R: A function to plot the shrunken class centroids, from the...

pamr.plotcen {pamr} | R Documentation

## 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

### 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.

### Author(s)

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

### Examples

    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)

[Package pamr version 1.55 Index]