| between.graph {made4} | R Documentation |
Plots a 1D graph, of results of between group analysis similar to that in Culhane et al., 2002.
between.graph(x, ax=1, cols=NULL, hor=TRUE, ...)
x |
Object of the class bga resulting from a bga analysis.
|
ax |
Numeric. The column number of principal component ($ls and $li) to be used. Default is 1. This is the first component of the analysis. |
cols |
Vector of colours. By default colours are obtained
using getcol |
hor |
Logical, indicating whether the graph should be plotted horizontally or vertically. The default is a horizontal plot. |
... |
further arguments passed to or from other methods |
This will produce a figure similar to Figure 1 in the paper by Culhane et al., 2002.
between.graph requires both samples and centroid co-ordinates ($ls, $li) which are passed
to it via an object of class bga. If cases are to be coloured by class, it also requires
a $fac factor which is also passed to it via an object of class bga.
To plot a 1D graph from other multivariate analysis such as PCA (dudi.pca),
COA (dudi.coa), or coinertia analysis. Please
use graph1D.
Aedin Culhane
Culhane AC, et al., 2002 Between-group analysis of microarray data. Bioinformatics. 18(12):1600-8.
data(khan)
if (require(ade4, quiet = TRUE)) {
khan.bga<-bga(khan$train, khan$train.classes)
}
between.graph(khan.bga)
between.graph(khan.bga, ax=2, lwd=3, hor=FALSE, cex=0.5, col=c("green",
"blue", "red", "yellow"))