MVA.pairplot: Paired plot of multivariate analyses

In RVAideMemoire: Testing and Plotting Procedures for Biostatistics

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 MVA.scoreplot). In this case these sets are automatically detected.
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.

Author(s)

Maxime HERVE <[e-mail]>

Examples

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

RVAideMemoire documentation built on Nov. 6, 2023, 5:07 p.m.