MVA.trajplot function

Trajectory plot of multivariate analyses

Displays a trajectory plot (i.e. a score plot with trajectories linking defined points) of a multivariate analysis.

MVA.trajplot(x, xax = 1, yax = 2, trajects, trajlab = NULL, scaling = 2,
  set = c(12, 1, 2), space = 1, xlab = NULL, ylab = NULL, main = NULL,
  pch = 16, cex = 1, trajlab.cex = 1, col = 1, lwd = 1, lty = 1,
  points = TRUE, allpoints = TRUE, arrows = TRUE, labels = NULL,
  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,
  legend.cex = 1, 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.
• trajects: vector or list of vectors identifying trajectories. Each vector should give the number of the individuals to be linked, ordered from the first to the last one.
• trajlab: optional traject labels.
• scaling: type of scaling. Only available with some analyses performed with the vegan package. See Details of MVA.scoreplot.
• set: scores to be displayed, when several sets are available (see Details of MVA.scoreplot). 12 (default) for both sets, 1 for rows or X, 2 for columns or Y.
• 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.
• 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.
• pch: symbols used for points. Can be a vector giving one value per trajectory (and a last one for non-linked points if allpoints=TRUE).
• cex: size of the labels. Can be a vector giving one value per trajectory (and a last one for non-linked points if allpoints=TRUE).
• trajlab.cex: size of trajectory labels. Can be a vector giving one value per trajectory.
• 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 trajectory segments. Can be a vector giving one value per trajectory.
• lty: type of trajectory segments. Can be a vector giving one value per trajectory.
• points: logical indicating if points should be displayed. If FALSE, points are replaced with their corresponding label (defined by labels).
• allpoints: logical indicating if points which do not belong to any trajectory should be drawn.
• arrows: logical indicating if trajectories should be oriented with arrows.
• labels: names of the individuals. If NULL (default), labels correspond to row names of the data used in the multivariate analysis.
• 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 trajlab is defined, values of trajlab are used.
• legend.cex: size of legend labels, if legend is TRUE.
• 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(olympic)
PCA <- dudi.pca(olympic$tab,scannf=FALSE)
MVA.plot(PCA,"traject",trajects=list(1:10,25:30),col=c(2,3,1),trajlab=c("T1","T2"))