axes {biplotEZ}

Aesthetics for biplot axes

Description

This function allows formatting changes to 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

refers to the column names of bp to specify which axes to label.

which

integer-valued vector specifying which biplot axes are shown in a biplot. By default all p biplot axes are shown.

col

vector of size p specifying colours of labels of biplot axes. The default is grey(0.7).

lwd

axis line width, with default 1.

lty

axis line type, with default 1.

label.dir

One of "Orthog" (default), "Hor" or "Paral" specifying titles of axes to appear orthogonal to the side of the figure; always horizontally or always parallel to the side of the figure.

label.col

axis label colour, with default, col.

label.cex

axis label expansion, with default 0.75.

label.line

axis label written on which margin line, with default 0.1.

label.offset

A four-component numeric vector controlling the distance a biplot axis title is printed from the side of the figure. Sides are numbered 1 to 4 according to R conventions clockwise starting from the bottom horizontal side. Default is rep(0,4)

ticks

integer-valued vector of size equal to the number of biplot axes to control the number of tickmarks on each individual biplot axis. Default is 5 for each axis.

tick.col

tick mark colour, with default col.

tick.size

positive integer-valued vector with specifying tick mark sizes, with default 1.

tick.label

logical, whether axes should be labelled or not, with default TRUE.

tick.label.side

character vector specifying position of the tick label "below" or "above" the axis.

tick.label.col

tick mark label colour, with default tick.col.

tick.label.cex

tick mark label expansion, with default 0.6.

predict.col

predicted samples colour, with default col.

predict.lwd

predicted samples line width, with default lwd.

predict.lty

predicted samples line type, with default lty.

ax.names

vector of size p containing user defined names for the variables.

orthogx

numeric vector of size p specifying the x-coordinate of the parallel transformation of each axis. Defaults to zero for each axis. Only used when the dimension of the biplot is two.

orthogy

numeric vector of size p specifying the y-coordinate of the parallel transformation of each axis. Defaults to zero for each axis. Only used when the dimension of the biplot is two.

vectors

logical, whether calibrated axes should be displayed on the biplot

unit.circle

logical, whether a unit circle should be displayed on the biplot

Value

A list with the following components is available:

which

vector of the columns displayed as axes.

col

vector of axis colours.

lwd

vector of axis line widths.

lty

vector of axis line types.

label.dir

direction of the axis labels.

label.col

vector of axis label colours.

label.cex

vector of axis labels expansions.

label.line

vector of axis label margin lines from axes.

ticks

vector representing the number of tick marks per axis.

tick.col

vector of tick mark colours.

tick.size

vector of tick mark sizes.

tick.label

vector of logical values indicating whether axes are labelled.

tick.label.side

vector specifying position of the tick label "below" or "above" the axis.

tick.label.col

vector of tick mark label colours.

tick.label.cex

vector of tick mark label expansions.

predict.col

vector of colours for the predicted samples.

predict.lty

vector of line types for the predicted samples.

predict.lwd

vector of line widths for the predicted samples.

names

vector of variable names defined by the user.

orthogx

vector of the horisontal translations for each axis.

orthogy

vector of the vertical translations for each axis.

calibrated.axis

whether to plot calibrated axis

Examples

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