traceplot {BioMark}

Plot the coefficient or stability trace for the lasso/elastic net biomarker selection.

Description

The function plots the coefficient or stability traces for the lasso element of a BioMark object.

Usage

traceplot(object, ...)

Arguments

object

An object of class BioMark.

...

Further plotting arguments.

Author(s)

Ron Wehrens

References

N. Meinshausen and P. Buhlmann: Stability Selection. J. R. Statist. Soc. B 72, 417-473 (2010)

See Also

get.biom

Examples

library(BioMark)
data(spikedApples)

mycols <- rep("gray", ncol(spikedApples$dataMatrix))
mycols[spikedApples$biom] <- "red"
myltys <- rep(2, ncol(spikedApples$dataMatrix))
myltys[spikedApples$biom] <- 1

par(mfrow = c(1,2))
apple.coef <- get.biom(X = spikedApples$dataMatrix,
                       Y = factor(rep(0:1, each = 10)),
                       ncomp = 2:3, type = "coef")
traceplot(apple.coef, col = mycols, lty = myltys)

apple.stab <- get.biom(X = spikedApples$dataMatrix,
                       Y = factor(rep(0:1, each = 10)),
                       fmethod = c("vip","lasso"), type = "stab")
traceplot(apple.stab, col = mycols, lty = myltys)