axes: Format aesthetics for the biplot axes

In biplotEZ: EZ-to-Use Biplots

Format aesthetics for the biplot axes

Description

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()

biplotEZ documentation built on April 4, 2025, 2:20 a.m.