plot {bpca} | R Documentation |
These are methods for objects of class bpca.2d
, bpca.3d
and
qbpca
.
## S3 method for class 'bpca.2d': plot(x, ref.lines=TRUE, ref.color='navy', ref.lty='dotted', var.factor=1, var.color='red3', var.lty='solid', var.pch=20, var.pos=4, var.cex=.6, var.offset=.2, obj.color='black', obj.pch=20, obj.pos=4, obj.cex=.6, obj.offset=.2, obj.names=TRUE, obj.labels=rownames(x$coord$objects), obj.identify=FALSE, ...) ## S3 method for class 'bpca.3d': plot(x, rgl.use=FALSE, ref.lines=TRUE, ref.color='navy', ref.lty=ifelse(rgl.use, NA, 'dotted'), clear3d=ifelse(rgl.use, TRUE, NULL), simple.axes=ifelse(rgl.use, TRUE, NULL), aspect=ifelse(rgl.use, c(1, 1, 1), NULL), var.factor=1, var.color='red3', var.lty=ifelse(rgl.use, NA, 'solid'), var.pch=ifelse(rgl.use, NULL, 20), var.pos=ifelse(rgl.use, 0, 4), var.cex=ifelse(rgl.use, .8, .6), var.offset=ifelse(rgl.use, NULL, .2), obj.color='black', obj.pch=ifelse(rgl.use, NULL, 20), obj.pos=ifelse(rgl.use, 0, 4), obj.cex=ifelse(rgl.use, .8, .6), obj.offset=ifelse(rgl.use, NULL, .2), obj.names=TRUE, obj.labels=rownames(x$coord$objects), obj.identify=FALSE, box=FALSE, angle=ifelse(rgl.use, NULL, 40), ...) ## S3 method for class 'qbpca': plot(x, xlab='Index', ylab='r', pch=c(1,8), col=c(4,2), ...)
x |
A bpca.2d , bpca.3d or qbpca object. |
rgl.use |
A logical value. If TRUE the 3d scatter will be done with the
rgl environment, in another way the scatterplot3d
will be used. |
ref.lines |
A logical value. If TRUE, the reference lines will be added to the biplot. |
ref.color |
Line color for reference lines. |
ref.lty |
Line type of the reference lines. |
clear3d |
A logical value. It clears (or not) a 3d biplot before making
a new one. Used only if rgl.use=TRUE . |
simple.axes |
A logical value to draw simple axes.
Used only if rgl.use=TRUE . |
aspect |
A vector of the apparent ratios of the x, y, and z axes of the
bounding box. Used only if rgl.use=TRUE . |
var.factor |
Factor of expansion/reduction of length lines of the variables. |
var.color |
A vector of colors for the variables representation. |
var.lty |
Line type for the variables. Used only if rgl.use=FALSE . |
var.pch |
A vector of plotting symbols or characters for the variables.
If too short, the values are recycled. Used only if rgl.use=FALSE . |
var.pos |
Position of labels for the variables. |
var.cex |
Character expansion for the variables. |
var.offset |
The distance (in character widths) which separates the
label from identified points of variables. Negative values are allowed.
Used only if rgl.use=FALSE . |
obj.color |
A vector of colors for the objects representation. |
obj.pch |
A vector of plotting symbols or characters for objects.
If too short, the values are recycled. Used only if rgl.use=FALSE . |
obj.pos |
Position of labels for objects. |
obj.cex |
Character expansion for objects. |
obj.offset |
The distance (in character widths) which separates the label
from identified points of objects. Negative values are allowed.
Used only if rgl.use=FALSE . |
obj.names |
A logical value to represent objects as spheres or points. |
obj.identify |
A logical value. If TRUE, it is possible, in interative way, to identify the objects with the mouse. |
obj.labels |
A vector of labels for objects. |
box |
A logical value to whether to draw a box. Used only if
rgl.use=TRUE . |
angle |
Angle between x and y axis (Attention: result depends on scaling).
For 180 < angle < 360 the returned functions xyz.convert and points3d will
not work properly. Used only if rgl.use=FALSE . |
xlab |
A label for the x axis. |
ylab |
A label for the y axis. |
pch |
A vector of plotting symbols or characters. |
col |
A vector of colors. |
... |
Other graphical parameters may also be passed as arguments to these functions. |
A biplot aims to represent both the observations and variables of a matrix of multivariate data on the same plot.
The methods plot.bpca.2d
draw a 2d biplot (PC1 and PC2 on axis x
and y, respectively). It uses the traditional graphics system.
The methods plot.bpca.3d
draw a 3d biplot (PC1, PC2 and PC3 on axis
x, y and z, respectively) in two ways:
scatterplot3d
based on
traditional graphic system. Use the parameter rgl.use=FALSE for it.rgl
: a 3D real-time rendering
device driver system for R. Use the parameter rgl.use=TRUE for it.
