Description Usage Arguments Value Note Author(s) See Also Examples
Plot the scaling coordinates of the proximity matrix from snpRF.
1 |
rf |
an object of class |
fac |
a factor that was used as response to train |
k |
number of dimensions for the scaling coordinates. |
palette |
colors to use to distinguish the classes; length must be the equal to the number of levels. |
pch |
plotting symbols to use. |
... |
other graphical parameters. |
The output of cmdscale
on 1 - rf$proximity
is
returned invisibly.
If k > 2
, pairs
is used to produce the
scatterplot matrix of the coordinates.
Robert Gentleman, with slight modifications by Andy Liaw and modifications for use with snpRF by Greg Jenkins
1 2 3 4 5 6 7 8 | set.seed(1)
data(snpRFexample)
eg.rf <- snpRF(x.autosome=autosome.snps,x.xchrom=xchrom.snps,
xchrom.names=xchrom.snps.names,x.covar=covariates,
y=phenotype, proximity=TRUE,keep.forest=FALSE)
MDSplot(eg.rf, phenotype)
## Using different symbols for the classes:
MDSplot(eg.rf, phenotype, palette=rep(1, 2), pch=as.numeric(phenotype))
|
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