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Simple Effect Plot

Source: R/simple_effect_plot.R
simple_effect_plot.Rd

Generates a clean and simple effect plot. Shows the relationship between genotype classes at a marker on a trait. Optionally includes annotation of medians and sample sizes, and allows flipping of axes. Works on polyploids.

Usage

simple_effect_plot(
  effects_df,
  marker_name,
  trait_name,
  genotype_levels = c("A", "H", "B"),
  annotate = TRUE,
  flip = FALSE,
  trait_label = NULL
)

Arguments

effects_df

A data frame containing at least the columns for marker genotypes and trait values. Usually the output of format_qtl_inputwith a few modifications (first two rows removed).

marker_name

A character string specifying the name of the marker column in effects_df.

trait_name

A character string specifying the name of the trait column in effects_df.

genotype_levels

A character vector indicating the expected genotype categories (factor levels). Default is c("A", "H", "B").

annotate

Logical; if TRUE, the plot includes annotations of median values and sample sizes per genotype. Default is TRUE.

flip

Logical; if TRUE, the coordinates of the plot are flipped (horizontal layout). Default is FALSE.

trait_label

Optional character string to use as the y-axis label. If NULL, the trait name is used.

Value

A ggplot2 object displaying the distribution of trait values across genotype classes (alleles) at the specified marker.

Details

The function performs the following:

  • Verifies the presence of marker and trait columns in the input data frame.

  • Removes rows with missing genotype data.

  • Converts the marker column to a factor with specified genotype levels.

  • Creates a boxplot with optional annotations of median values and counts.

  • Optionally flips the plot horizontally.

Note

Inspired by Fig. 2 Caraza-Harter & Endelman

Examples