GGE biplots with ggplot2

Source: R/GGE_Plot.R

GGE biplots are used for visual examination of the relationships between test environments, genotypes, and genotype-by-environment interactions. `GGEPlot()` produces a biplot as an object of class 'ggplot', using the output of the GGEmodel function. Several types of biplots are offered which focus on different aspects of the analysis. Customization options are also included. This function is a modification of GGEPlot from the GGEBiplots package.

GGEPlot(
  GGEModel,
  type = "Biplot",
  d1 = 1,
  d2 = 2,
  selectedE = NA,
  selectedG = NA,
  selectedG1 = NA,
  selectedG2 = NA,
  colGen = "gray47",
  colEnv = "darkred",
  colSegment = "gray30",
  colHull = "gray30",
  sizeGen = 4,
  sizeEnv = 4,
  largeSize = 4.5,
  axis_expand = 1.2,
  axislabels = TRUE,
  axes = TRUE,
  limits = TRUE,
  titles = TRUE,
  footnote = TRUE
)

Arguments

GGEModel

An object of class GGEModel.

type

type of biplot to produce.

  • "Biplot": Basic biplot.

  • "Selected Environmen"t: Ranking of cultivars based on their performance in any given environment.

  • "Selected Genotype": Ranking of environments based on the performance of any given cultivar.

  • "Relationship Among Environments".

  • "Comparison of Genotype".

  • "Which Won Where/What": Identifying the 'best' cultivar in each environment.

  • "Discrimination vs. representativeness": Evaluating the environments based on both discriminating ability and representativeness.

  • "Ranking Environments": Ranking environments with respect to the ideal environment.

  • "Mean vs. stability": Evaluating cultivars based on both average yield and stability.

  • "Ranking Genotypes": Ranking genotypes with respect to the ideal genotype.

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 evaluate when `type="Selected Environment"`.

selectedG

name of the genotype to evaluate when `type="Selected Genotype"`.

selectedG1,

name of the genotype to compare to `selectedG2` when `type="Comparison of Genotype"`.

selectedG2,

name of the genotype to compare to `selectedG1` when `type="Comparison of Genotype"`.

colGen

genotype attributes colour. Defaults to `"gray47"`.

colEnv

environment attributes colour. Defaults to `"darkred"`.

colSegment

segment or circle lines colour. Defaults to `"gray30"`.

colHull

hull colour when `type="Which Won Where/What"`. Defaults to "gray30".

sizeGen

genotype labels text size. Defaults to 4.

sizeEnv

environment labels text size. Defaults to 4.

largeSize

larger labels text size to use for two selected genotypes in `type="Comparison of Genotype"`, and for the outermost genotypes in `type="Which Won Where/What"`. 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 this argument is `TRUE` labels for axes are included. Defaults to `TRUE`.

axes

logical, if this argument is `TRUE` x and y axes going through the origin are drawn. Defaults to `TRUE`.

limits

logical, if this argument is `TRUE` the axes are re-scaled. Defaults to `TRUE`.

titles

logical, if this argument is `TRUE` a plot title is included. Defaults to `TRUE`.

footnote

logical, if this argument is `TRUE` a footnote is included. Defaults to `TRUE`.

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.

Sam Dumble (2017). GGEBiplots: GGE Biplots with 'ggplot2'. R package version 0.1.1. https://CRAN.R-project.org/package=GGEBiplots

Examples

 library(geneticae)

 # Data without replication
 library(agridat)
 data(yan.winterwheat)
 GGE1 <- GGEmodel(yan.winterwheat)
 GGEPlot(GGE1)


 # Data with replication
 data(plrv)
 GGE2 <- GGEmodel(plrv, genotype = "Genotype", environment = "Locality",
                  response = "Yield", rep = "Rep")
 GGEPlot(GGE2)