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

In PCLassoReg: Group Regression Models for Risk Protein Complex Identification

Description

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

Usage

## S3 method for class '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

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.PCLasso objects.

See Also

cv.PCLasso

Examples

# 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")

PCLassoReg documentation built on Oct. 26, 2021, 5:07 p.m.