R Under development (unstable) (2024-04-27 r86487 ucrt) -- "Unsuffered Consequences"
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> library(ClassDiscovery)
Loading required package: cluster
Loading required package: oompaBase
> suppressWarnings( RNGversion("3.5.3") )
> set.seed(581492)
> # simulate data from three groups
> d1 <- matrix(rnorm(100*10, rnorm(100, 0.5)), nrow=100, ncol=10, byrow=FALSE)
> d2 <- matrix(rnorm(100*10, rnorm(100, 0.5)), nrow=100, ncol=10, byrow=FALSE)
> d3 <- matrix(rnorm(100*10, rnorm(100, 0.5)), nrow=100, ncol=10, byrow=FALSE)
> dd <- cbind(d1, d2, d3)
> # colors that match the groups
> cols <- rep(c('red', 'green', 'blue'), each=10)
> 
> # compute teh PCanova object
> pan <- PCanova(dd, c('red', 'green', 'blue'), cols, cols)
> summary(pan)
An object of the PCanova class with 3 groups.
Call:
	PCanova(data = dd, classes = c("red", "green", "blue"), labels = cols, colors = cols)
> 
> # view the PC plots
> plot(pan)
> 
> # view the dendrograms
> pltree(pan, line=-0.5)
> 
> # compare teh results when there is no underlying group structure
> dd <- matrix(rnorm(100*50, rnorm(100, 0.5)), nrow=100, ncol=50, byrow=FALSE)
> cols <- rep(c('red', 'green', 'blue', 'orange', 'cyan'), each=10)
> pan <- PCanova(dd, unique(cols), cols, cols)
> plot(pan, mscale=1/sqrt(10))
> 
> pltree(pan, line=-0.5)
> 
> # cleanup
> rm(d1, d2, d3, dd, cols, pan)
> 
> proc.time()
   user  system elapsed 
   0.34    0.03    0.37