plotBiplot: The Default Biplot Function

In MorphoTools2: Multivariate Morphometric Analysis

The Default Biplot Function

Description

A generic function for plotting ordination scores and the character's contribution to ordination axes in a single plot.

Usage

plotBiplot(result, axes = c(1,2), xlab = NULL, ylab = NULL,
      pch = 16, col = "black", pt.bg = "white", breaks = 1,
      xlim = NULL, ylim = NULL, labels = FALSE, arrowLabels = TRUE,
      colArrowLabels = "black", angle = 15, length = 0.1, arrowCol = "red",
      legend = FALSE, legend.pos = "topright", ncol = 1, ...)

Arguments

result	an object of class pcadata, or cdadata.
axes	x, y axes of plot.
xlab, ylab	a title of the respective axes.
pch	a vector of plotting characters or symbols: see points.
col	the colours for points. Multiple colours can be specified so that each taxon can be given its own colour. If there are fewer colours than taxa, they are recycled in the standard fashion.
pt.bg	the background colours for points. Multiple colours can be specified, as above.
breaks	a numeric, giving the width of one histogram bar.
xlim, ylim	the range of x and y axes.
labels	logical, if TRUE, object's labels are displayed.
arrowLabels	logical, if TRUE, character's labels are displayed.
colArrowLabels	the colours for character's labels.
angle	angle from the shaft of the arrow to the edge of the arrow head.
length	length of the edges of the arrow head (in inches).
arrowCol	the colour for arrows.
legend	logical, if TRUE, legend is displayed. Only restricted number of legend parameters are supported. For more precise legend plotting, use plotAddLegend directly.
legend.pos	a single keyword from the list "bottomright", "bottom", "bottomleft", "left", "topleft", "top", "topright", "right", and "center", to be used to position the legend.
ncol	the number of columns in which to set the legend items.
...	further arguments to be passed to plot.default or other graphical parameters in par.

Details

This generic method holds separate implementations of plotting biplots for pcadata, and cdadata objects. If only one axis exists, sample scores are displayed as a histogram.

Value

None. Used for its side effect of producing a plot.

Examples

data(centaurea)
centaurea = naMeanSubst(centaurea)
centaurea = removePopulation(centaurea, populationName = c("LIP", "PREL"))

pcaRes = pca.calc(centaurea)

plotBiplot(pcaRes, axes = c(1,2), col = c("red", "green", "blue", "red"),
  pch = c(20, 17, 8, 21), pt.bg = "orange", legend = TRUE, legend.pos = "bottomright")

plotBiplot(pcaRes, main = "My PCA plot", cex = 0.8)

cdaRes = cda.calc(centaurea)

plotBiplot(cdaRes, col = c("red", "green", "blue", "red"),
  pch = c(20, 17, 8, 21), pt.bg = "orange", legend = TRUE)

MorphoTools2 documentation built on Oct. 2, 2024, 5:07 p.m.