Project Data onto Principal Components

Usage

project.pca(data, pca, angular = FALSE, fit = FALSE, ...)
z2xyz.pca(z.coord, pca)
xyz2z.pca(xyz.coord, pca)

Arguments

data

a numeric vector or row-wise matrix of data to be projected.

pca

an object of class "pca" as obtained from functions pca.xyz or pca.tor.

angular

logical, if TRUE the data to be projected is treated as torsion angle data.

fit

logical, if TRUE the data is first fitted to pca$mean.

...

other parameters for fit.xyz.

xyz.coord

a numeric vector or row-wise matrix of data to be projected.

z.coord

a numeric vector or row-wise matrix of PC scores (i.e. the z-scores which are centered and rotated versions of the origional data projected onto the PCs) for conversion to xyz coordinates.

Examples

attach(transducin)

The following objects are masked from transducin (pos = 3):

    annotation, core, pdbs


gaps.pos <- gap.inspect(pdbs$xyz)

#-- Do PCA without structures 2 and 7
pc.xray <- pca.xyz(pdbs$xyz[-c(2,7), gaps.pos$f.inds])

#-- Project structures 2 and 7 onto the PC space
d <- project.pca(pdbs$xyz[c(2,7), gaps.pos$f.inds], pc.xray)

plot(pc.xray$z[,1], pc.xray$z[,2],col="gray")
points(d[,1],d[,2], col="red")



detach(transducin)

See also

Author