Produces a ggplot2-based GGE-GT-GYT biplot based on a model fitted with the
functions gge()
, gtb()
, and gytb()
.
# S3 method for 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(),
...
)
A ggplot2-based biplot.
An object of class gg, ggplot
.
An object with classes gge
gtb
, or gytb
.
The variable to plot (useful for gge
objects. Defaults to
var = 1
the first variable of x
.
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).
If TRUE
(default), the text labels repel away from each
other and away from the data points.
Force of repulsion between overlapping text labels. Defaults
to 1
.
Exclude text labels that overlap too many things. Defaults to 20.
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.
The name of genotypes to compare between when
type = 9
. Must be a string present in the genotype's name.
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).
The line type to highlith the genotype's vectors.
Defaults to line.type.gen == "dotted
.
The size of the shape (both for genotypes and
environments). Defaults to 2.2
.
The size of the shape for winners genotypes when
type = 3
. Defaults to 3.2
.
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
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'
.
The alpha value for the color. Defaults to 1
. Values
must be between 0
(full transparency) to 1
(full color).
The color and alpha values for the circle
lines. Defaults to 'gray'
and 0.4
, respectively.
The labs of legend. Defaults to NULL
is c('Env', 'Gen')
.
The size of the text for genotypes, environments and labels, respectively.
The text size to use for winner genotypes where
type = 3
and for the two selected genotypes where type = 9
.
Defaults to 4.5.
The size of the line in biplots (Both for segments and circles).
multiplication factor to expand the axis limits by to enable fitting of labels. Defaults to 1.2
Logical values (Defaults to TRUE
) to include
automatically generated information in the plot such as singular value
partitioning, scaling and centering.
The graphical theme of the plot. Default is
plot_theme = theme_metan()
. For more details, see
ggplot2::theme()
.
Currently not used.
Tiago Olivoto tiagoolivoto@gmail.com
Yan, W., and M.S. Kang. 2003. GGE biplot analysis: a graphical tool for breeders, geneticists, and agronomists. CRC Press.
# \donttest{
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)
# }
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