plot.mtsi: Plot the multi-trait stability index

In TiagoOlivoto/WAASB: Multi Environment Trials Analysis

Plot the multi-trait stability index

Description

Makes a radar plot showing the multitrait stability index proposed by Olivoto et al. (2019)

Usage

## S3 method for class 'mtsi'
plot(
  x,
  SI = 15,
  type = "index",
  position = "fill",
  genotypes = "selected",
  title = TRUE,
  radar = TRUE,
  arrange.label = FALSE,
  x.lab = NULL,
  y.lab = NULL,
  size.point = 2.5,
  size.line = 0.7,
  size.text = 10,
  width.bar = 0.75,
  n.dodge = 1,
  check.overlap = FALSE,
  invert = FALSE,
  col.sel = "red",
  col.nonsel = "black",
  legend.position = "bottom",
  ...
)

Arguments

x	An object of class mtsi
SI	An integer (0-100). The selection intensity in percentage of the total number of genotypes.
type	The type of the plot. Defaults to "index". Use type = "contribution" to show the contribution of each factor to the MGIDI index of the selected genotypes.
position	The position adjustment when type = "contribution". Defaults to "fill", which shows relative proportions at each trait by stacking the bars and then standardizing each bar to have the same height. Use position = "stack" to plot the MGIDI index for each genotype.
genotypes	When type = "contribution" defines the genotypes to be shown in the plot. By default (genotypes = "selected" only selected genotypes are shown. Use genotypes = "all" to plot the contribution for all genotypes.)
title	Logical values (Defaults to TRUE) to include automatically generated titles.
radar	Logical argument. If true (default) a radar plot is generated after using coord_polar().
arrange.label	Logical argument. If TRUE, the labels are arranged to avoid text overlapping. This becomes useful when the number of genotypes is large, say, more than 30.
x.lab, y.lab	The labels for the axes x and y, respectively. x label is set to null when a radar plot is produced.
size.point	The size of the point in graphic. Defaults to 2.5.
size.line	The size of the line in graphic. Defaults to 0.7.
size.text	The size for the text in the plot. Defaults to 10.
width.bar	The width of the bars if type = "contribution". Defaults to 0.75.
n.dodge	The number of rows that should be used to render the x labels. This is useful for displaying labels that would otherwise overlap.
check.overlap	Silently remove overlapping labels, (recursively) prioritizing the first, last, and middle labels.
invert	Logical argument. If TRUE, rotate the plot.
col.sel	The colour for selected genotypes. Defaults to "red".
col.nonsel	The colour for nonselected genotypes. Defaults to "black".
legend.position	The position of the legend.
...	Other arguments to be passed from ggplot2::theme().

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, B.G. Sari, and M.I. Diel. 2019. Mean performance and stability in multi-environment trials II: Selection based on multiple traits. Agron. J. (in press).

Examples

library(metan)
mtsi_model <- waasb(data_ge, ENV, GEN, REP, resp = c(GY, HM))
mtsi_index <- mtsi(mtsi_model)
plot(mtsi_index)

TiagoOlivoto/WAASB documentation built on Oct. 19, 2024, 1:20 a.m.