GGEBiplots: GGEPlot – R documentation

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GGEPlot

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,
  colGen = "forestgreen", colEnv = "blue", colSegment = "red",
  colHull = "black", 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` 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
`colGen`	colour for genotype attributes on biplot. Defaults to "forestgreen"
`colEnv`	colour for environment attributes on biplot. Defaults to "blue"
`colSegment`	colour for segment or circle lines. Defaults to "red"
`colHull`	colour for hull when type=6. Defaults to "black"
`sizeGen`	text size for genotype labels. Defaults to 4
`sizeEnv`	text size for environment labels. Defaults to 4
`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 footbote

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

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

#using 'gge' instead

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

GGEBiplots

GGE Biplots with 'ggplot2'

v0.1.1

GPL-3

Authors

Sam Dumble [aut, cre], Elisa Frutos Bernal [ctb], Purificacion Galindo Villardon [ctb]

Initial release