PCLassoReg (version 1.0.0)

plot.cv.PCLasso: Plot the cross-validation curve from a cv.PCLasso object

Description

Plot the cross-validation curve from a cv.PCLasso object, along with standard error bars.

Usage

# S3 method for cv.PCLasso
plot(x, type = c("cve", "rsq", "snr", "all"), norm = NULL, ...)

Arguments

x

Fitted cv.PCLasso model.

type

What to plot on the vertical axis. "cve" plots the cross-validation error (deviance); "rsq" plots an estimate of the fraction of the deviance explained by the model (R-squared); "snr" plots an estimate of the signal-to-noise ratio; "all" produces all of the above.

norm

If TRUE, plot the norm of each group, rather than the individual coefficients.

...

Other graphical parameters to plot

Value

No return value, called for plotting of cv.PCLasso objects.

Details

Error bars representing approximate +/- 1 SE (68% confidence intervals) are plotted along with the estimates at value of lambda. See plot.cv.grpreg in the R package grpreg for details.

See Also

cv.PCLasso

Examples

# NOT RUN {
# load data
data(survivalData)
data(PCGroups)

x = survivalData$Exp
y = survivalData$survData

PC.Human <- getPCGroups(Groups = PCGroups, Organism = "Human",
Type = "EntrezID")

# fit model
cv.fit1 <- cv.PCLasso(x, y, group = PC.Human, penalty = "grLasso",
nfolds = 10)

# plot the norm of each group
plot(cv.fit1, norm = TRUE)

# plot the individual coefficients
plot(cv.fit1, norm = FALSE)

# plot the cross-validation error (deviance)
plot(cv.fit1, type = "cve")
# }