plotgenes: Graph xy plot of variable (gene) projections from PCA or COA....
In SamGG/made4: Multivariate analysis of microarray data using ADE4

Description Usage Arguments Details Value Note Author(s) See Also Examples

Graph xy plot of variables but only label variables at ends of X and Y axes. Useful for graphing genes coordinates (\$co) resulting from PCA or COA of microarray data.

1 2	plotgenes(coord, nlab = 10, axis1 = 1, axis2 = 2, genelabels = row.names(coord), boxes = TRUE, colpoints = "black", ...)

`coord`	a `data.frame` or `matrix` or object from `ord` `bga` or `cia` analysis with at least two columns, containing x, y coordinates to be plotted.
`nlab`	Numeric. An integer indicating the number of variables at ends of axes to be labelled.
`axis1`	An integer, the column number for the x-axis. Default is 1, so axis 1 is dudivar[,1].
`axis2`	An integer, the column number for the y-axis. Default is 2, so axis 2 is dudivar[,2].
`genelabels`	A vector of gene (variable) labels. Default is row.names(coord)
`boxes`	A logical, indicating whether a box should be plotted surrounding each variable label. The default is `TRUE`.
`colpoints`	The colour of the points on the plot. The default is "black".
`...`	further arguments passed to or from other method.

plotgenes calls the function genes which return an index of the "top" variables at the ends of the x and y axes.

If you wish to return a table or list of the top genes at the end of an axis, use the function topgenes.

An xy plot

plotgenes plots variables using s.var, which is a modified version of s.label.

Aedin Culhane

See Also as s.var and s.label

data(khan)
if (require(ade4, quiet = TRUE)) {
khan.ord<-ord(khan$train, classvec=khan$train.classes) 
}
par(mfrow=c(2,2))
#s.var(khan.ord$co, col=as.numeric(khan$train.classes), clabel=0.8)
plotgenes(khan.ord, colpoints="red")
plotgenes(khan.ord, colpoints="red", genelabels=khan$annotation$Symbol)
plotgenes(khan.ord, colpoints="gray", genelabels=khan$annotation$Symbol,boxes=FALSE)