Format aesthetics for the biplot axes

This function allows the user to format the aesthetics for the biplot axes.

Usage

axes(bp, X.names=colnames(bp$X), which = 1:bp$p, col = grey(0.7), lwd = 1, lty = 1,
label.dir = "Orthog", label.col = col, label.cex = 0.75, label.line = 0.1, 
label.offset=rep(0,4), ticks = 5, tick.col = col, tick.size = 1, tick.label = TRUE, 
tick.label.side = "below", tick.label.col = tick.col, tick.label.cex = 0.6,
predict.col = col, predict.lwd = lwd, predict.lty = lty, ax.names = X.names,
orthogx = 0, orthogy = 0, vectors = FALSE, unit.circle=FALSE)

Arguments

bp

an object of class biplot.

X.names

a vector of column names of bp to specify which axes should be labelled.

which

a vector containing the columns or variables for which the axes should be displayed, with default 1:p.

col

the colour(s) for the axes, with default grey(0.7). Alternatively, provide a vector of colours corresponding to X.names.

lwd

the line width(s) for the axes, with default 1.

lty

the line type(s) for the axes, with default 1.

label.dir

a character string indicating the placement of the axis titles to the side of the figure. One of "Orthog" for axis titles to appear orthogonal to the side of the figure (default) , "Hor" for axis titles to appear horizontally or "Paral" for axis titles to appear parallel to the side of the figure.

label.col

the colour(s) for the axis labels, with default, col.

label.cex

the label expansion for the axis labels, with default 0.75.

label.line

the distance of the axis title from the side of the figure, with default 0.1.

label.offset

a four-component numeric vector controlling the distances axis titles are displayed from the side of the figure, with default rep(0,4). Sides are numbered 1 to 4 according to R conventions.

ticks

an integer-valued vector indicating the number of tickmarks for each axis, with default 5 for each axis.

tick.col

the colour(s) for the tick marks, with default col.

tick.size

a vector specifying the sizes of tick marks for each axis, with default 1 for each .

tick.label

a logical value indicating whether the axes should be labelled, with default TRUE.

tick.label.side

a character string indicating the position of the tick label. One of "below" for the label to appear below the tick mark (default) or "above" for the label to appear above the tick mark.

tick.label.col

the colour(s) for the tick mark labels, with default tick.col.

tick.label.cex

the label expansion for the tick mark labels, with default 0.6.

predict.col

the colour(s) for the predicted samples, with default col.

predict.lwd

the line width(s) for the predicted samples, with default lwd.

predict.lty

the line type(s) for the predicted samples, with default lty.

ax.names

a vector of size p containing user defined titles for the axes.

orthogx

a numeric vector of size p specifying the x-coordinate of the parallel transformation of each axis, with default 0 for each axis. This is only used when dim.biplot = 2.

orthogy

a numeric vector of size p specifying the y-coordinate of the parallel transformation of each axis, with default 0 for each axis. This is only used when dim.biplot = 2.

vectors

a logical value indicating whether vector representation (calibrated axes) should be displayed on the biplot. This is only used when a PCA biplot is produced.

unit.circle

a logical value indicating whether a unit circle should be displayed on the biplot.

Value

The object of class biplot will be appended with a list called axes containing the following elements:

which

a vector containing the columns for which the axes are displayed.

col

the colour(s) of the axes.

lwd

the line width(s) of the axes.

lty

the line type(s) of the axes.

label.dir

the placement of the axis titles to the side of the figure.

label.col

the colour(s) of the axis titles.

label.cex

the label expansion(s) of the axis titles.

label.line

the distance(s) of the axis titles from the side of the figure.

ticks

the number of tick marks per axis.

tick.col

the colour(s) of the tick marks.

tick.size

the size(s) of the tick marks.

tick.label

logical value(s) indicating whether axes are labelled.

tick.label.side

the position of the tick mark labels.

tick.label.col

the colour(s) of the tick mark labels.

tick.label.cex

the expansion(s) of the tick mark labels.

predict.col

the colour(s) of the predicted samples.

predict.lty

the line type(s) of the predicted samples.

predict.lwd

the line width(s) of the predicted samples.

names

the user defined axis titles.

orthogx

the horizontal translations for each axis.

orthogy

the vertical translations for each axis.

vectors

a logical value indicating whether calibrated axes are plotted.

See also

biplot()

Examples

biplot(iris[,1:4]) |> PCA() |> axes(col="purple") |> plot()

biplot(iris[,1:4]) |> PCA() |> samples(col="purple",pch=15) |> axes() |> plot()