between.graph: Plot 1D graph of results from between group analysis
In SamGG/made4: Multivariate analysis of microarray data using ADE4

Description Usage Arguments Details Author(s) References See Also Examples

Plots a 1D graph, of results of between group analysis similar to that in Culhane et al., 2002.

1	between.graph(x, ax = 1, cols = NULL, hor = TRUE, scaled=TRUE, centnames=NULL, varnames=NULL, ...)

`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.
`scaled`	Logical, indicating whether the coordinates in the graph should be scaled to fit optimally in plot. Default is TRUE
`centnames`	A vector of variables labels. Default is NULL, if NULL the row names of the centroid \$li coordinates will be used.
`varnames`	A vector of variables labels. Default is NULL, if NULL the row names of the variable \$ls coordinates will be used.
`...`	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.

graph1D

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, cex=0.5, col=c("green","blue", "red", "yellow"))
between.graph(khan.bga, ax=2,  hor=FALSE, col=c("green","blue", "red", "yellow"))