MVA.pairplot function

Paired plot of multivariate analyses

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

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 maxime.herve@univ-rennes1.fr

Examples

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