MorphoTools2 (version 1.0.2.1)

plotPoints: The Default Scatterplot Function

Description

A generic function for plotting ordination scores stored in pcadata, pcoadata, nmdsdata, and cdadata objects.

Usage

plotPoints(result, axes = c(1,2), xlab = NULL, ylab = NULL,
      pch = 16, col = "black", pt.bg = "white", breaks = 1,
      ylim = NULL, xlim = NULL, labels = FALSE, legend = FALSE,
      legend.pos = "topright", ncol = 1, ...)

Value

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

Arguments

result

an object of class pcadata, pcoadata, nmdsdata, 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, labels are displayed. Only restricted number of parameters are supported. For more precise labels plotting, use plotAddLabels.points directly.

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 points for pcadata, pcoadata, nmdsdata, and cdadata objects. If only one axis exists, sample scores are displayed as a histogram.

Examples

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

pcaRes = pca.calc(centaurea)

plotPoints(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")

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

cdaRes = cda.calc(centaurea)

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