plot_scores: Plot scores in different graphical interpretations

In metan: Multi Environment Trials Analysis

Plot scores in different graphical interpretations

Description

Plot scores of genotypes and environments in different graphical interpretations.

Biplots type 1 and 2 are well known in AMMI analysis. In the plot type 3, the scores of both genotypes and environments are plotted considering the response variable and the WAASB, an stability index that considers all significant principal component axis of traditional AMMI models or all principal component axis estimated with BLUP-interaction effects (Olivoto et al. 2019). Plot type 4 may be used to better understand the well known 'which-won-where' pattern, facilitating the recommendation of appropriate genotypes targeted for specific environments, thus allowing the exploitation of narrow adaptations.

Usage

plot_scores(
  x,
  var = 1,
  type = 1,
  first = "PC1",
  second = "PC2",
  repel = TRUE,
  repulsion = 1,
  max_overlaps = 20,
  polygon = FALSE,
  title = TRUE,
  plot_theme = theme_metan(),
  axis.expand = 1.1,
  x.lim = NULL,
  y.lim = NULL,
  x.breaks = waiver(),
  y.breaks = waiver(),
  x.lab = NULL,
  y.lab = NULL,
  shape.gen = 21,
  shape.env = 23,
  size.shape.gen = 2.2,
  size.shape.env = 2.2,
  size.bor.tick = 0.1,
  size.tex.lab = 12,
  size.tex.gen = 3.5,
  size.tex.env = 3.5,
  size.line = 0.5,
  size.segm.line = 0.5,
  col.bor.gen = "black",
  col.bor.env = "black",
  col.line = "black",
  col.gen = "blue",
  col.env = "forestgreen",
  col.alpha.gen = 1,
  col.alpha.env = 1,
  col.segm.gen = transparent_color(),
  col.segm.env = "forestgreen",
  highlight = NULL,
  col.highlight = "red",
  col.alpha.highlight = 1,
  size.tex.highlight = 5.5,
  size.shape.highlight = 3.2,
  leg.lab = c("Env", "Gen"),
  line.type = "solid",
  line.alpha = 0.9,
  resolution = deprecated(),
  file.type = "png",
  export = FALSE,
  file.name = NULL,
  width = 8,
  height = 7,
  color = TRUE,
  ...
)

