coloredBiplot {compositions}

A biplot providing somewhat easier access to details of the plot.

Description

This function generates a simple biplot out of various sources and allows to give color and symbol to the x-objects individually.

Usage

## Default S3 method:
coloredBiplot(x, y, var.axes = TRUE, col, 
         cex = rep(par("cex"), 2), xlabs = NULL, ylabs = NULL, expand=1, 
         xlim = NULL, ylim = NULL, arrow.len = 0.1, main = NULL, sub = NULL, 
         xlab = NULL, ylab = NULL, xlabs.col = NULL, xlabs.bg = NULL, 
         xlabs.pc=NULL, ...)
## S3 method for class 'princomp'
coloredBiplot(x, choices = 1:2, scale = 1, 
         pc.biplot=FALSE, ...)
## S3 method for class 'prcomp'
coloredBiplot(x, choices = 1:2, scale = 1, 
         pc.biplot=FALSE, ...)
         

Arguments

x

a representation of the the co-information to be plotted, given by a result of princomp or prcomp; or the first set of coordinates to be plotted

y

optional, the second set of coordinates to be potted

var.axes

if 'TRUE' the second set of points have arrows representing them as (unscaled) axes

col

one color (to be used for the y set) or a vector of two colors (to be used for x and y sets respectively, if xlabs.col is NULL)

cex

the usual cex parameter for plotting; can be a length-2 vector to format differently x and y labels/symbols

xlabs

names to write for the points of the first set

ylabs

names to write for the points of the second set

expand

expansion factor to apply when plotting the second set of points relative to the first. This can be used to tweak the scaling of the two sets to a physically comparable scale

xlim

horizontal axis limits

ylim

vertical axis limits

arrow.len

length of the arrow heads on the axes plotted if 'var.axes' is true. The arrow head can be suppressed by 'arrow.len=0'

main

main title

sub

subtitle

xlab

horizontal axis title

ylab

vertical axis title

xlabs.col

the color(s) to draw the points of the first set, if xlabs is null

xlabs.bg

the filling color(s) to draw the points of the first set, if xlabs is null and xlabs.pc is between 21 and 25.

xlabs.pc

the plotting character(s) for the first set, if xlabs is null

scale

the way to distribute the singular values on the right or left singular vectors for princomp and prcomp objects (see biplot)

choices

the components to be plotted (see biplot)

pc.biplot

should be scaled by sqrt(nrow(X))? (see biplot)

...

further parameters for plot

Details

The functions is provided for convenience.

Value

The function is called only for the side effect of plotting. It is a modification of the standard R routine 'biplot'.

Author(s)

Raimon Tolosana-Delgado, K.Gerald v.d. Boogaart http://www.stat.boogaart.de

See Also

biplot, plot.acomp

Examples

data(SimulatedAmounts)
coloredBiplot(x=princomp(acomp(sa.outliers5)),pc.biplot=FALSE,
          xlabs.pc=c(1,2,3), xlabs.col=2:4, col="black")