pamr.plotcen

0th

Percentile

A function to plot the shrunken class centroids, from the nearest shrunken centroid classifier

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.

Aliases
  • pamr.plotcen
Examples
# NOT RUN {
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)
 
# }
Documentation reproduced from package pamr, version 1.56.1, License: GPL-2

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