This function plot the scores for genotypes obtained in the factor analysis to interpret the stability
Usage
# S3 method for 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 ofx
.- plot_theme
The graphical theme of the plot. Default is
plot_theme = theme_metan()
. For more details, seeggplot2::theme()
.- x.lim
The range of x-axis. Default is
NULL
(maximum and minimum values of the data set). New arguments can be inserted asx.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 asx.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 thanx.lim
can be used.- y.breaks
The breaks to be plotted in the x-axis. Default is
authomatic breaks
. The same arguments thanx.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 between21-25
:21
(circle),22
(square),23
(diamond),24
(up triangle), and25
(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 between0
(full transparency) to1
(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 besize.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..
Author
Tiago Olivoto tiagoolivoto@gmail.com