plot.gge: Create GGE, GT or GYT biplots

In metan: Multi Environment Trials Analysis

Create GGE, GT or GYT biplots

Description

Produces a ggplot2-based GGE-GT-GYT biplot based on a model fitted with the functions gge(), gtb(), and gytb().

Usage

## S3 method for class 'gge'
plot(
  x,
  var = 1,
  type = 1,
  repel = TRUE,
  repulsion = 1,
  max_overlaps = 20,
  sel_env = NA,
  sel_gen = NA,
  sel_gen1 = NA,
  sel_gen2 = NA,
  shape.gen = 21,
  shape.env = 23,
  line.type.gen = "dotted",
  size.shape = 2.2,
  size.shape.win = 3.2,
  size.stroke = 0.3,
  col.stroke = "black",
  col.gen = "blue",
  col.env = "forestgreen",
  col.line = "forestgreen",
  col.alpha = 1,
  col.circle = "gray",
  col.alpha.circle = 0.5,
  leg.lab = NULL,
  size.text.gen = 3.5,
  size.text.env = 3.5,
  size.text.lab = 12,
  size.text.win = 4.5,
  size.line = 0.5,
  axis_expand = 1.2,
  title = TRUE,
  plot_theme = theme_metan(),
  ...
)

Arguments

x	An object with classes gge gtb, or gytb.
var	The variable to plot (useful for gge objects. Defaults to var = 1 the first variable of x.
type	The type of biplot to produce. Basic biplot. Mean performance vs. stability (gge biplots) or the The Average Tester Coordination view for genotype-trait and genotype-yield*trait biplots. Which-won-where. Discriminativeness vs. representativeness. Examine an environment (or trait/yield*trait combination). Ranking environments (or trait/yield*trait combination). Examine a genotype. Ranking genotypes. Compare two genotypes. Relationship among environments (or trait/yield*trait combination).
repel	If TRUE (default), the text labels repel away from each other and away from the data points.
repulsion	Force of repulsion between overlapping text labels. Defaults to 1.
max_overlaps	Exclude text labels that overlap too many things. Defaults to 20.
sel_env, sel_gen	The name of the environment (or trait/yield*trait combination) and genotype to examine when type = 5 and type = 7, respectively. Must be a string which matches a environment or genotype label.
sel_gen1, sel_gen2	The name of genotypes to compare between when type = 9. Must be a string present in the genotype's name.
shape.gen, shape.env	The shape for genotype and environment indication in the biplot. Defaults to shape.gen = 21 (circle) for genotypes and shape.env = 23 (rhombus) for environments. Values must be between 21-25: 21 (circle), 22 (square), 23 (rhombus), 24 (up triangle), and 25 (low triangle).
line.type.gen	The line type to highlith the genotype's vectors. Defaults to line.type.gen == "dotted.
size.shape	The size of the shape (both for genotypes and environments). Defaults to 2.2.
size.shape.win	The size of the shape for winners genotypes when type = 3. Defaults to 3.2.
size.stroke, col.stroke	The width and color of the border, respectively. Default to size.stroke = 0.3 and col.stroke = "black". The size of the shape will be size.shape + size.stroke
col.gen, col.env, col.line	Color for genotype/environment labels and for the line that passes through the biplot origin. Defaults to col.gen = 'blue', col.env = 'forestgreen', and col.line = 'forestgreen'.
col.alpha	The alpha value for the color. Defaults to 1. Values must be between 0 (full transparency) to 1 (full color).
col.circle, col.alpha.circle	The color and alpha values for the circle lines. Defaults to 'gray' and 0.4, respectively.
leg.lab	The labs of legend. Defaults to NULL is c('Env', 'Gen').
size.text.gen, size.text.env, size.text.lab	The size of the text for genotypes, environments and labels, respectively.
size.text.win	The text size to use for winner genotypes where type = 3 and for the two selected genotypes where type = 9. Defaults to 4.5.
size.line	The size of the line in biplots (Both for segments and circles).
axis_expand	multiplication factor to expand the axis limits by to enable fitting of labels. Defaults to 1.2
title	Logical values (Defaults to TRUE) to include automatically generated information in the plot such as singular value partitioning, scaling and centering.
plot_theme	The graphical theme of the plot. Default is plot_theme = theme_metan(). For more details, see ggplot2::theme().
...	Currently not used.

Value

A ggplot2-based biplot.

An object of class gg, ggplot.

Author(s)

Tiago Olivoto [e-mail]

References

Yan, W., and M.S. Kang. 2003. GGE biplot analysis: a graphical tool for breeders, geneticists, and agronomists. CRC Press.

Examples

library(metan)
mod <- gge(data_ge, ENV, GEN, GY)
plot(mod)
plot(mod,
     type = 2,
     col.gen = 'blue',
     col.env = 'red',
     size.text.gen = 2)

metan documentation built on March 7, 2023, 5:34 p.m.