plot.prcurve: Plot a fitted principal curve in PCA space

In analogue: Analogue and Weighted Averaging Methods for Palaeoecology

Plot a fitted principal curve in PCA space

Description

Projects the principal curve into PCA space and draws it and the underlying data in a biplot.

Usage

## S3 method for class 'prcurve'
plot(x, axes = 1:2, scaling = 0, segments = TRUE,
     col = "red", col.seg = "forestgreen", lwd = 2,
     lwd.seg = 1, ...)

## S3 method for class 'prcurve'
lines(x, axes = 1:2, scaling = 0, segments = TRUE,
      col = "red", col.seg = "forestgreen", lwd = 2,
      lwd.seg = 1, ...)

Arguments

x	an object of class "prcurve".
axes	numeric vector of length 2; this is passed to the choices argument of the scores function.
scaling	numeric; the scaling to use. See scores.rda for the available options. The default is not to scale the scores, but scaling = 1 might be a useful alternative.
segments	logical; should segments be drawn between the observed points to the location on the principal curve on to which they project.
col	The colour to draw the principal curve in.
col.seg	The colour to draw the segments in.
lwd, lwd.seg	The line thickness used to draw the principal curve and segments respectively.
...	additional arguments passed on to points when drawing the observations in PCA space.

Value

A plot on the currently active device. The function does not return anything.

Author(s)

Gavin L. Simpson

See Also

prcurve; rda for the code used to perform the PCA.

Examples

## Load the Abernethy Forest data
data(abernethy)

## Remove the Depth and Age variables
abernethy2 <- abernethy[, -(37:38)]

## Fit the principal curve using varying complexity of smoothers
## for each species
aber.pc <- prcurve(abernethy2, method = "ca", trace = TRUE,
                   vary = TRUE, penalty = 1.4)

## Plot the curve
plot(aber.pc)

## The lines() method can be used to add the principal curve to an
## existing plot
ord <- rda(abernethy2)
plot(ord, scaling = 1)
lines(aber.pc, scaling = 1)

analogue documentation built on Sept. 30, 2024, 9:41 a.m.