plot.pca {bio3d} | R Documentation |
Produces a z-score plot (conformer plot) and an eigen spectrum plot (scree plot).
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 = "", ...)
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. |
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.
Called for its effect.
Barry Grant
Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.
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