plot_bars: Plot phenotypic effect for two markers as a bar plot

In TheJacksonLaboratory/CAPE: Combined Analysis of Pleiotropy and Epistasis for Diversity Outbred Mice

Plot phenotypic effect for two markers as a bar plot

Description

This internal function is called by plot_effects to generate a bar plot showing mean trait values for all combinations of genotypes for two markers. This function also indicates the predicted additive effects of the two markers with a dashed line, as well as the error of the predicted additive effect with an orange box. The true effect of the marker combination is shown with a gray bar. The effects can centered on the reference allele to better show relative effects of each allele and allele combination.

Usage

plot_bars(
  phenoV,
  marker1_vals,
  marker2_vals,
  pheno_name,
  marker1_label,
  marker2_label,
  ymin = NULL,
  ymax = NULL,
  error_bars,
  ref_centered
)

Arguments

phenoV	A vector of trait values
marker1_vals	A vector of genotype values for marker1
marker2_vals	A vector of genotype values for marker2.
pheno_name	A string indicating the name of the trait being plotted.
marker1_label	A string indicating the name of marker1
marker2_label	A string indicating the name of marker2
ymin	A numeric value indicating the minimum y value for the plot. If NULL, it will be calculated based on phenoV and error bars.
ymax	A numeric value indicating the maximum y value for the plot. If NULL, it will be calculated based on phenoV and error bars.
error_bars	A string indicating the type of error bars to draw. Can be "sd" for standard deviation, "se" for standard error, or "none".
ref_centered	Whether to center the effects on the reference genotype.

Value

None

TheJacksonLaboratory/CAPE documentation built on Feb. 12, 2024, 4:32 p.m.