GGEPlot: GGE biplots with 'ggplot2'

In stats4sd/GGEBiplots: GGE Biplots with 'ggplot2'

GGE biplots with ggplot2

Description

Produces the GGE biplot as an object of class 'ggplot' from a model produced by a call to either GGEModel or gge. Nearly all stylistic attributes of output can either be customised within the function or disabled so that the user can customise output to their own liking.

Usage

GGEPlot(
  GGEModel,
  type = 1,
  d1 = 1,
  d2 = 2,
  selectedE = NA,
  selectedG = NA,
  selectedG1 = NA,
  selectedG2 = NA,
  colSegment = "red",
  colHull = "black",
  largeSize = 4.5,
  axis_expand = 1.2,
  axislabels = TRUE,
  axes = TRUE,
  limits = TRUE,
  titles = TRUE,
  footnote = TRUE,
  textGen = element_text(family = "", face = 1, color = "forestgreen", size = 4, hjust
    = 0, vjust = 0, angle = 0),
  textEnv = element_text(family = "", face = 1, color = "blue", size = 4, hjust = 0,
    vjust = 0, angle = 0)
)

Arguments

GGEModel	An object of class GGEModel or gge
type	type of biplot to produce. Basic biplot. Examine environment. See ExamineEnv Examine genotype. See ExamineGen Relationship among environments. See EnvRelationship Compare two genotypes. See CompareGens Which won where/what. See WhichWon Discrimination vs. representativeness. See DiscRep Ranking environments. See RankEnv Mean vs. stability. See MeanStability Ranking gentoypes See RankGen
d1	PCA component to plot on x axis. Defaults to 1
d2	PCA component to plot on y axis. Defaults to 2
selectedE	name of the environment to examine when type=2. Must be a string which matches an environment label
selectedG	name of the genotype to examine when type=3. Must be a string which matches a genotype label
selectedG1	name of a genotype to compare when type=5. Must be a string which matches a genotype label
selectedG2	name of a genotype to compare when type=5. Must be a string which matches a genotype label and not equal to selectedG1
colSegment	colour for segment or circle lines. Defaults to "red"
colHull	colour for hull when type=6. Defaults to "black"
largeSize	text size to use for larger labels where type=5, used for the two selected genotypes, and where type=6, used for the outermost genotypes. Defaults to 4.5
axis_expand	multiplication factor to expand the axis limits by to enable fitting of labels. Defaults to 1.2
axislabels	logical. If TRUE then include automatically generated labels for axes
axes	logical. If TRUE then include x and y axes going through the origin
limits	logical. If TRUE then automatically rescale axes
titles	logical. If TRUE then include automatically generated titles
footnote	logical. If TRUE then include automatically generated footnote
textGen	element_text for genotype labels
textEnv	element_text for environment labels

Value

A biplot of class ggplot

References

Yan W, Kang M (2003). GGE Biplot Analysis: A Graphical Tool for Breeders, Geneticists, and Agronomists. CRC Press.

Examples

data(Ontario)
GGE1<-GGEModel(Ontario)
GGEPlot(GGE1)

#using 'gge' instead

library(gge)
GGE2<-gge(as.matrix(Ontario))
GGEPlot(GGE2)

stats4sd/GGEBiplots documentation built on March 18, 2023, 7:54 p.m.