A function to plot the shrunken class centroids, from the nearest shrunken centroid classifier produced by pamr.train
pamr.plotcen(fit, data, threshold)
The result of a call to pamr.train
The input data, in the same form as that used by pamr.train
,
The desired threshold value
Trevor Hastie, Robert Tibshirani, Balasubramanian Narasimhan, and Gilbert Chu
pamr.plotcen plots the shrunken class centroids for each
class,
for genes surviving the threshold for at least once class. If
genenames
are included in "data", they are added to the plot. Note: for many
classes
and long gene names, this plot may need some manual prettying.
suppressWarnings(RNGversion("3.5.0"))
set.seed(120)
x <- matrix(rnorm(1000*20),ncol=20)
y <- sample(c(1:4),size=20,replace=TRUE)
mydata <- list(x=x,y=y,genenames=as.character(1:1000))
mytrain <- pamr.train(mydata)
mycv <- pamr.cv(mytrain,mydata)
pamr.plotcen(mytrain, mydata,threshold=1.6)
Run the code above in your browser using DataLab