plotarrays {made4} | R Documentation |
Graph xy plot of variables using s.var, s.groups or s.match.col. Useful for visualising array coordinates ($li) resulting from ord, bga or cia of microarray data.
plotarrays(coord, axes1 = 1, axes2 = 2, arraylabels = NULL, classvec=NULL, graph = "auto", ...)
coord |
a data.frame or matrix or object from ord
bga or cia analysis with at least two
columns, containing x, y coordinates to be plotted |
axes1 |
An integer, the column number for the x-axis. Default is 1, so axes 1 is dudivar[,1] |
axes2 |
An integer, the column number for the y-axis. Default is 2, so axes 2 is dudivar[,2] |
arraylabels |
A vector of variables labels. Default is row.names(coord) |
classvec |
A factor or vector which describes the classes in
coord . Default is NULL. If included variables will be coloured by class. |
graph |
A character of type "auto", "s.var", "s.groups", or "s.match.col" which specifies the type of plot type or "graph" to be drawn. By default is "auto", that is graph will be selected depending on the class of cooord |
... |
further arguments passed to or from other method |
plotarrays
calls the function s.var
, s.groups
or s.match.col
.
If you wish to return a table or list of the top array at
the end of an axis, use the function topgenes
.
An xy plot
plotarrays
plots variables using s.var
, s.groups
,
s.match.col
which are modifieds version
of s.label
, s.class
. , and
s.match
.
Aedin Culhane
data(khan) if (require(ade4, quiet = TRUE)) { khan.bga<-bga(khan$train, khan$train.classes) } attach(khan.bga) par(mfrow=c(2,1)) plotarrays(khan.bga) plotarrays(khan.bga, graph="s.var")