plot.mtmps {metan}

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 'mtmps'
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 computed with mps().

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 MTMPS 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)
model <-
mps(data_ge,
    env = ENV,
    gen = GEN,
    rep = REP,
    resp = everything())
selection <- mtmps(model)
plot(selection)