RVAideMemoire (version 0.9-54)

MVA.trajplot: Trajectory plot of multivariate analyses

Description

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

Usage

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 o

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.\

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"))