between.graph {made4} | R Documentation

## Plot 1D graph of results from between group analysis

### Description

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

### Usage

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

### Arguments

`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

### Details

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`.

### Author(s)

Aedin Culhane

### References

Culhane AC, et al., 2002 Between-group analysis of microarray data. Bioinformatics. 18(12):1600-8.

### See Also

`graph1D`

### Examples

    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"))

[Package made4 version 1.66.0 Index]