plot.cv.PCLasso2 {PCLassoReg}

Plot the cross-validation curve from a cv.PCLasso2 object

Description

Plot the cross-validation curve from a cv.PCLasso2 object, along with standard error bars.

Usage

## S3 method for class 'cv.PCLasso2'
plot(x, type = c("cve", "rsq", "snr", "all"), norm = NULL, ...)

Arguments

x

Fitted cv.PCLasso2 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

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.

Value

No return value, called for plotting of cv.PCLasso2 objects.

See Also

cv.PCLasso2

Examples

# load data
data(classData)
data(PCGroups)

x = classData$Exp
y = classData$Label

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

# fit model
cv.fit1 <- cv.PCLasso2(x, y, group = PC.Human, penalty = "grLasso",
family = "binomial", 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")