mixOmics (version 2.9-2)

plot.valid: Validation Plot

Description

Function to plot validation statistics, such as MSEP, RMSEP or $R^2$, as a function of the number of components.

Usage

## S3 method for class 'valid':
plot(x, criterion = c("MSEP", "RMSEP", "R2"),
     xlab = "number of components", ylab = NULL,
     cTicks = 1:ncol(x[[1]]), layout = NULL, ...)

Arguments

x

an valid object.

criterion

character string. What type of validation criterion to plot. One of "MSEP", "RMSEP" or "R2".

xlab, ylab

titles for $x$ and $y$ axes. Typically character strings, but can be expressions (e.g., expression(R^2).

cTicks

integer vector. Axis tickmark locations for the used number of components. Default is from one to ncomp (see valid).

layout

numeric vector of length two giving the number of rows and columns in a multi panel display. If not specified, plot.valid tries to be intelligent.

...

Further arguments sent to xyplot function.

encoding

latin1

Details

plot.valid creates one plot for each response variable in the model, laid out in a multi panel display. It uses xyplot for performing the actual plotting.

See Also

pls, spls, predict.

Examples

require(lattice)

data(liver.toxicity)
X <- liver.toxicity$gene
Y <- liver.toxicity$clinic

liver.val <- valid(X, Y, ncomp = 5, mode = "regression", 
                   method = "pls", validation = "loo")
				   
plot.valid(liver.val, criterion = "RMSEP", type = "l", layout = c(2, 2))