plot.can_cor function

Plots an object of class can_cor

Graphs of the Canonical Correlation Analysis

## S3 method for class 'can_cor'
plot(
  x,
  type = 1,
  plot_theme = theme_metan(),
  size.tex.lab = 12,
  size.tex.pa = 3.5,
  x.lab = NULL,
  x.lim = NULL,
  x.breaks = waiver(),
  y.lab = NULL,
  y.lim = NULL,
  y.breaks = waiver(),
  axis.expand = 1.1,
  shape = 21,
  col.shape = "orange",
  col.alpha = 0.9,
  size.shape = 3.5,
  size.bor.tick = 0.3,
  labels = FALSE,
  main = NULL,
  ...
)

Arguments

• x: The waasb object

• type: The type of the plot. Defaults to type = 1 (Scree-plot of the correlations of the canonical loadings). Use type = 2, to produce a plot with the scores of the variables in the first group, type = 3 to produce a plot with the scores of the variables in the second group, or type = 4 to produce a circle of correlations.

• plot_theme: The graphical theme of the plot. Default is plot_theme = theme_metan(). For more details,see ggplot2::theme().

• size.tex.lab: The size of the text in axis text and labels.

• size.tex.pa: The size of the text of the plot area. Default is 3.5.

• x.lab: The label of x-axis. Each plot has a default value. New arguments can be inserted as x.lab = 'my label'.

• 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)

• y.lab: The label of y-axis. Each plot has a default value. New arguments can be inserted as y.lab = 'my label'.

• y.lim: The range of y-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.

• axis.expand: Multiplication factor to expand the axis limits by to enable fitting of labels. Default is 1.1.

• shape: The shape of points in the plot. Default is 21 (circle). Values must be between 21-25: 21 (circle), 22

  (square), 23 (diamond), 24 (up triangle), and 25 (low triangle).

• col.shape: A vector of length 2 that contains the color of shapes for genotypes above and below of the mean, respectively. Defaults to "orange". c("blue", "red").

• col.alpha: The alpha value for the color. Default is 0.9. Values must be between 0 (full transparency) to 1 (full color).

• size.shape: The size of the shape in the plot. Default is 3.5.

• 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

• labels: Logical arguments. If TRUE then the points in the plot will have labels.

• main: The title of the plot. Defaults to NULL, in which each plot will have a default title. Use a string text to create an own title or set to main = FALSE to omit the plot title.

• ...: Currently not used.

Returns

An object of class gg, ggplot.

Examples

library(metan)
cc1 = can_corr(data_ge2,
               FG = c(PH, EH, EP),
               SG = c(EL, ED, CL, CD, CW, KW, NR))
plot(cc1, 2)

cc2 <-
data_ge2 %>%
mean_by(GEN) %>%
column_to_rownames("GEN") %>%
can_corr(FG = c(PH, EH, EP),
               SG = c(EL, ED, CL, CD, CW, KW, NR))
plot(cc2, 2, labels = TRUE)

Author(s)

Tiago Olivoto tiagoolivoto@gmail.com