Plot the BLUPs for genotypes

Plot the predicted BLUP of the genotypes.

Usage

plot_blup(
  x,
  var = 1,
  which = "gen",
  ncol = NULL,
  nrow = NULL,
  prob = 0.05,
  export = FALSE,
  file.type = "pdf",
  file.name = NULL,
  plot_theme = theme_metan(),
  width = 6,
  height = 6,
  err.bar = TRUE,
  size.err.bar = 0.5,
  size.shape = 3.5,
  size.tex.lab = 12,
  height.err.bar = 0.3,
  x.lim = NULL,
  x.breaks = waiver(),
  col.shape = c("blue", "red"),
  y.lab = "Genotypes",
  x.lab = NULL,
  n.dodge = 1,
  check.overlap = FALSE,
  panel.spacing = 0.15,
  resolution = 300,
  ...
)

Arguments

x: The waasb object
var: The variable to plot. Defaults to var = 1 the first variable of x.
which: Which plot to shown. If which = "gen" (default) plots the BLUPs for genotypes. To create a plot showing the BLUPs for genotype-environment combinations, use which = "ge".
ncol, nrow: The number of columns and rows, respectively, to be shown in the plot when which = "ge".
prob: The probability error for constructing confidence interval.
export: Export (or not) the plot. Default is TRUE.
file.type: If export = TRUE, define the type of file to be exported. Default is pdf, Graphic can also be exported in *.tiff format by declaring file.type = "tiff".
file.name: The name of the file for exportation, default is NULL, i.e. the files are automatically named.
plot_theme: The graphical theme of the plot. Default is plot_theme = theme_metan(). For more details, see ggplot2::theme().
width: The width "inch" of the plot. Default is 6.
height: The height "inch" of the plot. Default is 6.
err.bar: Logical value to indicate if an error bar is shown. Defaults to TRUE.
size.err.bar: The size of the error bar for the plot. Default is 0.5.
size.shape: The size of the shape (both for genotypes and environments). Default is 3.5.
size.tex.lab: The size of the text in axis text and labels.
height.err.bar: The height for error bar. Default is 0.3.
x.lim: The range of x-axis. Default is NULL (maximum and minimum values of the data set). New arguments can be inserted as x.lim = c(x.min, x.max).
x.breaks: The breaks to be plotted in the x-axis. Default is authomatic breaks. New arguments can be inserted as x.breaks = c(breaks)
col.shape: A vector of length 2 that contains the color of shapes for genotypes above and below of the mean, respectively. Default is c("blue", "red").
y.lab: The label of the y-axis in the plot. Default is "Genotypes".
x.lab: The label of the x-axis in the plot. Default is NULL, i.e., the name of the selected variable.
n.dodge: The number of rows that should be used to render the Y 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.
panel.spacing: Defines the spacing between panels when which = "ge".
resolution: The resolution of the plot. Parameter valid if file.type = "tiff" is used. Default is 300 (300 dpi)
...: Currently not used.

Value

An object of class gg, ggplot.

Author

Tiago Olivoto tiagoolivoto@gmail.com

Examples

# \donttest{
library(metan)
BLUP <- waasb(data_ge2,
              resp = PH,
              gen = GEN,
              env = ENV,
              rep = REP)
#> Evaluating trait PH |============================================| 100% 00:00:00 

#> Method: REML/BLUP
#> Random effects: GEN, GEN:ENV
#> Fixed effects: ENV, REP(ENV)
#> Denominador DF: Satterthwaite's method
#> ---------------------------------------------------------------------------
#> P-values for Likelihood Ratio Test of the analyzed traits
#> ---------------------------------------------------------------------------
#>     model       PH
#>  COMPLETE       NA
#>       GEN 9.39e-01
#>   GEN:ENV 1.09e-13
#> ---------------------------------------------------------------------------
#> All variables with significant (p < 0.05) genotype-vs-environment interaction
plot_blup(BLUP)

plot_blup(BLUP, which = "ge")


# }

Usage

Arguments

Value

See also

Author

Examples