EpiTest.plot: Display variance component or directional epistasis graphs

In EpiTest: Test for Gene x Gene Interactions in Bi-Parental Populations

Display variance component or directional epistasis graphs

Description

Display variance component or directional epistasis graphs

Usage

EpiTest.plot(
  ETest,
  Title = NULL,
  Family_names = NULL,
  Colors = NULL,
  Type = "mean",
  Alpha = 5/100
)

Arguments

ETest	a list as obtained from the EpiTest.fit function
Title	(optional) a character string to be used as a title for the graph
Family_names	(optional) a character vector with family names
Colors	(optional) a character vector with three colors for the graphical display (for variance graphs only)
Type	a string with "mean" to display the directional epistasis plot or "var" to display the variance component graph
Alpha	type I error for the test, with 5% default value (for directional epistasis plot only)

Value

a ggplot graph

Examples

data(Pheno.list)
data(Ancestry.list)

## Full NAM analysis
Parent.list <- Parents$Genotype[-1]
names(Parent.list) <- Parents$Family[-1]
ETest.nam <- purrr::imap(Parent.list, ~ EpiTest.fit(Ancestry = Ancestry.list[[.y]],
                                                    Pheno = Pheno.list[[.y]],
                                                    ParentName = c(P0 = 'B73',P1 = .x),
                                                    Parents = Parents,
                                                    Trait = 'GDD_DTA',
                                                    Weight = TRUE))
## Variance component plot
EpiTest.plot(ETest.nam,Title = 'Days to anthesis',Type = "var")

## Directional epistasis plot
EpiTest.plot(ETest.nam,Title = 'Days to anthesis',Type = "mean",Alpha = 5/100)

EpiTest documentation built on Dec. 20, 2022, 5:35 p.m.