plot.waasb: Several types of residual plots

In metan: Multi Environment Trials Analysis

Several types of residual plots

Description

Residual plots for a output model of class waas and waasb. Six types of plots are produced: (1) Residuals vs fitted, (2) normal Q-Q plot for the residuals, (3) scale-location plot (standardized residuals vs Fitted Values), (4) standardized residuals vs Factor-levels, (5) Histogram of raw residuals and (6) standardized residuals vs observation order. For a waasb object, normal Q-Q plot for random effects may also be obtained declaring type = 're'

Usage

## S3 method for class 'waasb'
plot(
  x,
  var = 1,
  type = "res",
  position = "fill",
  trait.levels = NULL,
  percent = TRUE,
  percent.digits = 2,
  size.text.percent = 3.5,
  rotate = FALSE,
  conf = 0.95,
  out = "print",
  n.dodge = 1,
  check.overlap = FALSE,
  labels = FALSE,
  plot_theme = theme_metan(),
  alpha = 0.2,
  fill.hist = "gray",
  col.hist = "black",
  col.point = "black",
  col.line = "red",
  col.lab.out = "red",
  size.line = 0.7,
  size.text = 10,
  width.bar = 0.75,
  size.lab.out = 2.5,
  size.tex.lab = 10,
  size.shape = 1.5,
  bins = 30,
  which = c(1:4),
  ncol = NULL,
  nrow = NULL,
  ...
)

Arguments

x	An object of class waasb.
var	The variable to plot. Defaults to var = 1 the first variable of x.
type	One of the "res" to plot the model residuals (default), type = 're' to plot normal Q-Q plots for the random effects, or "vcomp" to create a bar plot with the variance components.
position	The position adjustment when type = "vcomp". 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 phenotypic variance for each trait.
trait.levels	By default, variables are ordered in the x-axis by alphabetic order. If a plot with two variables (eg., "GY" and "PH") "PH" should appers before "GY", one can use a comma-separated vector of variable names to relevel the variable's position in the plot (eg., trait.levels = "PH, GY").
percent	If TRUE (default) shows the y-axis as percent and the percentage values within each bar.
percent.digits	The significant figures for the percentage values. Defaults to 2.
size.text.percent	The size of the text for the percentage values. Defaults to 3.5.
rotate	Logical argument. If rotate = TRUE the plot is rotated, i.e., traits in y axis and value in the x axis.
conf	Level of confidence interval to use in the Q-Q plot (0.95 by default).
out	How the output is returned. Must be one of the 'print' (default) or 'return'.
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.
labels	Logical argument. If TRUE labels the points outside confidence interval limits.
plot_theme	The graphical theme of the plot. Default is plot_theme = theme_metan(). For more details, see ggplot2::theme().
alpha	The transparency of confidence band in the Q-Q plot. Must be a number between 0 (opaque) and 1 (full transparency).
fill.hist	The color to fill the histogram. Default is 'gray'.
col.hist	The color of the border of the the histogram. Default is 'black'.
col.point	The color of the points in the graphic. Default is 'black'.
col.line	The color of the lines in the graphic. Default is 'red'.
col.lab.out	The color of the labels for the 'outlying' points.
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".
size.lab.out	The size of the labels for the 'outlying' points.
size.tex.lab	The size of the text in axis text and labels.
size.shape	The size of the shape in the plots.
bins	The number of bins to use in the histogram. Default is 30.
which	Which graphics should be plotted. Default is which = c(1:4) that means that the first four graphics will be plotted.
ncol, nrow	The number of columns and rows of the plot pannel. Defaults to NULL
...	Additional arguments passed on to the function patchwork::wrap_plots().

Author(s)

Tiago Olivoto [e-mail]

Examples

library(metan)
x <- gamem_met(data_ge,
               gen = GEN,
               env = ENV,
               rep = REP,
               resp = everything())
plot(x)

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