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

In pamr: Pam: Prediction Analysis for Microarrays

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

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)
 

Example output

Loading required package: cluster
Loading required package: survival
1234567891011121314151617181920212223242526272829301234Fold 1 :123456789101112131415161718192021222324252627282930
Fold 2 :123456789101112131415161718192021222324252627282930
Fold 3 :123456789101112131415161718192021222324252627282930
Fold 4 :123456789101112131415161718192021222324252627282930

pamr documentation built on May 2, 2019, 12:35 p.m.