The method qb.pca
draws a scatterplot of the correlations observed
(in the data) and projected (under the biplot) related to the variables.
It uses the traditional graphics system.
qb.pca
is a simple (and graphical) measure of the quality of the biplot
reduction associated to the variables.
Jose Claudio Faria (joseclaudio.faria@gmail.com)
and
Clarice Garcia Borges Demetrio (clarice@esalq.usp.br)
Gabriel, K. R. (1971) The biplot graphical display of matrices with application to principal component analysis. Biometrika 58, 453-467.
Gower, J.C. and Hand, D. J. (1996) Biplots. Chapman & Hall.
Galindo, M. P. (1986) Una alternativa de representacion simultanea: HJ-Biplot. Questiio, 10(1):13-23, 1986.
Johnson, R. A. and Wichern, D. W. (1988) Applied multivariate statistical analysis. Prentice-Hall, Inc., Upper Saddle River, NJ, USA, 6 ed.
Yan, B. W. and Kang, M. S. (2003) GGE biplot analysis : a graphical tool for breeders, geneticists, and agronomists. CRC Press, New York, 288p.
## ## Example 1 ## Computing and ploting a bpca object with 'graphics' package - 2d ## library(bpca) bp <- bpca(gabriel1971) x11(w=5, h=5) plot(bp, var.factor=2) # Additional graphical parameters (nonsense) plot(bpca(gabriel1971, meth='sqrt'), main='gabriel1971 - sqrt', sub='The graphical parameters are working fine!', var.factor=2, var.cex=.6, var.col=rainbow(9), var.pch='v', obj.pch='o', obj.cex=.5, obj.col=rainbow(8), obj.pos=1, obj.offset=.5) ## ## Example 2 ## Computing and ploting a bpca object with 'scatterplot3d' package - 3d ## bp <- bpca(gabriel1971, lambda.end=3) x11(w=6, h=6) plot(bp, var.factor=3) # Additional graphical parameters (nonsense) plot(bpca(gabriel1971, lambda.end=3, meth='jk'), main='gabriel1971 - jk', sub='The graphical parameters are working fine!', var.factor=6, var.pch='+', var.cex=.6, var.col='green4', obj.pch='*', obj.cex=.8, obj.col=1:8, ref.lty='solid', ref.col='red', angle=70) ## ## Example 3 ## Computing and ploting a bpca object with 'rgl' package - 3d ## plot(bpca(gabriel1971, lambda.end=3), rgl.use=TRUE, var.factor=2) # Suggestion: Interact with the graphic with the mouse # left button: press, maintain and movement it to interactive rotation; # right button: press, maintain and movement it to interactive zoom. # Enjoy it! ## ## Example 4 ## Grouping objects with different symbols and colors - 2d and 3d ## x11(w=6, h=6) # 2d plot(bpca(iris[-5]), var.factor=.3, var.cex=.7, obj.names=FALSE, obj.cex=1.5, obj.col=c('red', 'green3', 'blue')[unclass(iris$Species)], obj.pch=c('+', '*', '-')[unclass(iris$Species)]) # 3d static plot(bpca(iris[-5], lambda.end=3), var.factor=.2, var.color=c('blue', 'red'), var.cex=1, obj.names=FALSE, obj.cex=1, obj.col=c('red', 'green3', 'blue')[unclass(iris$Species)], obj.pch=c('+', '*', '-')[unclass(iris$Species)]) # 3d dinamic plot(bpca(iris[-5], method='hj', lambda.end=3), rgl.use=TRUE, var.col='brown', var.factor=.3, var.cex=1.2, obj.names=FALSE, obj.cex=.8, obj.col=c('red', 'green3', 'orange')[unclass(iris$Species)], simple.axes=FALSE, box=TRUE) ## ## Example 5 ## Computing and ploting a bpca object with 'obj.identify=TRUE' parameter - 2d ## bp <- bpca(gabriel1971) # Normal labels if(interactive()) plot(bp, obj.names=FALSE, obj.identify=TRUE) # Alternative labels if(interactive()) plot(bp, obj.names=FALSE, obj.labels=c('toi', 'kit', 'bat', 'ele', 'wat', 'rad', 'tv', 'ref'), obj.identify=TRUE) ## ## Example 6 ## Computing and ploting a bpca object with 'obj.identify=TRUE' parameter - 3d ## bp <- bpca(gabriel1971, lambda.end=3) # Normal labels if(interactive()) plot(bp, obj.names=FALSE, obj.identify=TRUE) # Alternative labels if(interactive()) plot(bp, obj.names=FALSE, obj.labels=c('toi', 'kit', 'bat', 'ele', 'wat', 'rad', 'tv', 'ref'), obj.identify=TRUE)