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 |

`coord` |
a |

`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 |

`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

1 2 3 4 5 6 7 8 9 | ```
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)
``` |

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