RVAideMemoire (version 0.9-5)

MVA.pairplot: Paired plot of multivariate analyses

Description

Displays a paired plot (i.e. a score plot of paired points) of a multivariate analysis.

Usage

MVA.pairplot(x, xax = 1, yax = 2, pairs = NULL, scaling = 2, space = 1, fac = NULL,
  xlab = NULL, ylab = NULL, main = NULL, ident = TRUE, labels = NULL, cex = 0.7, col = 1,
  lwd = 1, main.pos = c("bottomleft", "topleft", "bottomright", "topright"),
  main.cex = 1.3, legend = FALSE, legend.pos = c("topleft", "topright", "bottomleft",
  "bottomright"), legend.title = NULL, legend.lab = NULL, drawextaxes = TRUE,
  drawintaxes = TRUE, xlim = NULL, ylim = NULL)

Arguments

x

a multivariate analysis (see Details).

xax

the horizontal axis.

yax

the vertical axis. Cannot be NULL, only two-dimensional graphs can be drawn.

pairs

two-level factor identifying paired individuals (in the same order in both sets of points). Can be omitted with multivariate analyses where two sets of points are available in the same space (see MV

scaling

type of scaling. Only available with some analyses performed with the vegan package. See Details of MVA.scoreplot.

space

scores to be displayed, when several spaces are available (see Details of MVA.scoreplot). space is the number of the space to be plotted.

fac

an optional factor defining groups pairs.

xlab

legend of the horizontal axis. If NULL (default), automatic labels are used depending on the multivariate analysis.

ylab

legend of the vertical axis. If NULL (default), automatic labels are used depending on the multivariate analysis.

main

optional title of the graph.

ident

logical indicating if variable names should be displayed.

labels

names of the individuals. If NULL (default), labels correspond to row names of the data used in the multivariate analysis.

cex

size of the labels. If fac is not NULL, can be a vector of length one or a vector giving one value per group. Otherwise a vector of any length can be defined, which is recycled if necessary.

col

color(s) used for arrows and labels. If fac is not NULL, can be a vector of length one or a vector giving one value per group. Otherwise a vector of any length can be defined, which is recycled if necessary.

lwd

width of arrows. If fac is not NULL, can be a vector of length one or a vector giving one value per group. Otherwise a vector of any length can be defined, which is recycled if necessary.

main.pos

position of the title, if main is not NULL. Default to "bottomleft".

main.cex

size of the title, if main is not NULL.

legend

logical indicating if a legend should be added to the graph.

legend.pos

position of the legend, if legend is TRUE. Default to "topleft".

legend.title

optional title of the legend, if legend is TRUE.

legend.lab

legend labels, if legend is TRUE. If NULL and fac is defined, levels of fac are used.

drawextaxes

logical indicating if external axes should be drawn..

drawintaxes

logical indicating if internal axes should be drawn.

xlim

limits of the horizontal axis. If NULL, limits are computed automatically.

ylim

limits of the vertical axis. If NULL, limits are computed automatically.

Details

This function should not be use directly. Prefer the general MVA.plot, to which all arguments can be passed. All multivariate analyses supported by MVA.scoreplot can be used for a paired plot.

Examples

require(ade4)
data(macaca)
PCIA <- procuste(macaca$xy1,macaca$xy2)
MVA.plot(PCIA,"pairs")