Generates a line plot showing QTL traces (LOD scores) across chromosomes for one or more traits. Supports customization of visual appearance and annotations such as significance thresholds and vertical lines.

Usage

plot_qtl_trace(
  qtl_df,
  thresholds_df,
  vline_df = NULL,
  use_physical_pos = FALSE,
  x_angle = 0,
  trait_colors = NULL,
  trait_labels = NULL,
  x_label = "Position (cM)",
  y_label = "LOD",
  plot_title = NULL,
  show_legend = TRUE,
  facet_nrow = 1
)

Arguments

qtl_df: A data frame containing QTL mapping results. Must include columns: pos (genetic position in cM), lod (LOD score), response_var (trait name), and chr (chromosome). Optional phys.pos (physical position in Mb).
thresholds_df: A data frame with LOD score thresholds per trait. Must include columns: chr, hline, and response_var.
vline_df: Optional. A data frame specifying positions for vertical lines. Must include chr and vline columns. Can also include a label column for text annotation at each vertical line.
use_physical_pos: Logical. If TRUE, use physical position (phys.pos) for the x-axis. If FALSE (default), use genetic position (pos).
x_angle: Integer. Angle of the x-axis text labels (default is 0).
trait_colors: Optional. A named vector of colors for each trait. If NULL (default), colors are automatically assigned.
trait_labels: Optional. A named vector of human-readable trait labels (can include expressions) to use in the legend.
x_label: Character. Label for the x-axis (default is "Position (cM)").
y_label: Character. Label for the y-axis (default is "LOD").
plot_title: Optional. Title for the plot (default is NULL).
show_legend: Logical. Whether to display the legend (defaults to TRUE).
facet_nrow: Integer. Number of rows in the facet layout (defaults to 1).

Value

A ggplot object displaying QTL traces per trait and chromosome, with optional custom styling.