Plot a principal-surface biplot

Draws the sample coordinates. If vars is given, draws one panel per named variable, each showing the sample coordinates together with that variable's contour lines - the surface's analogue of a biplot axis, read by interpolating between contour lines rather than by projection onto a single calibrated axis. With no vars, a single panel of sample coordinates is drawn with no contours.

Usage

# S3 method for class 'prinsurf'
plot(
  x,
  vars = NULL,
  group = NULL,
  col_contour = "grey40",
  nlevels = 6,
  pch = 16,
  cex = 0.7,
  asp = 1,
  main = NULL,
  outer_main = NULL,
  ...
)

Arguments

x

A "prinsurf" object.

vars

Variables to contour, one panel each (default: none – a bare scatter of sample coordinates).

group

Optional factor to colour the sample points.

col_contour

Colour for the contour lines.

nlevels

Number of contour levels per panel.

pch, cex

Point symbol and size for samples.

asp

Aspect ratio of each panel; the default 1 keeps the two surface coordinates on a common scale, so distances in the biplot are comparable in every direction.

main

Panel title(s), replacing the default (the variable's name, or no title when vars is not given). A single string titles every panel; a vector titles the panels in the order of vars and is recycled to that length. Use "" for no panel titles.

outer_main

A single title for the figure as a whole, drawn in the outer margin above the panels. Can be combined with main, which titles the individual panels.

...

Passed to each panel's initial plot.

Value

Invisibly, vars.

Examples

set.seed(1)
s <- runif(120, -1, 1); t <- runif(120, -1, 1)
X <- cbind(x = s, y = t, z = 0.7 * s + 0.9 * t^2) +
     matrix(rnorm(360, 0, 0.03), 120, 3)
fit <- prinsurf(X, max.iter = 6)

## default: each panel is titled with its variable's name
plot(fit, vars = c("x", "z"))


## your own panel titles, and a title for the figure as a whole
plot(fit, vars = c("x", "z"),
     main = c("First coordinate", "Third coordinate"),
     outer_main = "Principal-surface biplot")


## a title on a single, contour-free panel
plot(fit, main = "Sample coordinates")