plotgenes {made4} | R Documentation

## Graph xy plot of variable (gene) projections from PCA or COA. Only label variables at ends of axes

### Description

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.

### Usage

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

### Arguments

`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.

### Details

`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`.

### Value

An xy plot

### Note

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

### Author(s)

Aedin Culhane

### See Also

See Also as `s.var` and `s.label`

### Examples

    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)

[Package made4 version 1.66.0 Index]