plot.pca {bio3d}R Documentation

Plot PCA Results

Description

Produces a z-score plot (conformer plot) and an eigen spectrum plot (scree plot).

Usage

plot.pca(x, pch = 16, col = par("col"), ...)
plot.pca.scree(x, y = NULL, type = "o", pch = 18,
         main = "", sub = "", xlim = c(0, 20), ylim = NULL,
         ylab = "Proporton of Variance (%)",
         xlab = "Eigenvalue Rank", axes = TRUE, ann = par("ann"),
         col = par("col"), lab = TRUE, ...)
plot.pca.score(x, start.row = 1, end.row = nrow(x), col=rainbow(nrow(x)), lab = "", ...)

Arguments

x the results of principal component analysis obtained with pca.xyz.
pch a vector of plotting characters or symbols: see ‘points’.
col a character vector of plotting colors.
start.row row index of the first conformer to colour.
end.row row index of the last conformer to colour.
lab a character vector of plot labels.
y the y coordinates for the scree plot.
type one-character string giving the type of plot desired.
main a main title for the plot, see also 'title'.
sub a sub-title for the plot.
xlim the x limits of the plot.
ylim the y limits of the plot.
ylab a label for the y axis.
xlab a label for the x axis.
axes a logical value indicating whether both axes should be drawn.
ann a logical value indicating whether the default annotation (title and x and y axis labels) should appear on the plot.
... extra plotting arguments.

Details

plot.pca is a wrapper calling both plot.pca.score and plot.pca.scree resulting in a 2x2 plot with three score plots and one scree plot.

Value

Called for its effect.

Author(s)

Barry Grant

References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.

See Also

pca.xyz, plot.bio3d

Examples

data(kinesin)
attach(kinesin)

plot(pc.xray)

## change colors
plot(pc.xray,col=rainbow(length(pc.xray$z[,1])), cex=1.5)

## add labels

## color by seq identity


[Package bio3d version 1.0-5 Index]