koplsPlotScores {kopls}R Documentation

Plots scores from trained K-OPLS models

Description

Produces score plots from K-OPLS models. If model components are unspecified, all possible combinations are displayed as a scatter plot matrix. Otherwise, two selected components will be shown using a traditional 2D scatter plot.

Usage

koplsPlotScores(model, x = NA, xsub = "p", y = NA, ysub = "o")

Arguments

model K-OPLS model (see koplsModel).
x x-axis score vector index.
xsub Identifying value for x: Either 'p' for predictive component or 'o' for Y-orthogonal component.
y y-axis score vector index.
ysub Identifying value for y: Either 'p' for predictive component or 'o' for Y-orthogonal component .

Details

The diagnol of the scatter plot matrix depicts the kernel density of that particular score vector. Any additional parameters will be passed on to the plot() function, which can be used to e.g. set the color or shape of the displayed data points.

Author(s)

Max Bylesjo and Mattias Rantalainen

References

Rantalainen M, Bylesjo M, Cloarec O, Nicholson JK, Holmes E and Trygg J. Kernel-based orthogonal projections to latent structures (K-OPLS), J Chemometrics 2007; 21:376-385. doi:10.1002/cem.1071.

Examples


## Load data set
data(koplsExample)

## Define kernel function parameter
sigma<-25

## Define number of Y-orthogonal components
nox<-3

## Construct kernel
Ktr<-koplsKernel(Xtr,NULL,'g',sigma)

## Model 
model<-koplsModel(Ktr,Ytr,1,nox,'mc','mc');

#### Visualize results

## Shows all scores as scatter plot matrix
## col.vec defines class colors and is loaded by data(koplsExample)
koplsPlotScores(model, col=col.vec)

## Shows tp1 vs to1, colored by class
## pch.vec defines class glyph types and is loaded by data(koplsExample)
koplsPlotScores(model, x=1, xsub='p', y=1, ysub='o', col=col.vec, pch=pch.vec)

## Shows to1 vs to2
koplsPlotScores(model, x=1, xsub='o', y=2, ysub='o', col=col.vec, pch=pch.vec)


[Package kopls version 1.0.3 Index]