Arguments

x	An object fitted with the functions performs_ammi(), waas(), waas_means(), or waasb().
var	The variable to plot. Defaults to var = 1 the first variable of x.
type	type of biplot to produce type = 1 The default. Produces an AMMI1 biplot (Y x PC1) to make inferences related to stability and productivity. type = 2 Produces an AMMI2 biplot (PC1 x PC2) to make inferences related to the interaction effects. Use the arguments first or second to change the default IPCA shown in the plot. type = 3 Valid for objects of class waas or waasb, produces a biplot showing the GY x WAASB. type = 4 Produces a plot with the Nominal yield x Environment PC.
first, second	The IPCA to be shown in the first (x) and second (y) axis. By default, IPCA1 is shown in the x axis and IPCA2 in the y axis. For example, use second = "PC3" to shown the IPCA3 in the y axis.
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.
polygon	Logical argument. If TRUE, a polygon is drawn when type = 2.
title	Logical values (Defaults to TRUE) to include automatically generated titles
plot_theme	The graphical theme of the plot. Default is plot_theme = theme_metan(). For more details, see ggplot2::theme().
axis.expand	Multiplication factor to expand the axis limits by to enable fitting of labels. Default is 1.1.
x.lim, y.lim	The range of x and y axes, respectively. Default is NULL (maximum and minimum values of the data set). New values can be inserted as x.lim = c(x.min, x.max) or y.lim = c(y.min, y.max).
x.breaks, y.breaks	The breaks to be plotted in the x and y axes, respectively. Defaults to waiver() (automatic breaks). New values can be inserted, for example, as x.breaks = c(0.1, 0.2, 0.3) or x.breaks = seq(0, 1, by = 0.2)
x.lab, y.lab	The label of x and y axes, respectively. Defaults to NULL, i.e., each plot has a default axis label. New values can be inserted as x.lab = 'my label'.
shape.gen, shape.env	The shape for genotypes and environments indication in the biplot. Default is 21 (circle) for genotypes and 23 (diamond) for environments. Values must be between 21-25: 21 (circle), 22 (square), 23 (diamond), 24 (up triangle), and 25 (low triangle).
size.shape.gen, size.shape.env	The size of the shapes for genotypes and environments respectively. Defaults to 2.2.
size.bor.tick	The size of tick of shape. Default is 0.1. The size of the shape will be max(size.shape.gen, size.shape.env) + size.bor.tick
size.tex.lab, size.tex.gen, size.tex.env	The size of the text for axis labels (Defaults to 12), genotypes labels, and environments labels (Defaults to 3.5).
size.line	The size of the line that indicate the means in the biplot. Default is 0.5.
size.segm.line	The size of the segment that start in the origin of the biplot and end in the scores values. Default is 0.5.
col.bor.gen, col.bor.env	The color of the shape's border for genotypes and environments, respectively.
col.line	The color of the line that indicate the means in the biplot. Default is 'gray'
col.gen, col.env	The shape color for genotypes (Defaults to 'blue') and environments ('forestgreen'). Must be length one or a vector of colors with the same length of the number of genotypes/environments.
col.alpha.gen, col.alpha.env	The alpha value for the color for genotypes and environments, respectively. Defaults to NA. Values must be between 0 (full transparency) to 1 (full color).
col.segm.gen, col.segm.env	The color of segment for genotypes (Defaults to transparent_color()) and environments (Defaults to 'forestgreen'), respectively. Valid arguments for plots with type = 1 or type = 2 graphics.
highlight	Genotypes/environments to be highlight in the plot. Defaults to NULL.
col.highlight	The color for shape/labels when a value is provided in highlight. Defaults to "red".
col.alpha.highlight	The alpha value for the color of the highlighted genotypes. Defaults to 1.
size.tex.highlight	The size of the text for the highlighted genotypes. Defaults to 5.5.
size.shape.highlight	The size of the shape for the highlighted genotypes. Defaults to 3.2.
leg.lab	The labs of legend. Default is Gen and Env.
line.type	The type of the line that indicate the means in the biplot. Default is 'solid'. Other values that can be attributed are: 'blank', no lines in the biplot, 'dashed', 'dotted', 'dotdash', 'longdash', and 'twodash'.
line.alpha	The alpha value that combine the line with the background to create the appearance of partial or full transparency. Default is 0.4. Values must be between '0' (full transparency) to '1' (full color).
resolution	deprecated
file.type	The type of file to be exported. Currently recognises the extensions eps/ps, tex, pdf, jpeg, tiff, png (default), bmp, svg and wmf (windows only).
export	Export (or not) the plot. Default is FALSE. If TRUE, calls the ggplot2::ggsave() function.
file.name	The name of the file for exportation, default is NULL, i.e. the files are automatically named.
width	The width 'inch' of the plot. Default is 8.
height	The height 'inch' of the plot. Default is 7.
color	Should type 4 plot have colors? Default to TRUE.
...	Currently not used.

Value

An object of class gg, ggplot.

Author(s)

Tiago Olivoto [e-mail]

References

Olivoto, T., A.D.C. L\'ucio, J.A.G. da silva, V.S. Marchioro, V.Q. de Souza, and E. Jost. 2019. Mean performance and stability in multi-environment trials I: Combining features of AMMI and BLUP techniques. Agron. J. 111:2949-2960. doi: 10.2134/agronj2019.03.0220

See Also

plot_eigen()

Examples

library(metan)
# AMMI model
model <- waas(data_ge,
             env = ENV,
             gen = GEN,
             rep = REP,
             resp = everything())

# GY x PC1 for variable GY (default plot)
plot_scores(model)

# PC1 x PC2 (variable HM)
#
plot_scores(model,
            polygon = TRUE,            # Draw a convex hull polygon
            var = "HM",                # or var = 2 to select variable
            highlight = c("G1", "G2"), # Highlight genotypes 2 and 3
            type = 2)                  # type of biplot

# PC3 x PC4 (variable HM)
# Change size of plot fonts and colors
# Minimal theme
plot_scores(model,
           var = "HM",
           type = 2,
           first = "PC3",
           second = "PC4",
           col.gen = "black",
           col.env = "gray",
           col.segm.env = "gray",
           size.tex.gen = 5,
           size.tex.env = 2,
           size.tex.lab = 16,
           plot_theme = theme_metan_minimal())

# WAASB index
waasb_model <- waasb(data_ge, ENV, GEN, REP, GY)

# GY x WAASB
# Highlight genotypes 2 and 8
plot_scores(waasb_model,
            type = 3,
            highlight = c("G2", "G8"))

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