot showing genome completeness vs contamination with optional marginal density plots to display distributions.

Usage

plot_checkm2_res(
  checkm2_df,
  add_marginal = TRUE,
  marginal_type = "density",
  point_size = 0.6,
  base_size = 14,
  quality_thresholds = list(high_comp = 90, high_contam = 5, med_comp = 70, med_contam =
    10),
  filter_data = TRUE,
  min_quality_score = 50,
  min_completeness = 50,
  max_contamination = 10
)

Value

A ggplot object or ggExtra plot object if marginal plots are added.

Arguments

checkm2_df: Data frame. CheckM2 results containing at least columns: 'Completeness', 'Contamination', and 'Name'.
add_marginal: Logical. Whether to add marginal density plots using ggExtra. Default is TRUE.
marginal_type: Character. Type of marginal plot: "density", "histogram", "boxplot", or "violin". Default is "density".
point_size: Numeric. Size of points in scatter plot. Default is 0.6.
base_size: Numeric. Base font size for the plot. Default is 14.
quality_thresholds: List. Custom thresholds for quality classification. Default list(high_comp = 90, high_contam = 5, med_comp = 70, med_contam = 10)
filter_data: Logical. Whether to filter low-quality genomes. Default is TRUE.
min_quality_score: Numeric. Minimum quality score for filtering. Default is 50.
min_completeness: Numeric. Minimum completeness for filtering. Default is 50.
max_contamination: Numeric. Maximum contamination for filtering. Default is 10.