Plot the ge_factanal model

This function plot the scores for genotypes obtained in the factor analysis to interpret the stability

Usage

# S3 method for class 'ge_factanal'
plot(
  x,
  var = 1,
  plot_theme = theme_metan(),
  x.lim = NULL,
  x.breaks = waiver(),
  x.lab = NULL,
  y.lim = NULL,
  y.breaks = waiver(),
  y.lab = NULL,
  shape = 21,
  col.shape = "gray30",
  col.alpha = 1,
  size.shape = 2.2,
  size.bor.tick = 0.3,
  size.tex.lab = 12,
  size.tex.pa = 3.5,
  force.repel = 1,
  line.type = "dashed",
  line.alpha = 1,
  col.line = "black",
  size.line = 0.5,
  ...
)

Arguments

x: An object of class ge_factanal
var: The variable to plot. Defaults to var = 1 the first variable of x.
plot_theme: The graphical theme of the plot. Default is plot_theme = theme_metan(). For more details, see ggplot2::theme().
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)
x.lab: The label of x-axis. Each plot has a default value. New arguments can be inserted as x.lab = "my label".
y.lim: The range of x-axis. Default is NULL. The same arguments than x.lim can be used.
y.breaks: The breaks to be plotted in the x-axis. Default is authomatic breaks. The same arguments than x.breaks can be used.
y.lab: The label of y-axis. Each plot has a default value. New arguments can be inserted as y.lab = "my label".
shape: The shape for genotype indication in the plot. Default is 1 (circle). Values between 21-25: 21 (circle), 22 (square), 23 (diamond), 24 (up triangle), and 25 (low triangle) allows a color for fill the shape.
col.shape: The shape color for genotypes. Must be one value or a vector of colors with the same length of the number of genotypes. Default is "gray30". Other values can be attributed. For example, transparent_color(), will make a plot with only an outline around the shape area.
col.alpha: The alpha value for the color. Default is 1. Values must be between 0 (full transparency) to 1 (full color).
size.shape: The size of the shape (both for genotypes and environments). Default is 2.2.
size.bor.tick: The size of tick of shape. Default is 0.3. The size of the shape will be size.shape + size.bor.tick
size.tex.lab: The size of the text in the axes text and labels. Default is 12.
size.tex.pa: The size of the text of the plot area. Default is 3.5.
force.repel: Force of repulsion between overlapping text labels. Defaults to 1.
line.type: The type of the line that indicate the means in the biplot. Default is "solid". Other values that can be attributed are: "blank", no lines in the biplot, "dashed", "dotted", "dotdash", "longdash", and "twodash".
line.alpha: The alpha value that combine the line with the background to create the appearance of partial or full transparency. Default is 0.4. Values must be between "0" (full transparency) to "1" (full color).
col.line: The color of the line that indicate the means in the biplot. Default is "gray"
size.line: The size of the line that indicate the means in the biplot. Default is 0.5.
...: Currently not used..

Value

An object of class gg, ggplot.

Author

Tiago Olivoto tiagoolivoto@gmail.com

Examples

# \donttest{
library(metan)
library(ggplot2)
model = ge_factanal(data_ge2,
                    env = ENV,
                    gen = GEN,
                    rep = REP,
                    resp = PH)
plot(model)


plot(model,
     size.shape = 3,
     force.repel = 10,
     col.shape = "orange",
     col.line = "red")

# }

Usage

Arguments

Value

See also

Author

Examples