MVA.trajplot: Trajectory plot of multivariate analyses

In RVAideMemoire: Testing and Plotting Procedures for Biostatistics

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 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 <[e-mail]>

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"))

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