plot_blup: Plot the BLUPs for genotypes

In TiagoOlivoto/metan: Multi Environment Trials Analysis

Plot the BLUPs for genotypes

Description

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(s)

Tiago Olivoto [e-mail]

See Also

plot_scores(), plot_waasby()

Examples

library(metan)
BLUP <- waasb(data_ge2,
              resp = PH,
              gen = GEN,
              env = ENV,
              rep = REP)
plot_blup(BLUP)
plot_blup(BLUP, which = "ge")

TiagoOlivoto/metan documentation built on Oct. 16, 2024, 8:22 p.m.