plotgenes {made4} | R Documentation |
Graph xy plot of variables but only label variables at ends of X and Y axes. Useful for graphing genes coordinates ($co) resulting from PCA or COA of microarray data.
plotgenes(coord, nlab = 10, axis1 = 1, axis2 = 2, genelabels = row.names(coord), boxes = TRUE, colpoints = "black", ...)
coord |
a data.frame or matrix or object from ord
bga or cia analysis with at least two
columns, containing x, y coordinates to be plotted. |
nlab |
Numeric. An integer indicating the number of variables at ends of axes to be labelled. |
axis1 |
An integer, the column number for the x-axis. Default is 1, so axis 1 is dudivar[,1]. |
axis2 |
An integer, the column number for the y-axis. Default is 2, so axis 2 is dudivar[,2]. |
genelabels |
A vector of gene (variable) labels. Default is row.names(coord) |
boxes |
A logical, indicating whether a box should be plotted surrounding
each variable label. The default is TRUE . |
colpoints |
The colour of the points on the plot. The default is "black". |
... |
further arguments passed to or from other method. |
plotgenes
calls the function genes
which return an index of the "top"
variables at the ends of the x and y axes.
If you wish to return a table or list of the top genes at
the end of an axis, use the function topgenes
.
An xy plot
plotgenes
plots variables using s.var
, which is a modified version
of s.label
.
Aedin Culhane
data(khan) if (require(ade4, quiet = TRUE)) { khan.ord<-ord(khan$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)