pamr (version 1.57)

pamr.plotcen: A function to plot the shrunken class centroids, from the nearest shrunken centroid classifier

Description

A function to plot the shrunken class centroids, from the nearest shrunken centroid classifier produced by pamr.train

Usage

pamr.plotcen(fit, data, threshold)

Arguments

fit

The result of a call to pamr.train

data

The input data, in the same form as that used by pamr.train

threshold

The desired threshold value

Author

Trevor Hastie, Robert Tibshirani, Balasubramanian Narasimhan, and Gilbert Chu

Details

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.

Examples

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)