calibrate {calibrate}R Documentation

Calibration of Biplot and Scatterplot Axis

Description

Routine for the calibration of any axis (variable vector) in a biplot or a scatterplot

Usage

calibrate(g,y,tm,Fr,tmlab=tm,tl=0.05,dt=TRUE,dp=FALSE,lm=TRUE,
verb=TRUE,axislab="",reverse=FALSE,shift=0,alpha=NULL,labpos=1,
weights=diag(rep(1,length(y))),axiscol="blue",cex.axislab=0.75,
graphics=TRUE,where=3,laboffset=c(0,0),m=matrix(c(0,0),nrow=1),
markerpos=3,showlabel=TRUE,lwd=1)

Arguments

g the vector to be calibrated (2 x 1).
y the data vector corresponding to g, appropriately centred and/or standardized.
tm the vector of tick marks, appropiately centred and/or scaled.
Fr the coordinates of the rows markers in the biplot.
tmlab a list or vector of tick mark labels.
tl the tick length. By default, the tick markers have length 0.05.
dt draw ticks. By default, ticks markers are drawn. Set dt=F in order to compute calibration results without actually drawing the calibrated scale.
dp drop perpendiculars. With dp=T perpendicular lines will be drawn from the row markers specified by Fr onto the calibrated axis. This is a graphical aid to read off the values in the corresponding scale.
lm label markers. By default, all tick marks are labelled. Setting lm=F turns off the labelling of the tick marks. This allows for creating tick marks without labels. It is particularly useful for creating finer scales of tickmarks without labels.
verb verbose parameter (F=be quiet, T=show results).
axislab a label for the calibrated axis.
reverse puts the tick marks and tick mark labels on the other side of the axis.
shift a scalar that shifts the calibrated axis by a fixed distance.
alpha a value for the calibration factor. This parameter should only be specified if a calibration is required that is different from the one that is optimal for data recovery.
labpos position of the label for the calibrated axis (1,2,3 or 4).
laboffset offset vector for the axis label. If specified, shifts the label by the specified amounts with respect to the current position.
weights a matrix of weights (optional).
axiscol color of the calibrated axis.
cex.axislab character expansion factor for axis label and tick mark labels.
graphics do graphics or not (F=no graphical output, T=draws calibrated scale).
where label placement (1=beginning,2=middle,3=end).
m vector of means.
markerpos position specifier for the tick mark labels (1,2,3 or 4).
showlabel show axis label in graph (T) or not (F).
lwd line with for the calibrated axis

Details

This program calibrates variable vectors in biplots and scatterplots, by drawing tick marks along a given the vector and labelling the tick marks with specified values. The optimal calibration is found by (generalized) least squares. Non-optimal calibrations are possible by specifying a calibration factor (alpha).

Value

Returns a list with calibration results

useralpha calibration factor specified by the user
optalpha optimal calibration factor
lengthoneunit length in the plot of one unit in the scale of the calibrated variable
gof goodness of fit (as in regression)
gos goodness of scale
M coordinates of the tick markers
ang angle in degrees of the biplot axis with the positive x-axis
yt fitted values for the variable according to the calibration
e errors according to the calibration
Fpr coordinates of the projections of the row markers onto the calibrated axis
Mn coordinates of the tick marker end points

Author(s)

Jan Graffelman jan.graffelman@upc.edu

References

Gower, J.C. and Hand, D.J., (1996) Biplots. Chapman & Hall, London

Graffelman, J. and van Eeuwijk, F.A. (2005) Calibration of multivariate scatter plots for exploratory analysis of relations within and between sets of variables in genomic research Biometrical Journal, 47(6) pp. 863-879.

Graffelman, J. (2006) A guide to biplot calibration.

See Also

biplot

Examples

x <- rnorm(20,1)
y <- rnorm(20,1)
x <- x - mean(x)
y <- y - mean(y)
z <- x + y
b <- c(1,1)
plot(x,y,asp=1,pch=19)
tm<-seq(-2,2,by=0.5)
Calibrate.z <- calibrate(b,z,tm,cbind(x,y),axislab="Z",graphics=TRUE)

[Package calibrate version 1.5 Index]